HALOZYME THERAPEUTICS INC, 10-K filed on 3/1/2013
Annual Report
Document and Entity Information (USD $)
In Millions, except Share data, unless otherwise specified
12 Months Ended
Dec. 31, 2012
Feb. 25, 2013
Jun. 30, 2012
Document and Entity Information [Abstract]
 
 
 
Entity Registrant Name
HALOZYME THERAPEUTICS INC 
 
 
Entity Central Index Key
0001159036 
 
 
Document Type
10-K 
 
 
Document Period End Date
Dec. 31, 2012 
 
 
Amendment Flag
false 
 
 
Document Fiscal Year Focus
2012 
 
 
Document Fiscal Period Focus
FY 
 
 
Current Fiscal Year End Date
--12-31 
 
 
Entity Well-known Seasoned Issuer
Yes 
 
 
Entity Voluntary Filers
No 
 
 
Entity Current Reporting Status
Yes 
 
 
Entity Filer Category
Large Accelerated Filer 
 
 
Entity Public Float
 
 
$ 784.5 
Entity Common Stock, Shares Outstanding
 
113,122,900 
 
Consolidated Balance Sheets (USD $)
Dec. 31, 2012
Dec. 31, 2011
Current assets:
 
 
Cash and cash equivalents
$ 99,901,264 
$ 52,825,527 
Accounts receivable, net
15,703,087 
2,262,465 
Inventories
2,670,696 
567,263 
Prepaid expenses and other assets
12,752,888 
8,332,242 
Total current assets
131,027,935 
63,987,497 
Property and equipment, net
3,700,462 
1,771,048 
Total Assets
134,728,397 
65,758,545 
Current liabilities:
 
 
Accounts payable
2,271,689 
7,556,859 
Accrued expenses
7,783,447 
5,615,574 
Deferred revenue, current portion
8,891,017 
4,129,407 
Total current liabilities
18,946,153 
17,301,840 
Deferred revenue, net of current portion
34,954,966 
36,754,583 
Long-term debt, net
29,661,680 
Lease financing obligation
1,450,000 
Deferred rent, net of current portion
861,879 
802,006 
Commitments and contingencies (Note 9)
   
   
Stockholders' equity:
 
 
Preferred stock — $0.001 par value; 20,000,000 shares authorized; no shares issued and outstanding
   
   
Common stock — $0.001 par value; 150,000,000 shares authorized; 112,709,174 and 103,989,272 shares issued and outstanding at December 31, 2012 and 2011, respectively
112,709 
103,990 
Additional paid-in capital
347,314,658 
255,817,772 
Accumulated deficit
(298,573,648)
(245,021,646)
Total stockholders' equity
48,853,719 
10,900,116 
Total Liabilities and Stockholders' Equity
$ 134,728,397 
$ 65,758,545 
Consolidated Balance Sheets (Parenthetical) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Statement of Financial Position [Abstract]
 
 
Preferred stock, par value
$ 0.001 
$ 0.001 
Preferred stock, shares authorized
20,000,000 
20,000,000 
Preferred stock, shares issued
Preferred stock, shares outstanding
Common stock, par value
$ 0.001 
$ 0.001 
Common stock, shares authorized
150,000,000 
150,000,000 
Common stock, shares issued
112,709,174 
103,989,272 
Common stock, shares outstanding
112,709,174 
103,989,272 
Consolidated Statements of Comprehensive Loss (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Revenues:
 
 
 
Product sales, net
$ 2,887,442 
$ 1,836,102 
$ 895,518 
Revenues under collaborative agreements
39,437,784 
54,250,334 
12,728,597 
Total revenues
42,325,226 
56,086,436 
13,624,115 
Operating expenses:
 
 
 
Cost of product sales
1,094,400 
257,834 
985,283 
Research and development
70,044,073 
57,563,470 
51,773,504 
Selling, general and administrative
24,812,199 
18,104,073 
15,122,960 
Total operating expenses
95,950,672 
75,925,377 
67,881,747 
Operating income (loss)
(53,625,446)
(19,838,941)
(54,257,632)
Other Income (Expense)
 
 
 
Interest income, net
59,028 
63,530 
49,015 
Other Income, net
14,416 
5,560 
966,967 
Total other income, net
73,444 
69,090 
1,015,982 
NET LOSS
(53,552,002)
(19,769,851)
(53,241,650)
Basic and diluted net loss per share (In dollars per share)
$ (0.48)
$ (0.19)
$ (0.56)
Shares used in computing basic and diluted net loss per share
111,077,105 
102,566,089 
94,357,695 
Comprehensive Loss
$ (53,552,002)
$ (19,769,851)
$ (53,241,650)
Consolidated Statements of Cash Flows (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Operating activities:
 
 
 
Net Loss
$ (53,552,002)
$ (19,769,851)
$ (53,241,650)
Adjustments to reconcile net loss to net cash used in operating activities:
 
 
 
Share-based compensation
8,348,587 
5,569,899 
4,866,325 
Depreciation and amortization
1,079,424 
1,095,823 
1,507,925 
Long-term debt, non-cash interest expense
8,625 
Loss (gain) on disposal of equipment
7,370 
(1,566)
13,542 
Changes in operating assets and liabilities:
 
 
 
Accounts receivable, net
(13,440,622)
65,803 
1,915,641 
Inventories
(2,103,433)
(373,841)
966,129 
Prepaid expenses and other assets
(4,420,646)
(4,611,346)
(2,147,119)
Accounts payable and accrued expenses
(3,263,487)
711,777 
3,437,089 
Deferred rent
44,895 
172,438 
(314,747)
Deferred revenue
2,961,993 
(17,209,561)
(2,388,641)
Net cash used in operating activities
(64,329,296)
(34,350,425)
(45,385,506)
Investing activities:
 
 
 
Purchases of property and equipment
(1,412,585)
(828,508)
(646,544)
Net cash used in investing activities
(1,412,585)
(828,508)
(646,544)
Financing activities:
 
 
 
Proceeds from issuance of common stock, net
81,476,845 
59,965,059 
Proceeds from issuance of long-term debt, net
29,660,600 
Proceeds from issuance of common stock under equity incentive plans, net
1,680,173 
4,748,612 
1,858,333 
Net cash provided by financing activities
112,817,618 
4,748,612 
61,823,392 
Net increase (decrease) in cash and cash equivalents
47,075,737 
(30,430,321)
15,791,342 
Cash and cash equivalents at beginning of period
52,825,527 
83,255,848 
67,464,506 
Cash and cash equivalents at end of period
99,901,264 
52,825,527 
83,255,848 
Supplemental disclosure of cash flow information:
 
 
 
Interest Paid
18,875 
Supplemental disclosure of noncash investing and financing activities:
 
 
 
Capitalized property and liability associated with a build-to-suit lease arrangement
1,450,000 
Accounts payable for purchases of property and equipment
$ 153,623 
$ 189,898 
$ 13,806 
Consolidated Statements of Stockholders' Equity (USD $)
Total
Common Stock
Additional Paid-in Capital
Accumulated Deficit
Stockholders' Equity, Total at Dec. 31, 2009
$ 6,903,389 
$ 91,682 
$ 178,821,852 
$ (172,010,145)
Shares at Dec. 31, 2009
 
91,681,756 
 
 
Share-based compensation expense
4,866,325 
 
4,866,325 
 
Issuance of common stock for cash, net, shares
 
8,300,000 
 
 
Issuance of common stock for cash, net
59,965,059 
8,300 
59,956,759 
 
Issuance of common stock, stock option exercises, shares
479,093 
479,093 
 
 
Issuance of common stock pursuant to exercise of stock options
1,858,213 
479 
1,857,734 
 
Issuance of restricted stock awards, shares
120,000 
120,000 
 
 
Issuance of restricted stock awards
120 
120 
 
Net Loss
(53,241,650)
 
 
(53,241,650)
Stockholders' Equity, Total at Dec. 31, 2010
20,351,456 
100,581 
245,502,670 
(225,251,795)
Shares at Dec. 31, 2010
 
100,580,849 
 
 
Share-based compensation expense
5,569,899 
 
5,569,899 
 
Issuance of common stock, stock option exercises, shares
3,137,056 
3,060,540 
 
 
Issuance of common stock pursuant to exercise of stock options
4,748,492 
3,060 
4,745,432 
 
Issuance of restricted stock awards, shares
347,883 
347,883 
 
 
Issuance of restricted stock awards
120 
349 
(229)
 
Net Loss
(19,769,851)
 
 
(19,769,851)
Stockholders' Equity, Total at Dec. 31, 2011
10,900,116 
103,990 
255,817,772 
(245,021,646)
Shares at Dec. 31, 2011
 
103,989,272 
 
 
Share-based compensation expense
8,348,587 
 
8,348,587 
 
Issuance of common stock for cash, net, shares
 
7,820,000 
 
 
Issuance of common stock for cash, net
81,476,845 
7,820 
81,469,025 
 
Issuance of common stock, stock option exercises, shares
444,637 
525,707 
 
 
Issuance of common stock pursuant to exercise of stock options
1,680,173 
525 
1,679,648 
 
Issuance of restricted stock awards, shares
374,195 
374,195 
 
 
Issuance of restricted stock awards
374 
(374)
 
Net Loss
(53,552,002)
 
 
(53,552,002)
Stockholders' Equity, Total at Dec. 31, 2012
$ 48,853,719 
$ 112,709 
$ 347,314,658 
$ (298,573,648)
Shares at Dec. 31, 2012
 
112,709,174 
 
 
Organization and Business
Organization and Business
Organization and Business
Halozyme Therapeutics, Inc. is a science-driven, biopharmaceutical company committed to making molecules into medicines for patients in need. Our research focuses primarily on human enzymes that alter the extracellular matrix. The extracellular matrix is a complex matrix of proteins and carbohydrates surrounding the cell that provides structural support in tissues and orchestrates many important biological activities, including cell migration, signaling and survival. Over many years, we have developed unique technology and scientific expertise enabling us to pursue this target-rich environment for the development of therapies.
Our proprietary enzymes can be used to facilitate the delivery of injected drugs and fluids, thus enhancing the efficacy and the convenience of other drugs or to alter abnormal tissue structures for clinical benefit. We have chosen to exploit our technology and expertise in a balanced way to modulate both risk and spend by: (1) developing our own proprietary products in therapeutic areas with significant unmet medical needs, such as diabetes, oncology and dermatology, and (2) licensing our technology to biopharmaceutical companies to collaboratively develop products which combine our technology with the collaborators' proprietary compounds.
The majority of the product candidates in our current pipeline are based on rHuPH20, a patented human recombinant hyaluronidase enzyme. rHuPH20 temporarily breaks down hyaluronic acid - a naturally occurring substance that is a major component of the extracellular matrix in tissues throughout the body such as skin and cartilage. Our proprietary pipeline consists of multiple clinical stage products in diabetes, oncology and dermatology. We currently have collaborations with F. Hoffmann-La Roche, Ltd. and Hoffmann-La Roche, Inc. (Roche), Pfizer Inc. (Pfizer), Baxter Healthcare Corporation (Baxter), ViroPharma Incorporated (ViroPharma) and Intrexon Corporation (Intrexon), with three product candidates which have been submitted for regulatory approval in the U.S. and/or Europe as well as several others at various stages of development.
We were founded in 1998 and reincorporated from the State of Nevada to the State of Delaware in November 2007. Except where specifically noted or the context otherwise requires, the use of terms such as "Halozyme," "we," "our," and "us" in these Notes to Consolidated Financial Statements refers to Halozyme Therapeutics, Inc.
Summary of Significant Accounting Policies
Summary of Significant Accounting Policies
Summary of Significant Accounting Policies
Basis of Presentation
The consolidated financial statements include the accounts of Halozyme Therapeutics, Inc. and our wholly owned subsidiary, Halozyme, Inc. All intercompany accounts and transactions have been eliminated.
Use of Estimates
The preparation of consolidated financial statements in conformity with U.S. generally accepted accounting principles (“U.S. GAAP”) requires management to make estimates and assumptions that affect the amounts reported in our consolidated financial statements and accompanying notes. On an ongoing basis, we evaluate our estimates and judgments, which are based on historical and anticipated results and trends and on various other assumptions that management believes to be reasonable under the circumstances. By their nature, estimates are subject to an inherent degree of uncertainty and, as such, actual results may differ from management’s estimates.
 
Cash and Cash Equivalents
Cash and cash equivalents consist of highly liquid investments with original maturities of three months or less from the original purchase date.
Concentrations of Credit Risk, Sources of Supply and Significant Customers
Financial instruments that potentially subject us to a significant concentration of credit risk consist of cash and cash equivalents and accounts receivable. We maintain our cash and cash equivalent balances with one major commercial bank. Deposits held with the bank exceed the amount of insurance provided on such deposits.
We have license and collaborative agreements with pharmaceutical companies under which we receive payments for license fees, milestone payments for specific achievements designated in the collaborative agreements, reimbursements of research and development services and supply of bulk formulation of rHuPH20. In addition, we sell Hylenex® recombinant in the United States to a limited number of established wholesale distributors in the pharmaceutical industry. Credit is extended based on an evaluation of the customer’s financial condition, and collateral is not required. Management monitors our exposure to accounts receivable by periodically evaluating the collectibility of the accounts receivable based on a variety of factors including the length of time the receivables are past due, the financial health of the customer and historical experience. Based upon the review of these factors, we recorded no allowance for doubtful accounts at December 31, 2012 and 2011. Approximately 86% of accounts receivable balance as of December 31, 2012 represents amounts due from Roche and Pfizer. Approximately 82% of the accounts receivable balance as of December 31, 2011 represents amounts due from Roche, Baxter and ViroPharma. For the years ended December 31, 2012, 2011 and 2010, 45%, 19% and 52% of total revenues were from Roche and 17%, 42% and 42% of total revenues were from Baxter, respectively. For the year ended December 31, 2012, 22% of total revenues were from Pfizer. In addition, for the year ended December 31, 2011, 22% and 16% of total revenues were from ViroPharma and Intrexon, respectively.
Worldwide revenues from external customers for the years ended December 31, 2012, 2011 and 2010 consisted of domestic revenues of approximately $22.7 million, $44.9 million and $6.0 million, respectively, and foreign revenues of approximately $19.6 million, $11.2 million and $7.6 million, respectively. Of our total foreign revenues for the years ended December 31, 2012, 2011 and 2010, approximately $18.9 million, $10.4 million, $7.2 million, respectively, were attributable to Switzerland. We attribute revenues under collaborative agreements to the individual countries where the collaborator is headquartered. We attribute revenues from product sales to the individual countries to which the product is shipped. For the years ended December 31, 2012, 2011 and 2010, we had no foreign based operations, and we had no long-lived assets located in foreign countries.
We rely on two third-party manufacturers for the supply of the bulk formulation of rHuPH20 which is the active pharmaceutical ingredient (“API”) in Hylenex recombinant and each of our collaborators’ product candidates. Payments due to these suppliers represent 20% and 59% of the accounts payable balance at December 31, 2012 and 2011, respectively. We also rely on a third-party manufacturer for the fill and finish of Hylenex recombinant product under a contract we entered in June 2011. Payments due to this supplier represent 8.0% and 3.7% of the accounts payable balance at December 31, 2012 and 2011, respectively.
Accounts Receivable, Net
Accounts receivable is recorded at the invoiced amount and is non-interest bearing. Accounts receivable is recorded net of allowances for doubtful accounts, cash discounts for prompt payment, distribution fees and chargebacks. We recorded no allowance for doubtful accounts at December 31, 2012 and 2011, as the collectibility of accounts receivable is reasonably assured. Allowances for prompt payment discounts, distribution fees and chargebacks as of December 31, 2012 and 2011 were immaterial.
Inventories
Inventories are stated at lower of cost or market. Cost is determined on a first-in, first-out basis. Inventories are reviewed periodically for potential excess, dated or obsolete status. Management evaluates the carrying value of inventories on a regular basis, taking into account such factors as historical and anticipated future sales compared to quantities on hand, the price we expect to obtain for products in their respective markets compared with historical cost and the remaining shelf life of goods on hand.
Raw materials inventories consist of raw materials used in the manufacture of our bulk drug material for Hylenex recombinant product. Work-in-process inventories consist of in-process Hylenex recombinant. Finished goods inventories consist of finished Hylenex recombinant product.
We expense costs relating to the purchase and production of pre-approval inventories for which the sole use is pre-approval products as research and development expense in the period incurred until such time as we believe future commercialization is probable and future economic benefit is expected to be realized. For products that have been approved by the regulatory bodies such as the U.S. Food and Drug Administration ("FDA"), inventories used in clinical trials are expensed at the time the inventories are packaged for the clinical trial. Prior to receiving approval from the FDA or comparable regulatory agencies in foreign countries, costs related to purchases of the API and the manufacturing of the product candidate is recorded as research and development expense. All direct manufacturing costs incurred after approval are capitalized as inventory.
Property and Equipment, Net
Property and equipment are recorded at cost, less accumulated depreciation and amortization. Equipment is depreciated using the straight-line method over their estimated useful lives of three years and leasehold improvements are amortized using the straight-line method over the estimated useful life of the asset or the lease term, whichever is shorter. Leased buildings under build-to-suit lease arrangements are capitalized and included in property and equipment when we are involved in the construction of the structural improvements or take construction risk prior to the commencement of the lease. Upon occupancy of facilities under the build-to-suit leases, we assess whether those arrangements qualify for sales recognition under the sale-leaseback accounting guidance. If we continue to be the deemed owner, the facilities would be accounted for as financing leases.
Impairment of Long-Lived Assets
We account for long-lived assets in accordance with authoritative guidance for impairment or disposal of long-lived assets. Long-lived assets are reviewed for events or changes in circumstances, which indicate that their carrying value may not be recoverable. For the years ended December 31, 2012 and 2011, there has been no impairment of the value of such assets.
Fair Value of Financial Instruments
We follow the authoritative guidance for fair value measurements and disclosures, which among other things, defines fair value, establishes a consistent framework for measuring fair value and expands disclosure for each major asset and liability category measured at fair value on either a recurring or nonrecurring basis. Fair value is defined as an exit price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or liability.
The framework for measuring fair value provides a hierarchy that prioritizes the inputs to valuation techniques used in measuring fair value as follows:
 
 
 
 
 
Level 1
  
Quoted prices (unadjusted) in active markets for identical assets or liabilities,
 
 
 
Level 2
  
Inputs other than quoted prices included within Level 1 that are either directly or indirectly observable, and
 
 
 
Level 3
  
Unobservable inputs in which little or no market activity exists, therefore requiring an entity to develop its own assumptions about the assumptions that market participants would use in pricing.
Our financial instruments include cash and cash equivalents, accounts receivable, prepaid expenses, accounts payable, accrued expenses and long-term debt. Fair value estimates of these instruments are made at a specific point in time, based on relevant market information. These estimates may be subjective in nature and involve uncertainties and matters of significant judgment and therefore cannot be determined with precision. The carrying amount of cash and cash equivalents, accounts receivable, prepaid expenses, accounts payable and accrued expenses are generally considered to be representative of their respective fair values because of the short-term nature of those instruments. . Further, based on the borrowing rates currently available to us for loans with similar terms, we believe the fair value of long-term debt approximates its carrying value. Cash equivalents of approximately $98.4 million and $51.8 million at December 31, 2012 and 2011, respectively, are carried at fair value and are classified within Level 1 of the fair value hierarchy because they are valued based on quoted market prices for identical securities. We have no instruments that are classified within Level 2 and Level 3.
Deferred Rent
Rent expense is recorded on a straight-line basis over the initial term of the lease. The difference between rent expense accrued and amounts paid under lease agreements is recorded as deferred rent in the accompanying consolidated balance sheets.
Comprehensive Income/Loss
Comprehensive income (loss) is defined as the change in equity during a period from transactions and other events and circumstances from non-owner sources. Comprehensive loss was the same as our net loss for all periods presented.
Revenue Recognition
We generate revenues from product sales and collaborative agreements. Payments received under collaborative agreements may include nonrefundable fees at the inception of the agreements, license fees, milestone payments for specific achievements designated in the collaborative agreements, reimbursements of research and development services and supply of bulk rHuPH20, and/or royalties on sales of products resulting from collaborative arrangements.
We recognize revenues in accordance with the authoritative guidance for revenue recognition. We recognize revenue when all of the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the seller’s price to the buyer is fixed or determinable; and (4) collectibility is reasonably assured.
Product Sales, Net. Hylenex recombinant was approved for marketing by the FDA in December 2005. From 2005 through January 7, 2011, we granted Baxter the worldwide market rights for Hylenex recombinant under the terms of the amended and restated development and supply agreement with Baxter ("Hylenex Collaboration"). Baxter commercially launched Hylenex recombinant in October 2009. Effective January 7, 2011, we and Baxter mutually agreed to terminate the collaboration. During the second quarter of 2011, we submitted the data that the FDA had requested to support the reintroduction of Hylenex recombinant to the market. The FDA approved the submitted data and granted the reintroduction of Hylenex recombinant.
In December 2011, we reintroduced Hylenex recombinant to the market, shipped initial orders to our wholesaler customers and began promoting Hylenex recombinant through our sales force. We sell Hylenex recombinant in the United States to wholesale pharmaceutical distributors, who sell the product to hospitals and other end-user customers. The wholesale distributors take title to the product, bear the risk of loss of ownership and have economic substance to the inventory. Further, we have no significant obligations for future performance to generate pull-through sales; however, we allow the wholesale distributors to return product that is damaged or received in error. In addition, we allow for product to be returned beginning six months prior to and ending twelve months following product expiration.
Given our limited history of selling Hylenex recombinant and the lengthy return period, we currently cannot reliably estimate expected returns and chargebacks of Hylenex recombinant at the time the product is received by the wholesale distributors. Therefore, we do not recognize revenue upon delivery of Hylenex recombinant to the wholesale distributor until the point at which we can reliably estimate expected product returns and chargebacks from the wholesale distributors. Shipments of Hylenex recombinant are recorded as deferred revenue until evidence exists to confirm that pull-through sales to the hospitals or other end-user customers have occurred. We recognize revenue when the product is sold through from the distributors to the distributors’ customers. In addition, the costs of manufacturing Hylenex recombinant associated with the deferred revenue are recorded as deferred costs, which are included in inventory, until such time as the related deferred revenue is recognized. We estimate sell-through revenue and certain gross to net sales adjustments based on analysis of third-party information including information obtained from certain distributors with respect to their inventory levels and sell-through to the distributors’ customers. At the time we can reliably estimate product returns and chargebacks from the wholesale distributors, we will record a one-time increase in net product sales revenue related to the recognition of product sales revenue previously deferred.
We recognize product sales allowances as a reduction of product sales in the same period the related revenue is recognized. Product sales allowances are based on amounts owed or to be claimed on the related sales. These estimates take into consideration the terms of our agreements with wholesale distributors and hospitals and the levels of inventory within the distribution channels that may result in future discounts taken. We must make significant judgments in determining these allowances. If actual results differ from our estimates, we will be required to make adjustments to these allowances in the future, which could have an effect on product sales revenue in the period of adjustment. Our product sales allowances include:
Distribution Fees.    The distribution fees, based on contractually determined rates, arise from contractual agreements we have with certain wholesale distributors for distribution services they provide with respect to Hylenex recombinant. At the time the sale is made to the respective wholesale distributors, we record an allowance for distribution fees by reducing our accounts receivable and deferred revenue associated with such product sales.
Prompt Payment Discounts.    We offer cash discounts to certain wholesale distributors as an incentive to meet certain payment terms. We expect our customers will take advantage of this discount; therefore, at the time the sale is made to the respective wholesale distributors, we accrue the entire prompt payment discount, based on the gross amount of each invoice, by reducing our accounts receivable and deferred revenue associated with such product sales.
Chargebacks.    We provide discounts to end-user members of certain group purchasing organizations ("GPO") under collective purchasing contracts between us and the GPOs. We also provide discounts to certain hospitals, who are members of the GPOs with which we do not have contracts. The end-user members purchase products from the wholesale distributors at a contracted discounted price, and the wholesale distributors then charge back to us the difference between the current retail price and the price the end-users paid for the product. Given our lack of historical sales data, we recognize chargebacks in the same period the related product sales revenue is recognized and reduce our accounts receivable accordingly. We incur GPO fees for these transactions which are also recorded in the same period the related product sales revenue is recognized and are included in accrued expenses.
Product Returns.    The product returns reserve is based on management’s best estimate of the product sales recognized as revenue during the period that are anticipated to be returned. The product returns reserve is recorded as a reduction of product sales revenue in the same period the related product sales revenue is recognized and is included in accrued expenses.
For the years ended December 31, 2012 and 2011, we recorded product sales revenue of approximately $2.2 million and $35,000, respectively, related to Hylenex recombinant, net of estimated distribution fees, prompt payment discounts, chargebacks and product returns totaling approximately $1.1 million and $8,000, respectively. We have a deferred revenue balance of approximately $624,000 and $167,000 at December 31, 2012 and 2011, respectively, for Hylenex recombinant shipments, which is net of estimated distribution fees, prompt pay discounts and product returns. In addition, inventory at December 31, 2012 and 2011 included a deferred cost of product sales of approximately $178,000 and $31,000, respectively, associated with Hylenex recombinant shipments to wholesalers. At the time we can reliably estimate product returns and chargebacks from the wholesalers, we will record a one-time increase in net product sales revenue related to the recognition of product sales revenue previously deferred.
Revenues under Collaborative Agreements. We have license and collaboration agreements under which the collaborators obtained worldwide rights for the use of our proprietary rHuPH20 enzyme in the development and commercialization of the collaborators’ biologic compounds. The collaborative agreements contain multiple elements including nonrefundable payments at the inception of the arrangement, license fees, exclusivity fees, payments based on achievement of specified milestones designated in the collaborative agreements, annual maintenance fees, reimbursements of research and development services, payments for supply of rHuPH20 API for the collaborator and/or royalties on sales of products resulting from collaborative agreements. We analyze each element of our collaborative agreements and consider a variety of factors in determining the appropriate method of revenue recognition of each element.
Effective January 1, 2011, we adopted Accounting Standards Update ("ASU") No. 2009-13, Multiple-Deliverable Revenue Arrangements ("ASU 2009-13"). In order to account for the multiple-element arrangements, we identify the deliverables included within the agreement and evaluate which deliverables represent units of accounting. Analyzing the arrangement to identify deliverables requires the use of judgment, and each deliverable may be an obligation to deliver services, a right or license to use an asset, or another performance obligation. The deliverables under our collaborative agreements include (i) the license to our rHuPH20 technology, (ii) at the collaborator’s request, research and development services which are reimbursed at contractually determined rates, and (iii) at the collaborator’s request, supply of rHuPH20 API which is reimbursed at our cost plus a margin. A delivered item is considered a separate unit of accounting when the delivered item has value to the collaborator on a standalone basis based on the consideration of the relevant facts and circumstances for each arrangement. Factors considered in this determination include the research capabilities of the collaborator and the availability of research expertise in this field in the general marketplace.
Arrangement consideration is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”), of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence of selling price exists, we use our best estimate of the selling price for the deliverable. The amount of allocable arrangement consideration is limited to amounts that are not contingent upon the delivery of additional items or meeting other specified performance conditions. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. Changes in the allocation of the sales price between delivered and undelivered elements can impact revenue recognition but do not change the total revenue recognized under any agreement.
Nonrefundable upfront license fee payments are recognized upon delivery of the license if facts and circumstances dictate that the license has standalone value from the undelivered items, which generally include research and development services and the manufacture of rHuPH20 API, the relative selling price allocation of the license is equal to or exceeds the upfront license fee, persuasive evidence of an arrangement exists, our price to the collaborator is fixed or determinable and collectibility is reasonably assured. Upfront license fee payments are deferred if facts and circumstances dictate that the license does not have standalone value. The determination of the length of the period over which to defer revenue is subject to judgment and estimation and can have an impact on the amount of revenue recognized in a given period.
Prior to the adoption of ASU No. 2009-13 on January 1, 2011, in order for a delivered item to be accounted for separately from other deliverables in a multiple-element arrangement, the following three criteria had to be met: (i) the delivered item had standalone value to the customer, (ii) there was objective and reliable evidence of fair value of the undelivered items and (iii) if the arrangement included a general right of return relative to the delivered item, delivery or performance of the undelivered items was considered probable and substantially in the control of the vendor. For the collaborative agreements entered into prior to January 1, 2011, there was no objective and reliable evidence of fair value of the undelivered items. Thus, the delivered licenses did not meet all of the required criteria to be accounted for separately from undelivered items. Therefore, we recognize revenue on nonrefundable upfront payments and license fees from these collaborative agreements over the period of significant involvement under the related agreements.
The terms of our collaborative agreements provide for milestone payments upon achievement of certain development and regulatory events and/or specified sales volumes of commercialized products by the collaborator. Effective January 1, 2011, we adopted, on a prospective basis, ASU No. 2010-17, Revenue Recognition - Milestone Method (“Milestone Method”). Under the Milestone Method, we recognize consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:
1.
The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the entity’s performance to achieve the milestone,
2.
The consideration relates solely to past performance, and
3.
The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.
A milestone is defined as an event (i) that can only be achieved based in whole or in part on either the entity’s performance or on the occurrence of a specific outcome resulting from the entity’s performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved and (iii) that would result in additional payments being due to the vendor.
Prior to our adoption of the Milestone Method, we recognized milestone payments upon the achievement of specified milestones if: (1) the milestone was substantive in nature and the achievement of the milestone was not reasonably assured at the inception of the agreement, (2) the fees were nonrefundable and (3) our performance obligations after the milestone achievement would continue to be funded by our collaborator at a level comparable to the level before the milestone achievement.
Reimbursements of research and development services are recognized as revenue during the period in which the services are performed as long as there is persuasive evidence of an arrangement, the fee is fixed or determinable and collection of the related receivable is reasonably assured. Revenue from the manufacture of rHuPH20 API is recognized when the API has met all specifications required for the collaborator's acceptance and title and risk of loss have transferred to the collaborator. We do not directly control when any collaborator will request research and development services or supply of rHuPH20 API; therefore, we cannot predict when we will recognize revenues in connection with research and development services and supply of rHuPH20 API. Royalties to be received based on sales of licensed products by our collaborators will be recognized as earned.
The collaborative agreements typically provide the collaborators the right to terminate such agreement in whole or on a product-by-product or target-by-target basis at any time upon 30 to 90 days prior written notice to us. There are no performance, cancellation, termination or refund provisions in any of our collaborative agreements that contain material financial consequences to us.
Refer to Note 3, “Collaborative Agreements,” and Note 5, “Deferred Revenue,” for further discussion on our collaborative arrangements.
Cost of Product Sales
Cost of product sales consists primarily of raw materials, third-party manufacturing costs, fill and finish costs, freight costs, internal costs and manufacturing overhead associated with the production of Hylenex recombinant. Cost of product sales also consists of the write-down of excess, dated and obsolete inventories. As a result of the termination of the Baxter Hylenex Collaboration in January 2011, we recorded write-down of inventory obsolescence of $166,000 and $875,000 for Hylenex recombinant API for the years ended December 31, 2011 and 2010, respectively. There was no write-down of inventories for the year ended December 31, 2012.
Research and Development Expenses
Research and development expenses include salaries and benefits, facilities and other overhead expenses, external clinical trial expenses, research related manufacturing services, contract services and other outside expenses. Research and development expenses are charged to operations as incurred when these expenditures relate to our research and development efforts and have no alternative future uses. 
In accordance with certain research and development agreements, we are obligated to make certain upfront payments upon execution of the agreement. Advance payments, including nonrefundable amounts, for goods or services that will be used or rendered for future research and development activities are deferred and capitalized. Such amounts will be recognized as an expense as the related goods are delivered or the related services are performed or such time when we do not expect the goods to be delivered or services to be performed.
Milestone payments that we make in connection with in-licensed technology or product candidates are expensed as incurred when there is uncertainty in receiving future economic benefits from the licensed technology or product candidates. We consider the future economic benefits from the licensed technology or product candidates to be uncertain until such licensed technology or product candidates are approved for marketing by the regulatory bodies such as the FDA or when other significant risk factors are abated. Management has viewed future economic benefits for all of our licensed technology or product candidates to be uncertain and has expensed these amounts as incurred.
Clinical Trial Expenses
Payments in connection with our clinical trials are often made under contracts with multiple contract research organizations that conduct and manage clinical trials on our behalf. The financial terms of these agreements are subject to negotiation and vary from contract to contract and may result in uneven payment flows. Generally, these agreements set forth the scope of work to be performed at a fixed fee, unit price or on a time-and-material basis. Payments under these contracts depend on factors such as the successful enrollment or treatment of patients or the completion of other clinical trial milestones.
Expenses related to clinical trials are accrued based on our estimates and/or representations from service providers regarding work performed, including actual level of patient enrollment, completion of patient studies and progress of the clinical trials. Other incidental costs related to patient enrollment or treatment are accrued when reasonably certain. If the contracted amounts are modified (for instance, as a result of changes in the clinical trial protocol or scope of work to be performed), we modify our accruals accordingly on a prospective basis. Revisions in the scope of a contract are charged to expense in the period in which the facts that give rise to the revision become reasonably certain. Historically, we have had no material changes in clinical trial expense accruals that would have had a material impact on our consolidated results of operations or financial position.
Share-Based Compensation
We record compensation expense associated with stock options and other share-based awards in accordance with the authoritative guidance for stock-based compensation. The cost of employee services received in exchange for an award of an equity instrument is measured at the grant date, based on the estimated fair value of the award, and is recognized as expense on a straight-line basis, net of estimated forfeitures, over the requisite service period of the award. Share-based compensation expense recognized during the period is based on the value of the portion of share-based payment awards that is ultimately expected to vest during the period. Share-based compensation expense for an award with a performance condition is recognized when the achievement of such performance condition is determined to be probable. If the outcome of such performance condition is not determined to be probable or is not met, no compensation expense is recognized and any recognized compensation expense is reversed. As share-based compensation expense recognized is based on awards ultimately expected to vest, it has been reduced for estimated forfeitures. The guidance requires forfeitures to be estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Pre-vesting forfeitures were estimated to be approximately 10% for employees in the years ended December 31, 2012, 2011 and 2010 based on our historical experience for the years then ended.
Total share-based compensation expense related to share-based awards for the years ended December 31, 2012, 2011 and 2010 was comprised of the following: 
 
 
Year Ended December 31,
 
 
2012
 
2011
 
2010
Research and development
 
$
4,190,938

 
$
2,815,362

 
$
2,517,172

Selling, general and administrative
 
4,157,649

 
2,754,537

 
2,349,153

Share-based compensation expense
 
$
8,348,587

 
$
5,569,899

 
$
4,866,325

Net share-based compensation expense, per basic and diluted share
 
$
0.08

 
$
0.05

 
$
0.05

Share-based compensation expense from:
 

 

 

Stock options
 
$
4,722,629

 
$
3,230,822

 
$
4,022,790

Restricted stock awards and restricted stock units
 
3,625,958

 
2,339,077

 
843,535

 
 
$
8,348,587

 
$
5,569,899

 
$
4,866,325


Cash flows resulting from tax deductions in excess of the cumulative compensation cost recognized for options exercised (excess tax benefits) are classified as cash inflows provided by financing activities and cash outflows used in operating activities. Due to our net loss position, no tax benefits have been recognized in the consolidated statements of cash flows.
Income Taxes
We provide for income taxes using the liability method. Under this method, deferred income tax assets and liabilities are determined based on the differences between the financial statement carrying amounts of existing assets and liabilities at each year end and their respective tax bases and are measured using enacted tax rates in effect for the year in which the differences are expected to affect taxable income. Deferred tax assets and other tax benefits are recorded when it is more likely than not that the position will be sustained upon audit. Valuation allowances have been established to reduce our net deferred tax assets to zero, as we believe that it is more likely than not that such assets will not be realized.
Other Income
Other income for the year ended December 31, 2010 consisted of one-time grants of approximately $978,000 received under the Qualifying Therapeutic Discovery Project program administered under section 48D of the Internal Revenue Code. 
Net Loss Per Share
Basic net loss per common share is computed by dividing net loss for the period by the weighted average number of common shares outstanding during the period, without consideration for common stock equivalents. Stock options, unvested stock awards and restricted stock units are considered to be common equivalents and are only included in the calculation of diluted earnings per common share when their effect is dilutive. Because of our net loss, outstanding stock options, outstanding restricted stock units and unvested stock awards totaling 7,444,333, 6,365,667 and 8,095,365 were excluded from the calculation of diluted net loss per common share for the years ended December 31, 2012, 2011 and 2010, respectively, because their effect is anti-dilutive.
Segment Information
We operate our business in one segment, which includes all activities related to the research, development and commercialization of human enzymes that either transiently modify tissue under the skin to facilitate the delivery of injected drugs and fluids or to alter abnormal tissue structures for clinical benefit. This segment also includes revenues and expenses related to (1) research and development activities conducted under our collaborative agreements with third parties and (ii) product sales of Hylenex recombinant. The chief operating decision maker reviews the operating results on an aggregate basis and manages the operations as a single operating segment.
Adoption of Recent Accounting Pronouncements
Effective January 1, 2012, we adopted Financial Accounting Standards Board's (“FASB”) Accounting Standards Update (“ASU”) No. 2011-05, Comprehensive Income (Topic 220): Presentation of Comprehensive Income and ASU No. 2011-12, Comprehensive Income (Topic 220): Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in ASU No. 2011-5. In these updates, an entity has the option to present the total of comprehensive income, the components of net income, and the components of other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. In both choices, an entity is required to present each component of net income along with total net income, each component of other comprehensive income along with a total for other comprehensive income, and a total amount for comprehensive income. ASU No. 2011-05 eliminates the option to present the components of other comprehensive income as part of the statement of changes in stockholders' equity. The amendments in ASU No. 2011-05 do not change the items that must be reported in other comprehensive income or when an item of other comprehensive income must be reclassified to net income. The amendments in these updates are effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The adoption of ASU Nos. 2011-05 and 2011-12 did not have a material impact on our consolidated financial position or results of operations. We have presented comprehensive loss in our consolidated statements of comprehensive loss.
Effective January 1, 2012, we prospectively adopted FASB's ASU No. 2011-04, “Fair Value Measurement (Topic 820) - Amendments to Achieve Common Fair Value Measurement and Disclosure Requirements in U.S. GAAP and IFRS”. The amendments in ASU 2011-04 result in common fair value measurement and disclosure requirements in GAAP and International Financial Reporting Standards (“IFRS”). Consequently, the amendments change the wording used to describe many of the requirements in U.S. GAAP for measuring fair value and for disclosing information about fair value measurements. This pronouncement is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The adoption of ASU No. 2011-04 did not have a material effect on our consolidated financial position or results of operations.
Collaborative Agreements
Collaborative Agreements
Collaborative Agreements
Roche Collaboration
In December 2006, we and Roche entered into a license and collaborative agreement under which Roche obtained a worldwide, exclusive license to develop and commercialize product combinations of rHuPH20 and up to thirteen Roche target compounds (the “Roche Collaboration”). As of December 31, 2012, Roche has elected a total of five exclusive targets and retains the option to develop and commercialize rHuPH20 with three additional targets, provided that Roche continues to pay annual maintenance fees to us. As of December 31, 2012, we have received $61.75 million from Roche, including the $20.0 million upfront license fee payment for the application of rHuPH20 to the initial three Roche exclusive targets, $20.75 million in connection with Roche's election of two additional exclusive targets and annual license maintenance fees for the right to designate the remaining targets as exclusive targets, $13.0 million in clinical development milestone payments and $8.0 million in regulatory milestone payments. We are also entitled to receive reimbursements for providing research and development services and rHuPH20 API to Roche at its request.
Under the terms of the Roche Collaboration, Roche will pay us a royalty on each product commercialized under the agreement consisting of a mid-single digit percent of the net sales of such product. Unless terminated earlier in accordance with its terms, the Roche Collaboration continues in effect until the expiration of Roche's obligation to pay royalties. Roche has the obligation to pay royalties with respect to each product in each country, during the period equal to the longer of: (a) the duration of any valid claim of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers the product in such country or (b) ten years following the date of the first commercial sale of such product in such country. Pursuant to the terms of the Roche Collaboration, we scaled up the production of rHuPH20 and identified a second source manufacturer that would help meet anticipated production obligations arising from the Roche Collaboration.
Due to our continuing involvement obligations (for example, support activities associated with rHuPH20), revenues from the upfront payment, exclusive designation fees and annual license maintenance fees were deferred and are being recognized over the term of the Roche Collaboration. Refer to Note 5 for a further discussion on deferred revenue associated with the Roche Collaboration. We determined that the clinical and regulatory milestones were substantive; therefore, we recognized the clinical and regulatory milestone payments as revenue upon achievement of such milestones.
For the years ended December 31, 2012 and 2011, we recognized $8.0 million and $5.0 million, respectively, as revenues under collaborative agreements in accordance with the Milestone Method related to the achievement of certain regulatory and clinical milestones pursuant to the terms of the Roche Collaboration. There were no milestone payments recognized as revenues under collaborative agreements under the Roche Collaboration for the year ended December 31, 2010.
Gammagard Collaboration
In September 2007, we entered into a license and collaborative agreement with Baxter, under which Baxter obtained a worldwide, exclusive license to develop and commercialize a product candidate (currently named HyQ) consisting of rHuPH20 combined with a current Baxter product, GAMMAGARD LIQUID (the “Gammagard Collaboration”). As of December 31, 2012, we have received $13.0 million under the Gammagard Collaboration, including the $10.0 million upfront license fee payment and a $3.0 million regulatory milestone payment. Baxter will pay us a royalty on each product commercialized under the agreement consisting of a mid-single digit percent of the net sales of such product.
The Gammagard Collaboration is applicable to both kit and formulation combinations. Baxter assumes all development, manufacturing, clinical, regulatory, sales and marketing costs under the Gammagard Collaboration, while we are responsible for the supply of rHuPH20 enzyme. We perform research and development activities and supply rHuPH20 enzyme at the request of Baxter, which are reimbursed by Baxter under the terms of the Gammagard Collaboration. In addition, Baxter has certain product development and commercialization obligations in major markets identified in the Gammagard Collaboration.
Unless terminated earlier in accordance with its terms, the Gammagard Collaboration continues in effect until the expiration of Baxter's obligation to pay royalties. Baxter has the obligation to pay royalties, with respect to each product in each country, during the period equal to the longer of: (a) the duration of any valid claim of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers the product in such country or (b) ten years following the date of the first commercial sale of such product in such country.
Due to our continuing involvement obligations (for example, support activities associated with rHuPH20 enzyme), the upfront payment was deferred and is being recognized over the term of the Gammagard Collaboration. For the year ended December 31, 2011, we recognized $3.0 million as revenues under collaborative agreements under the Gammagard Collaboration in accordance with the Milestone Method. There were no milestone payments recognized as revenues under collaborative agreements under the Gammagard Collaboration for the years ended December 31, 2012 and 2010.
Other Collaborations
In December 2012, we and Pfizer entered into a collaboration and license agreement, under which Pfizer has the worldwide license to develop and commercialize products combining rHuPH20 enzyme with Pfizer proprietary biologics directed to up to six targets (the “Pfizer Collaboration”). Targets may be selected on an exclusive or non-exclusive basis. As of December 31, 2012, we have recognized a nonrefundable upfront payment of $9.5 million for the licenses to three specified exclusive targets and three additional targets which Pfizer has the right to elect in the future upon payment of additional fees. Unless terminated earlier in accordance with its terms, the Pfizer Collaboration continues in effect until the later of (i) expiration of the last to expire of the valid claims of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers a product developed under the collaboration, and (ii) expiration of the last to expire royalty term for a product developed under the collaboration. The royalty term of a product developed under the Pfizer Collaboration, with respect to each country, consists of the period equal to the longer of: (a) the duration of any valid claim of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers the product in such country or (b) ten years following the date of the first commercial sale of such product in such country. Pfizer may terminate the agreement prior to expiration for any reason in its entirety or on a target-by-target basis upon 30 days prior written notice to us. Upon any such termination, the license granted to Pfizer (in total or with respect to the terminated target, as applicable) will terminate, provided, however, that in the event of expiration of the agreement, the licenses granted will become perpetual, non-exclusive and fully-paid-up.
In May 2011, we and ViroPharma entered into a collaboration and license agreement, under which ViroPharma obtained a worldwide exclusive license for the use of rHuPH20 enzyme in the development of a subcutaneous injectable formulation of ViroPharma's commercialized product, Cinryze® (C1 esterase inhibitor [human]) (the “ViroPharma Collaboration”). In addition, the license provides ViroPharma with exclusivity to C1 esterase inhibitor and to the hereditary angioedema indication, along with three additional orphan indications. As of December 31, 2012, we have received $13.0 million from ViroPharma, including the $9.0 million nonrefundable upfront license fee payment and a $3.0 million clinical development milestone payment. We are entitled to receive a royalty on each product commercialized under the agreement consisting of ten percent of the net sales of such product. Unless terminated earlier in accordance with its terms, the ViroPharma Collaboration continues in effect until the later of (i) expiration of the last to expire of the valid claims of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers a product developed under the collaboration, and (ii) expiration of the last to expire royalty term for a product developed under the collaboration. The royalty term of a product developed under the ViroPharma Collaboration, with respect to each country, consists of the period equal to the longer of: (a) the duration of any valid claim of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers the product in such country or (b) ten years following the date of the first commercial sale of such product in such country. ViroPharma may terminate the agreement prior to expiration for any reason on a product-by-product basis upon 90 days prior written notice to us. Upon any such termination, the license granted to ViroPharma (in total or with respect to the terminated product, as applicable) will terminate.
In June 2011, we and Intrexon entered into a collaboration and license agreement, under which Intrexon obtained a worldwide exclusive license for the use of rHuPH20 enzyme in the development of a subcutaneous injectable formulation of Intrexon's recombinant human alpha 1-antitrypsin (rHuA1AT) (the “Intrexon Collaboration”). In addition, the license provides Intrexon with exclusivity for a defined indication (“Exclusive Field”). As of December 31, 2012, we have received $10.0 million from Intrexon, including a nonrefundable upfront license fee payment of $9.0 million. We are entitled to receive a royalty on each product commercialized under the agreement consisting of a percentage of the net sales of such product ranging from mid-single digits up to a low double-digit percentage. Unless terminated earlier in accordance with its terms, the Intrexon Collaboration continues in effect until the later of (i) expiration of the last to expire of the valid claims of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers a product developed under the collaboration, and (ii) expiration of the last to expire royalty term for a product developed under the collaboration. The royalty term of a product developed under the Intrexon Collaboration, with respect to each country, consists of the period equal to the longer of: (a) the duration of any valid claim of our patents covering rHuPH20 or other specified patents developed under the collaboration which valid claim covers the product in such country or (b) ten years following the date of the first commercial sale of such product in such country. Intrexon may terminate the agreement prior to expiration for any reason on a product-by-product basis upon 90 days prior written notice to us. Upon any such termination, the license granted to Intrexon (in total or with respect to the terminated product, as applicable) will terminate. Intrexon's chief executive officer, chairman of its board of directors and major shareholder is also a member of our board of directors.
We identified the deliverables at the inception of the Pfizer, ViroPharma and Intrexon agreements which are the license, research and development services and API supply. We have determined that the license, research and development services and API supply individually represent separate units of accounting, because each deliverable has standalone value. The estimated selling prices for these units of accounting were determined based on market conditions, the terms of comparable collaborative arrangements for similar technology in the pharmaceutical and biotech industry and entity-specific factors such as the terms of our previous collaborative agreements, our pricing practices and pricing objectives and the nature of the research and development services to be performed for the collaborators. The arrangement consideration was allocated to the deliverables based on the relative selling price method.
The amount allocable to the delivered unit or units of accounting is limited to the amount that is not contingent upon the delivery of additional items or meeting other specified performance conditions (the noncontingent amount). As such, we excluded from the allocable arrangement consideration the milestone payments, annual exclusivity fees and royalties regardless of the probability of receipt. Based on the results of our analysis, we allocated the $9.5 million license fees from Pfizer, the $9.0 million upfront license fee from ViroPharma and the $9.0 million upfront license fee from Intrexon to the license fee deliverable under each of the arrangements. We determined that the upfront payments were earned upon the granting of the worldwide, exclusive right to our technology to the collaborators in these arrangements. As a result, we recognized the $9.5 million license fee under the Pfizer Collaboration for the year ended December 31, 2012, the $9.0 million upfront license fee received under the ViroPharma Collaboration and the $9.0 million upfront license fee received under the Intrexon Collaboration for the year ended December 31, 2011, as revenues under collaborative agreements.
Pfizer, ViroPharma and Intrexon are each solely responsible for the development, manufacturing and marketing of any products resulting from their respective collaborations. We are entitled to receive payments for research and development services and supply of rHuPH20 API to these collaborators if requested by such collaborator. We recognize amounts allocated to research and development services as revenues under collaborative agreements as the related services are performed. We recognize amounts allocated to the sales of API as revenues under collaborative agreements when such API has met all required specifications by the collaborators and the related title and risk of loss and damages have passed to the collaborators. We cannot predict the timing of delivery of research and development services and API as they are at the collaborators' requests.
For the year ended December 31, 2011, we recognized a $3.0 million milestone payment as revenues under collaborative agreements in accordance with the Milestone Method related to the achievement of a development milestone pursuant to the terms of the ViroPharma Collaboration. There were no milestone payments recognized as revenues under collaborative agreements associated with these collaborations for the year ended December 31, 2012. There were no milestone payments recognized as revenues under collaborative agreements associated with the Intrexon Collaboration for the years ended December 31, 2012 and 2011.
Pursuant to the terms of our existing collaborations collectively, we are entitled to receive additional milestone payments for the successful development of the elected targets in the aggregate of up to approximately $58.5 million upon achievement of specified clinical development milestone events and up to approximately $84.0 million upon achievement of specified regulatory milestone events in connection with specified regulatory filings and receipt of marketing approvals.
Certain Balance Sheet Items
Certain Balance Sheet Items
Certain Balance Sheet Items
Inventories consist of the following:
 
 
December 31,
2012
 
December 31,
2011
Raw materials
 
$
1,127,061

 
$
201,822

Work-in-process
 
792,257

 
290,647

Finished goods
 
751,378

 
74,794

 
 
$
2,670,696

 
$
567,263


Property and equipment consists of the following:
 
 
December 31,
2012
 
December 31,
2011
Research equipment
 
$
6,360,004

 
$
5,231,763

Computer and office equipment
 
1,432,975

 
1,266,041

Leasehold improvements
 
1,138,110

 
1,019,147

Building (1)
 
1,450,000

 

 
 
10,381,089

 
7,516,951

Accumulated depreciation and amortization
 
(6,680,627
)
 
(5,745,903
)
 
 
$
3,700,462

 
$
1,771,048

________________________
(1)
Represents capitalized building under a build-to-suit lease arrangement where we are considered the owner (for accounting purposes only) during the construction period.
Depreciation and amortization expense was approximately $1.1 million, $1.1 million and $1.5 million, for the years ended December 31, 2012, 2011 and 2010, respectively.
Accrued expenses consist of the following:
 
 
December 31,
2012
 
December 31,
2011
Accrued outsourced research and development expenses
 
$
2,223,242

 
$
1,910,273

Accrued compensation and payroll taxes
 
4,053,590

 
3,223,936

Other accrued expenses
 
1,506,615

 
481,365

 
 
$
7,783,447

 
$
5,615,574

Deferred Revenue
Deferred Revenue
Deferred Revenue
Deferred revenue consists of the following:
 
 
December 31,
2012
 
December 31,
2011
Collaborative agreements
 
$
43,222,473

 
$
40,716,806

Product sales
 
623,510

 
167,184

Total deferred revenue
 
43,845,983

 
40,883,990

Less current portion
 
8,891,017

 
4,129,407

Deferred revenue, net of current portion
 
$
34,954,966

 
$
36,754,583


Roche Collaboration.    In December 2006, we and Roche entered into the Roche Collaboration under which Roche obtained a worldwide, exclusive license to develop and commercialize product combinations of rHuPH20 and certain Roche target compounds. Under the terms of the Roche Collaboration, Roche paid $20.0 million to us in December 2006 as an initial upfront payment for the application of rHuPH20 to three pre-defined Roche biologic targets. Through December 31, 2012, Roche has paid an aggregate of $20.75 million in connection with Roche’s election of two additional exclusive targets and annual license maintenance fees for the right to designate the remaining targets as exclusive targets. Roche currently retains the option to develop and commercialize rHuPH20 with three additional targets, provided that Roche continues to pay annual license maintenance fees to us.
Due to our continuing involvement obligations (for example, support activities associated with rHuPH20 enzyme), revenues from the upfront payment, exclusive designation fees and annual license maintenance fees were deferred and are being recognized over the term of the Roche Collaboration. We recognized revenue from the upfront payment, exclusive designation fees and annual license maintenance fees under the Roche Collaboration in the amounts of approximately $2.0 million for each of the years ended December 31, 2012, 2011 and 2010. Deferred revenue relating to the upfront payment, exclusive designation fees and annual license maintenance fees under the Roche Collaboration was $30.4 million and $31.7 million as of December 31, 2012 and 2011, respectively.
During the year ended December 31, 2012, we received approximately $7.0 million in deferred revenue relating to the manufacture of rHuPH20 API for Roche. We recognized approximately $1.4 million as revenues under collaborative agreements from deferred revenue relating to the manufacture of rHuPH20 API for the year ended December 31, 2012. Deferred revenue relating to the manufacture of rHuPH20 API under the Roche Collaboration was $5.6 million and zero as of December 31, 2012 and 2011, respectively.
Baxter Gammagard Collaboration.    In September 2007, we and Baxter entered into the Gammagard Collaboration, under which Baxter obtained a worldwide, exclusive license to develop and commercialize product combinations of rHuPH20 with GAMMAGARD LIQUID. Under the terms of the Gammagard Collaboration, Baxter paid us a nonrefundable upfront payment of $10.0 million. Due to our continuing involvement obligations (for example, support activities associated with rHuPH20 enzyme), the $10.0 million upfront payment was deferred and is being recognized over the term of the Gammagard Collaboration. We recognized revenue from the upfront payment under the Gammagard Collaboration in the amounts of approximately $483,000, $483,000 and $521,000 for the years ended December 31, 2012, 2011 and 2010, respectively. Deferred revenue relating to the upfront payment under the Gammagard Collaboration was $7.1 million and $7.6 million as of December 31, 2012 and 2011, respectively.
Baxter Hylenex Collaboration.    In February 2007, we and Baxter amended certain existing agreements for Hylenex recombinant and entered into the Hylenex Collaboration for kits and formulations with rHuPH20. Under the terms of the Hylenex Collaboration, Baxter paid us a nonrefundable upfront payment of $10.0 million. In addition, Baxter would make payments to us based on sales of the products covered under the Hylenex Collaboration. Baxter had prepaid nonrefundable product-based payments totaling $10.0 million in connection with the execution of the Hylenex Collaboration. Due to our continuing involvement obligations (for example, support activities associated with rHuPH20 enzyme), the $10.0 million upfront payment was initially deferred and was being recognized over the term of the Hylenex Collaboration. The prepaid product-based payments were also deferred and were being recognized as product sales revenues as we earned such revenues from the sales of Hylenex recombinant by Baxter.
In January 2011, we and Baxter mutually agreed to terminate the Hylenex Collaboration and the associated agreements. The termination of these agreements does not affect the other relationships between the parties, including the application of our Enhanze technology to Baxter’s GAMMAGARD LIQUID.
In July 2011, we and Baxter entered into an agreement (the “Transition Agreement”) setting forth certain rights, data and assets to be transferred by Baxter to us during a transition period. Effective July 2011, we had no future performance obligations to Baxter in connection with the Hylenex Collaboration. Therefore, we recognized the unamortized deferred revenue of approximately $9.3 million relating to the prepaid product-based payments, and the unamortized deferred revenue of approximately $7.8 million relating to the deferred upfront payment from the Hylenex Collaboration as revenues under collaborative agreements for the year ended December 31, 2011. For the year ended December 31, 2010, we recognized revenues under the Hylenex Collaboration from the upfront payment in the amounts of approximately $503,000, and from the product-based payments in the amounts of approximately $332,000. There were no deferred revenues relating to the Hylenex Collaboration at December 31, 2012 and 2011.
As a result of the termination of the Hylenex Collaboration, at December 31, 2010 we had recharacterized deferred revenue of approximately $991,000 as a reserve for product returns for HYLENEX API previously delivered to Baxter that could be returned (“Delivered Products”). Pursuant to the terms of the Transition Agreement, Baxter no longer had the right to return the Hylenex recombinant API previously delivered to Baxter. Accordingly, we recharacterized the reserve for product returns for the Delivered Products of approximately $991,000 to current deferred revenue and recognized such deferred revenue as product sales revenue for the year ended December 31, 2011.
Long-Term Debt, Net
Long-term Debt, Net
Long-Term Debt, Net
In December 2012, we entered into a Loan and Security Agreement (the “Loan Agreement”) with Oxford Finance LLC (“Oxford”) and Silicon Valley Bank (“SVB”) (collectively, the “Lenders”) for a $30 million secured single-draw term loan facility with a maturity date, as amended, of January 1, 2017. On December 28, 2012, we drew down $30 million under the Loan Agreement. The proceeds are to be used for working capital and general business requirements. The term loan bears a fixed interest rate of 7.55% per annum. The monthly repayment schedule includes interest only payments in arrears for the first year followed by equal principal and interest payments for the subsequent 36 months. The term loan requires a final payment of $2.55 million which is due when the term loan becomes due or upon the prepayment of the facility. We have the option to prepay the outstanding balance of the term loan in full, subject to a prepayment fee of 1% to 3% depending upon when the prepayment occurs.
In connection with the term loan, we received proceeds of $29.7 million, net of debt offering costs. The debt offering costs have been recorded as debt discount on our consolidated balance sheet which together with the final $2.55 million payment and fixed interest rate payments will be amortized to interest expense throughout the life of the term loan using the effective interest rate method.
The term loan facility is secured by substantially all of the assets of the Company and Halozyme, Inc., except that the collateral does not include any intellectual property (including all licensing, collaboration and similar agreements relating thereto), and certain other excluded assets. The Loan Agreement contains customary representations, warranties and covenants by us, as well as customary events of default and our indemnification obligations. One of the events of default is a material adverse change which is defined as a material adverse change in our business, operations, or condition (financial or otherwise); a material impairment of the prospect of repayment of any portion of the loan; or a material impairment in the perfection or priority of lender's lien in the collateral or in the value of such collateral. As of December 31, 2012, we were in compliance with all material covenants under the Loan Agreement and there was no material adverse change.
Future maturities and interest payments under the term loan as of December 31, 2012, are as follows:
2013
 
$
2,076,250

2014
 
10,461,382

2015
 
11,206,507

2016
 
11,206,507

2017
 
3,483,876

Total minimum payments
 
38,434,522

Less amount representing interest
 
(8,434,522
)
Gross balance of long-term debt
 
30,000,000

Less unamortized debt discount
 
(338,320
)
Present value of long-term debt
 
29,661,680

Less current portion of long-term debt, less discount
 

Long-term debt, less current portion and discount
 
$
29,661,680


Interest expense, including amortization of debt discount, related to the long-term debt for the year ended December 31, 2012 was $28,000.
Stockholders' Equity
Stockholders' Equity
Stockholders’ Equity
During 2012, we issued an aggregate of 444,637 shares of common stock, in connection with the exercises of stock options for cash in the aggregate amount of approximately $2.0 million. In addition, we issued 374,195 shares of common stock, net of restricted stock awards canceled, in connection with the grants of restricted stock awards and 81,070 shares of common stock upon vesting of certain restricted stock units. The restricted stock unit holders surrendered 46,930 restricted stock units to pay for minimum withholding taxes totaling approximately $347,000.
In February 2012, we completed an underwritten public offering and issued 7,820,000 shares of common stock, including 1,020,000 shares sold pursuant to the full exercise of an over-allotment option granted to the underwriter. All of the shares were offered at a public offering price of $10.61 per share, generating approximately $81.5 million in net proceeds. Of the 7,820,000 shares of common stock sold, Randal J. Kirk, a member of our board of directors, through his affiliates, purchased 1,360,000 shares of common stock in this offering at the public offering price of $10.61 per share for a total of approximately $14.4 million.
During 2011, we issued an aggregate of 3,045,540 shares of common stock in connection with the exercises of 3,137,056 shares of stock options for cash in the aggregate amount of approximately $4.7 million. In addition, we issued 347,883 shares of common stock in connection with the grants of restricted stock awards and 15,000 shares of common stock upon vesting of certain restricted stock units.
In September 2010, we issued 8.3 million shares of common stock in a public offering at a public offering price of $7.50 per share, generating approximately $60.0 million in net proceeds. In connection with this financing, we granted to an underwriter an option to purchase 1,245,000 shares of common stock at a price of $7.25 per share. The option was exercisable in the event that the underwriter sold more than 8.3 million shares of common stock. The option expired unexercised on October 8, 2010.
During 2010, we issued an aggregate of 479,093 shares of common stock in connection with the exercises of stock options, for cash in the aggregate amount of approximately $1.9 million, and 120,000 shares of common stock for the grants of restricted stock awards.
Equity Incentive Plans
Equity Incentive Plans
Equity Incentive Plans
We have two equity incentive plans (the “Current Plans”) under which we currently grant stock options, restricted stock awards and restricted stock units: the 2011 Stock Plan and the 2008 Outside Directors’ Stock Plan. In May 2011, our stockholders approved our 2011 Stock Plan, which provides for the granting of up to a total of 6,000,000 shares of common stock (subject to certain limitations as described in the 2011 Stock Plan) to selected employees, consultants and non-employee members of our Board of Directors ("Outside Directors") as stock options, stock appreciation rights, restricted stock awards, restricted stock unit awards and performance awards. The 2011 Stock Plan replaced our prior stock plans, consisting of our 2008 Stock Plan, 2006 Stock Plan and 2004 Stock Plan (“Prior Plans”, collectively with the Current Plans, the “Plans”). The Prior Plans were terminated such that no additional awards could be granted under the Prior Plans, but the terms of the Prior Plans remain in effect with respect to outstanding awards until they are exercised, settled or canceled. The Plans were approved by the stockholders. Awards are subject to terms and conditions established by the Compensation Committee of our Board of Directors.
During the year ended December 31, 2012, we granted share-based awards under the 2011 Stock Plan and the 2008 Outside Directors’ Stock Plan. At December 31, 2012, 7,062,013 shares were subject to outstanding awards and 2,730,059 shares were available for future grants of share-based awards. At the present time, management intends to issue new common shares upon the exercise of stock options, issuance of restricted stock awards and settlement of restricted stock units.
Stock Options.    Options granted under each of the Plans must have an exercise price equal to at least 100% of the fair market value of our common stock on the date of grant. The options will generally have a maximum contractual term of ten years and vest at the rate of one-fourth of the shares on the first anniversary of the date of grant and 1/48 of the shares monthly thereafter. Certain option awards provide for accelerated vesting if there is a change in control (as defined in the Plans).
A summary of our stock option award activity as of and for the years ended December 31, 2012, 2011 and 2010 is as follows: 

 
Shares
Underlying
Stock Options

Weighted
Average Exercise
Price per Share

Weighted Average
Remaining
Contractual  Term (yrs)
 
Aggregate
Intrinsic
Value
Outstanding at January 1, 2010
 
7,804,266

 
$3.73
 
 
 
 
Granted
 
1,332,714

 
$5.94
 
 
 
 
Exercised
 
(479,093
)
 
$3.88
 
 
 
 
Canceled/forfeited
 
(682,522
)
 
$6.29
 
 
 
 
Outstanding at December 31, 2010
 
7,975,365

 
$3.87
 
 
 
 
Granted
 
1,624,768

 
$7.79
 
 
 
 
Exercised
 
(3,137,056
)
 
$1.71
 
 
 
 
Canceled/forfeited
 
(593,293
)
 
$6.72
 
 
 
 
Outstanding at December 31, 2011
 
5,869,784

 
$5.82
 
 
 
 
Granted
 
1,215,442

 
$9.90
 
 
 
 
Exercised
 
(444,637
)
 
$4.56
 
 
 
 
Canceled/forfeited
 
(260,722
)
 
$8.34
 
 
 
 
Outstanding at December 31, 2012
 
6,379,867

 
$6.59
 
6.5
 

$7.4
 million
Vested and expected to vest at December 31, 2012
 
6,086,988

 
$6.49
 
6.3
 

$7.4
 million
Exercisable at December 31, 2012
 
3,958,125

 
$5.34
 
5.1
 

$6.8
 million

The weighted average grant-date fair values of options granted during the years ended December 31, 2012, 2011 and 2010 were $5.63 per share, $4.57 per share and $3.69 per share, respectively. As of December 31, 2012, approximately $9.0 million of total unrecognized compensation costs related to non-vested stock option awards was expected to be recognized over a weighted average period of approximately 2.7 years. The intrinsic value of options exercised during the years ended December 31, 2012, 2011 and 2010 was approximately $2.9 million, $16.6 million and $1.8 million, respectively. Cash received from stock option exercises for the years ended December 31, 2012, 2011 and 2010 was approximately $2.0 million, $4.7 million and $1.9 million, respectively.
The fair value of each option award is estimated on the date of grant using a Black-Scholes-Merton option pricing model (“Black-Scholes model”) that uses the assumptions noted in the following table. Expected volatility is based on historical volatility of our common stock. The expected term of options granted is based on analyses of historical employee termination rates and option exercises. The risk-free interest rate is based on the U.S. Treasury yield for a period consistent with the expected term of the option in effect at the time of the grant. The dividend yield assumption is based on the expectation of no future dividend payments by us. Assumptions used in the Black-Scholes model were as follows:
 
 
Year Ended December 31,
 
 
2012

2011

2010
Expected volatility
 
64.0-69.2%


64.0-65.1%


65.8-70.8%

Average expected term (in years)
 
5.6


5.8


5.7

Risk-free interest rate
 
0.80-1.15%


1.14-2.55%


1.39-2.80%

Expected dividend yield
 
0
%

0
%

0
%

Restricted Stock Awards.    Restricted stock awards are grants that entitle the holder to acquire shares of our common stock at zero or a fixed price, which is typically nominal. The shares covered by a restricted stock award cannot be sold, pledged, or otherwise disposed of until the award vests and any unvested shares may be reacquired by us for the original purchase price following the awardee’s termination of service. Annual grants of restricted stock awards under the Outside Directors’ Stock Plans typically vest in full the first day the awardee may trade our stock in compliance with our insider trading policy following the date immediately preceding the first annual meeting of stockholders following the grant date.
The following table summarizes our restricted stock award activity during the years ended December 31, 2012, 2011 and 2010:

 
Number of
Shares

Weighted  Average
Grant Date
Fair Value
Unvested at January 1, 2010
 
120,000

 
$
5.81

Granted
 
120,000

 
$
7.67

Vested
 
(120,000
)
 
$
5.81

Forfeited
 

 
$

Unvested at December 31, 2010
 
120,000

 
$
7.67

Granted
 
353,508

 
$
6.51

Vested
 
(120,000
)
 
$
7.67

Forfeited
 
(5,625
)
 
$
6.67

Unvested at December 31, 2011
 
347,883

 
$
6.51

Granted
 
380,158

 
$
10.29

Vested
 
(339,758
)
 
$
6.51

Forfeited
 
(5,963
)
 
$
10.81

Unvested at December 31, 2012
 
382,320

 
$
10.21


The fair value of the restricted stock awards is based on the market value of our common stock on the date of grant. The total grant-date fair value of restricted stock awards vested during the years ended December 31, 2012, 2011 and 2010 was approximately $2.2 million, $0.9 million and $0.7 million, respectively. We recognized approximately $2.1 million, $1.7 million and $0.8 million of share-based compensation expense related to the restricted stock awards for the years ended December 31, 2012, 2011 and 2010. As of December 31, 2012, total unrecognized compensation cost related to unvested shares was approximately $2.0 million, which is expected to be recognized over a weighted-average period of approximately 2.2 years.
Restricted Stock Units.    A restricted stock unit is a promise by us to issue a share of our common stock upon vesting of the unit. During the year ended December 31, 2012 and 2011, we granted 682,146 and 163,000 shares of restricted stock units, respectively, at no purchase price, to certain employees under the 2011 Stock Plan. Of the total 163,000 shares of restricted stock units granted during the year ended December 31, 2011, 148,000 shares were subject to percentage vesting based upon achievement of certain corporate goals and the employees’ continuing services through May 2012. No restricted stock units were granted during the year ended December 31, 2010.
The following table summarizes our restricted stock unit activity during the years ended December 31, 2012 and 2011:

 
Number of
Shares

Weighted
Average
Purchase  Price

Weighted
Average  Remaining
Contractual Term (yrs)
 
Aggregate
Intrinsic
Value
Unvested at January 1, 2011
 

 
$

 
 
 
 
Granted
 
163,000

 
$

 
 
 
 
Vested
 
(15,000
)
 
$

 
 
 
 
Forfeited
 

 
$

 
 
 
 
Unvested at December 31, 2011
 
148,000

 
$

 
 
 
 
Granted
 
682,146

 
$

 
 
 
 
Vested
 
(128,000
)
 
$

 
 
 
 
Forfeited
 
(20,000
)
 
$

 
 
 
 
Unvested at December 31, 2012
 
682,146

 
$

 
2.03
 

$4.6
 million
Expected to vest at December 31, 2012
 
556,377

 
$

 
1.84
 

$3.7
 million

The estimated fair value of the restricted stock units was based on the market value of our common stock on the date of grant. The weighted average grant-date fair value of restricted stock units granted during the years ended December 31, 2012 and 2011 was $10.61 and $6.71 per share, respectively. The total intrinsic value of restricted stock units vested during the year ended December 31, 2012 and 2011 was approximately $0.9 million and $0.1 million, respectively. We recognized approximately $1.5 million and $0.7 million of share-based compensation expense related to the restricted stock units for the year ended December 31, 2012 and 2011, respectively. As of December 31, 2012, total unrecognized estimated unamortized compensation cost related to non-vested restricted stock units outstanding as of that date was approximately $4.2 million, with a weighted average amortization period of approximately 3.9 years.
Commitments and Contingencies
Commitments and Contingencies
Commitments and Contingencies
Operating Leases
Our administrative offices and research facilities are located in San Diego, California. We lease an aggregate of approximately 76,000 square feet of office and research space.
In June 2011, we entered into an amended and restated lease (the “11388 Lease”) with BMR-11388 Sorrento Valley Road LP for the office and research facilities located at 11388 Sorrento Valley Road, San Diego, California ("11388 Property"). The 11388 Lease commenced in June 2011 and continues through January 2018. The 11388 Lease supersedes the lease agreement with BC Sorrento, LLC entered into in July 2007. Under the terms of the 11388 Lease, the initial monthly rent payment was approximately $38,000 net of costs and property taxes associated with the operation and maintenance of the leased facilities, commencing in December 2011 and increases to approximately $65,000 starting in January 2013. Thereafter, the annual base rent is subject to approximately 2.5% annual increases each year throughout the term of the 11388 Lease. In addition, we received a cash incentive of approximately $98,000, a tenant improvement allowance of $300,000 and free and reduced rent totaling approximately $744,000 under the terms of the 11388 Lease. Combined with the unamortized deferred rent under the Original Lease, unamortized deferred rent associated with the 11388 Lease of $1.1 million and $854,000 was included in deferred rent as of December 31, 2012 and 2011, respectively.
In July 2007, we entered into a sublease agreement (the “11404 Sublease”) with Avanir Pharmaceuticals, Inc. (“Avanir”) for Avanir’s excess leased facilities located at 11404 Sorrento Valley Road, San Diego, California for office and research space (“11404 Property”) for a monthly rent payment of approximately $54,000, net of costs and property taxes associated with the operation and maintenance of the subleased facilities. The 11404 Sublease expires in January 2013. The annual base rent is subject to approximately 4% annual increases each year throughout the terms of the 11404 Sublease. In addition, we received free rent totaling approximately $492,000, of which approximately $4,000 and $149,000 was included in deferred rent as of December 31, 2012 and 2011, respectively.
In April 2009, we entered into a sublease agreement (the “11408 Sublease”) with Avanir for office and research space located at 11408 Sorrento Valley Road, San Diego, California (“11408 Property”), which expires in January 2013. The monthly rent payments, which commenced in January 2010, were approximately $21,000 and are subject to an annual increase of approximately 3%.
In June 2011, we entered into a lease agreement (the “11404/11408 Lease”) with BMR-Sorrento Plaza LLC (“BMR-Sorrento”) for the 11404 Property and 11408 Property commencing in January 2013 through January 2018. Pursuant to the terms of the 11404/11408 Lease, the initial monthly rent payment is approximately $71,000 net of costs and property taxes associated with the operation and maintenance of the leased facilities, commencing in January 2013 and is subject to approximately 2.5% annual increases each year throughout the term of the 11404/11408 Lease.
In October 2012, we entered into a lease agreement (the “11436 Lease”) with Cal-Sorrento, Ltd. for the 11436 Sorrento Valley Road, San Diego, California ("11436 Property"). The 11436 Lease requires the lessor to complete and pay for certain improvements on the building before the commencement of the lease which is estimated to be approximately May 2013. This lease expires in January 2018. Pursuant to the terms of the 11436 Lease, the initial monthly rent payment will be approximately $24,300 net of costs and property taxes associated with the operation and maintenance of the leased facilities, commencing approximately May 2013 and will be subject to approximately 3% annual increases each year throughout the term of the 11436 Lease. In addition, we will receive free and reduced rent totaling approximately $158,000. Under the terms of the 11436 Lease, we are the “deemed owner” (for accounting purposes only) of the facility during the construction period. As such, we recorded an asset of $1.5 million, representing the fair value of the building with a corresponding long-term lease financing obligation.
We pay a pro rata share of operating costs, insurance costs, utilities and real property taxes incurred by the landlords for the subleased facilities.
Additionally, we lease certain office equipment under operating leases. Total rent expense was approximately $1.6 million, $1.5 million and $1.5 million for the years ended December 31, 2012, 2011 and 2010, respectively.
 
Approximate annual future minimum operating lease payments as of December 31, 2012 are as follows: 
Year:
 
Operating
Leases
2013
 
$
1,865,000

2014
 
2,052,000

2015
 
2,049,000

2016
 
2,073,000

2017
 
2,126,000

Thereafter
 
80,000

Total minimum lease payments
 
$
10,245,000


Other Commitments
Under the terms of the Roche Collaboration, we were obligated to scale up the production of rHuPH20 and to identify a second source manufacturer that would help meet anticipated production obligations arising from the collaboration. To that end, during 2008, we entered into a Technology Transfer Agreement and a Clinical Supply Agreement with a second rHuPH20 manufacturer, Cook Pharmica LLC (“Cook”). Cook manufactures certain batches of the API that will be used in clinical trials of certain product candidates. Cook has the capacity to produce the quantities we were required to deliver under the terms of the Roche Collaboration. The technology transfer was completed in 2008. In 2009, multiple batches of rHuPH20 were produced to support planned future clinical studies. In 2010, we initiated process validation activities in support of potential future commercialization. The process validation was completed in 2011.
In March 2010, we entered into a Commercial Supply Agreement with Cook (the “Cook Commercial Supply Agreement”). Under the terms of the Cook Commercial Supply Agreement, Cook will manufacture certain batches of the API that will be used for potential commercial supply of certain product candidates. Under the terms of the Cook Commercial Supply Agreement, we are committed to certain minimum annual purchases of API equal to four quarters of forecasted supply. At December 31, 2012, we have $7.7 million minimum purchase obligation in connection with the Cook Commercial Supply Agreement.
In March 2010, we amended our Commercial Supply Agreement (the “March 2010 Avid Amendment”) with Avid Bioservices, Inc. ("Avid") which was originally entered into in February 2005 and amended in December 2006. Under the terms of the March 2010 Avid Amendment, we are committed to certain minimum annual purchases of API equal to three quarters of forecasted supply. In addition, Avid has the right to manufacture and supply a certain percentage of the API that will be used in Hylenex recombinant. At December 31, 2012, we had a minimum purchase obligation of approximately $217,000.
In March 2010, we entered into a second Commercial Supply Agreement with Avid (the “Avid Commercial Supply Agreement”). Under the terms of the Avid Commercial Supply Agreement, we are committed to certain minimum annual purchases of API equal to three quarters of forecasted supply. In addition, Avid has the right to manufacture and supply a certain percentage of the API that will be used in certain product candidates. At December 31, 2012, we had $7.7 million minimum purchase obligation in connection with this agreement.
In June 2011, we entered into a commercial manufacturing and supply agreement with Baxter, under which Baxter provides the final fill and finish steps in the production process of Hylenex recombinant for a limited period of time. The initial term of the agreement with Baxter extends expires on December 31, 2013; however, upon regulatory approval of a second filling line, the initial term will automatically be extended to December 31, 2015, subject to further extensions in accordance with the terms and conditions of the agreement. At December 31, 2012, we had a minimum purchase obligation of approximately $9.5 million. 
In June 2011, we entered into a services agreement with another third party manufacturer for the technology transfer and manufacture of Hylenex recombinant. At December 31, 2012, we had no minimum purchase obligation in connection with this agreement.
Legal Contingencies
From time to time, we may be involved in disputes, including litigation, relating to claims arising out of operations in the normal course of our business. Any of these claims could subject us to costly legal expenses and, while we generally believe that we have adequate insurance to cover many different types of liabilities, our insurance carriers may deny coverage or our policy limits may be inadequate to fully satisfy any damage awards or settlements. If this were to happen, the payment of any such awards could have a material adverse effect on our consolidated results of operations and financial position. Additionally, any such claims, whether or not successful, could damage our reputation and business. We currently are not a party to any legal proceedings, the adverse outcome of which, in management’s opinion, individually or in the aggregate, would have a material adverse effect on our consolidated results of operations or financial position.
Income Taxes
Income Taxes
Income Taxes
Significant components of our net deferred tax assets at December 31, 2012 and 2011 are shown below. A valuation allowance of $128.4 million and $107.5 million has been established to offset the net deferred tax assets as of December 31, 2012 and 2011, respectively, as realization of such assets is uncertain.

 
2012

2011
Deferred tax assets:
 



Net operating loss carryforwards
 
$
86,732,000

 
$
69,912,000

Deferred revenue
 
17,345,000

 
15,338,000

Research and development credits
 
20,286,000

 
19,270,000

Share-based compensation
 
2,975,000

 
2,122,000

Depreciation
 
179,000

 
76,000

Other, net
 
926,000

 
771,000

Total deferred tax assets
 
128,443,000

 
107,489,000

Valuation allowance for deferred tax assets
 
(128,443,000
)
 
(107,489,000
)
Net deferred tax assets
 
$

 
$


The provision for income taxes on earnings subject to income taxes differs from the statutory federal income tax rate at December 31, 2012, 2011 and 2010, due to the following:

 
2012

2011

2010
Federal income tax at 34%
 
$
(18,208,000
)
 
$
(6,722,000
)
 
$
(18,102,000
)
State income tax, net of federal benefit
 
(3,023,000
)
 
(1,153,000
)
 
(3,106,000
)
Increase in valuation allowance
 
20,954,000

 
9,935,000

 
22,469,000

Tax effect on non-deductible expenses and other
 
1,293,000

 
1,671,000

 
2,118,000

Research and development credits
 
(1,016,000
)
 
(3,731,000
)
 
(3,379,000
)

 
$

 
$

 
$


At December 31, 2012, we had federal and California tax net operating loss carryforwards of approximately $245.3 million and $247.0 million, respectively. Included in these amounts are federal and California net operating losses of approximately $27.9 million attributable to stock option deductions of which the tax benefit will be credited to equity when realized. The federal and California tax loss carryforwards will begin to expire in 2018 and 2013, respectively, unless previously utilized.
At December 31, 2012, we also had federal and California research and development tax credit carryforwards of approximately $14.3 million and $9.0 million, respectively. The federal research and development tax credits will begin to expire in 2024 unless previously utilized. The California research and development tax credits will carryforward indefinitely until utilized.
The American Taxpayer Relief Act of 2012, which retroactively reinstated the United States federal research and development tax credit from January 1, 2012 through December 31, 2013, was not enacted into law until the first quarter of 2013. Therefore the deferred tax asset and corresponding increase in the valuation allowance for the amount of the credit generated in 2012 will not be reflected until 2013.
Pursuant to Internal Revenue Code Section 382, the annual use of the net operating loss carryforwards and research and development tax credits could be limited by any greater than 50% ownership change during any three-year testing period. As a result of any such ownership change, portions of our net operating loss carryforwards and research and development tax credits are subject to annual limitations. We recently completed an updated Section 382 analysis regarding the limitation of the net operating losses and research and development credits as of December 31, 2012. Based upon the analysis, we determined that ownership changes occurred in prior years. However, the annual limitations on net operating loss and research and development tax credit carryforwards will not have a material impact on the future utilization of such carryforwards.
At December 31, 2012 and 2011, our unrecognized income tax benefits and uncertain tax positions were not material and would not, if recognized, affect the effective tax rate. Interest and/or penalties related to uncertain income tax positions are recognized by us as a component of income tax expense. For the years ended December 31, 2012, 2011 and 2010, we recognized no interest or penalties.
We are subject to taxation in the U.S. and in various state jurisdictions. Our tax years for 1998 and forward are subject to examination by the U.S. and California tax authorities due to the carryforward of unutilized net operating losses and research and development credits.
Employee Savings Plan
Employee Savings Plan
Employee Savings Plan
We have an employee savings plan pursuant to Section 401(k) of the Internal Revenue Code. All employees are eligible to participate, provided they meet the requirements of the plan. We are not required to make matching contributions under the plan. However, we voluntarily contributed to the plan approximately $508,000, $355,000 and $433,000 in the years ended December 31, 2012, 2011 and 2010, respectively.
Restructuring Expense
Restructuring Expense
Restructuring Expense
In October 2010, we completed a corporate reorganization to focus our resources on advancing our core proprietary programs and supporting strategic alliances with Roche and Baxter. This reorganization resulted in a reduction in the workforce of approximately 25 percent primarily in the discovery research and preclinical areas. We recorded approximately $1.3 million of severance pay and benefits expenses in connection with the reorganization, of which $1.2 million and $76,000 was included in research and development expense and selling, general and administrative expense, respectively, in the consolidated statement of comprehensive loss for the year ended December 31, 2010. No other restructuring charges were incurred. We made cash payments of $1.2 million during the year ended December 31, 2010 and paid the remaining balance in full during the year ended December 31, 2011.
Related Party Transactions
Related Party Transactions
Related Party Transactions
In June 2011, we and Intrexon entered into the Intrexon Collaboration, under which Intrexon obtained a worldwide exclusive license for the use of rHuPH20 enzyme in the development of a subcutaneous injectable formulation of Intrexon’s recombinant human alpha 1-antitrypsin (rHuA1AT). Intrexon’s chief executive officer and chairman of its board of directors, Randal J. Kirk, is also a member of our Board of Directors. The collaborative arrangement with Intrexon was reviewed and approved by our Board of Directors in accordance with our related party transaction policy. For the years ended December 31, 2012 and 2011, we recognized $1.0 million and $9.0 million, respectively, in revenue under collaborative agreements pursuant to the terms of the Intrexon Collaboration. See Note 3 for a further discussion of the Intexon Collaboration.
Connie L. Matsui, a member of our Board of Directors, and her husband had a controlling ownership interest (and therefore a financial interest) in an entity that held a minority ownership position in BC Sorrento, an entity that leased the 11388 Property to us until September 2010. The transaction with BC Sorrento was reviewed and approved by our Board of Directors in accordance with our related party transaction policy. Effective September 2010, BC Sorrento sold the 11388 Property to an unrelated party. As such, we no longer had any business transactions with BC Sorrento effective September 2010. We paid BC Sorrento approximately $982,000 for the year ended December 31, 2010. No payments were made to BC Sorrento for the years ended December 31, 2012 and 2011.
Summary of Unaudited Quarterly Financial Information
Summary of Unaudited Quarterly Financial Information
Summary of Unaudited Quarterly Financial Information
The following is a summary of our unaudited quarterly results for the years ended December 31, 2012 and 2011:
 
 
Quarter Ended
2012 (Unaudited):
 
March 31,
 
June 30,
 
September 30,
 
December 31,
Total revenues (a)
 
$
7,440,179

 
$
7,757,175

 
$
5,334,323

 
$
21,793,549

Total operating expenses
 
$
22,580,577

 
$
21,805,273

 
$
25,364,160

 
$
26,200,662

Net loss
 
$
(15,119,181
)
 
$
(14,021,119
)
 
$
(20,005,846
)
 
$
(4,405,856
)
Net loss per share, basic and diluted
 
$
(0.14
)
 
$
(0.13
)
 
$
(0.18
)
 
$
(0.04
)
Shares used in computing net loss per share, basic and diluted
 
107,589,514

 
112,063,665

 
112,305,002

 
112,323,056

 
 
Quarter Ended
2011 (Unaudited):
 
March 31,
 
June 30,
 
September 30,
 
December 31,
Total revenues (b)
 
$
7,543,894

 
$
23,188,948

 
$
22,942,428

 
$
2,411,166

Total operating expenses
 
$
17,203,480

 
$
20,093,017

 
$
17,789,595

 
$
20,839,285

Net income (loss)
 
$
(9,635,717
)
 
$
3,116,288

 
$
5,165,193

 
$
(18,415,615
)
Net income (loss) per share, basic and diluted
 
$
(0.10
)
 
$
0.03

 
$
0.05

 
$
(0.18
)
Shares used in computing net income (loss) per share:
 
 
 
 
 
 
 
 
Basic
 
100,927,402

 
102,671,410

 
103,223,352

 
103,406,407

Diluted
 
100,927,402

 
104,393,835

 
105,009,189

 
103,406,407

 
 
(a)
Revenues for the quarter ended December 31, 2012 included $9.5 million in revenue under collaborative agreements from the Pfizer Collaboration.
(b)
Revenues for the quarter ended June 30, 2011 included revenue under collaborative agreements totaling $18.0 million from the ViroPharma and Intrexon Collaborations. Revenues for the quarter ended September 30, 2011 included revenue from collaborative agreements totaling $17.9 million related to recognition of unamortized deferred prepaid product-based payments and unamortized deferred upfront payment pursuant to the termination of the Hylenex Collaboration with Baxter in July 2011.
Summary of Significant Accounting Policies (Policies)
Basis of Presentation
The consolidated financial statements include the accounts of Halozyme Therapeutics, Inc. and our wholly owned subsidiary, Halozyme, Inc. All intercompany accounts and transactions have been eliminated.
Use of Estimates
The preparation of consolidated financial statements in conformity with U.S. generally accepted accounting principles (“U.S. GAAP”) requires management to make estimates and assumptions that affect the amounts reported in our consolidated financial statements and accompanying notes. On an ongoing basis, we evaluate our estimates and judgments, which are based on historical and anticipated results and trends and on various other assumptions that management believes to be reasonable under the circumstances. By their nature, estimates are subject to an inherent degree of uncertainty and, as such, actual results may differ from management’s estimates.
Cash and Cash Equivalents
Cash and cash equivalents consist of highly liquid investments with original maturities of three months or less from the original purchase date.
Concentrations of Credit Risk, Sources of Supply and Significant Customers
Financial instruments that potentially subject us to a significant concentration of credit risk consist of cash and cash equivalents and accounts receivable. We maintain our cash and cash equivalent balances with one major commercial bank. Deposits held with the bank exceed the amount of insurance provided on such deposits.
We have license and collaborative agreements with pharmaceutical companies under which we receive payments for license fees, milestone payments for specific achievements designated in the collaborative agreements, reimbursements of research and development services and supply of bulk formulation of rHuPH20. In addition, we sell Hylenex® recombinant in the United States to a limited number of established wholesale distributors in the pharmaceutical industry. Credit is extended based on an evaluation of the customer’s financial condition, and collateral is not required. Management monitors our exposure to accounts receivable by periodically evaluating the collectibility of the accounts receivable based on a variety of factors including the length of time the receivables are past due, the financial health of the customer and historical experience. Based upon the review of these factors, we recorded no allowance for doubtful accounts at December 31, 2012 and 2011. Approximately 86% of accounts receivable balance as of December 31, 2012 represents amounts due from Roche and Pfizer. Approximately 82% of the accounts receivable balance as of December 31, 2011 represents amounts due from Roche, Baxter and ViroPharma. For the years ended December 31, 2012, 2011 and 2010, 45%, 19% and 52% of total revenues were from Roche and 17%, 42% and 42% of total revenues were from Baxter, respectively. For the year ended December 31, 2012, 22% of total revenues were from Pfizer. In addition, for the year ended December 31, 2011, 22% and 16% of total revenues were from ViroPharma and Intrexon, respectively.
Worldwide revenues from external customers for the years ended December 31, 2012, 2011 and 2010 consisted of domestic revenues of approximately $22.7 million, $44.9 million and $6.0 million, respectively, and foreign revenues of approximately $19.6 million, $11.2 million and $7.6 million, respectively. Of our total foreign revenues for the years ended December 31, 2012, 2011 and 2010, approximately $18.9 million, $10.4 million, $7.2 million, respectively, were attributable to Switzerland. We attribute revenues under collaborative agreements to the individual countries where the collaborator is headquartered. We attribute revenues from product sales to the individual countries to which the product is shipped. For the years ended December 31, 2012, 2011 and 2010, we had no foreign based operations, and we had no long-lived assets located in foreign countries.
We rely on two third-party manufacturers for the supply of the bulk formulation of rHuPH20 which is the active pharmaceutical ingredient (“API”) in Hylenex recombinant and each of our collaborators’ product candidates. Payments due to these suppliers represent 20% and 59% of the accounts payable balance at December 31, 2012 and 2011, respectively. We also rely on a third-party manufacturer for the fill and finish of Hylenex recombinant product under a contract we entered in June 2011. Payments due to this supplier represent 8.0% and 3.7% of the accounts payable balance at December 31, 2012 and 2011, respectively.
Accounts Receivable, Net
Accounts receivable is recorded at the invoiced amount and is non-interest bearing. Accounts receivable is recorded net of allowances for doubtful accounts, cash discounts for prompt payment, distribution fees and chargebacks. We recorded no allowance for doubtful accounts at December 31, 2012 and 2011, as the collectibility of accounts receivable is reasonably assured. Allowances for prompt payment discounts, distribution fees and chargebacks as of December 31, 2012 and 2011 were immaterial.
Inventories
Inventories are stated at lower of cost or market. Cost is determined on a first-in, first-out basis. Inventories are reviewed periodically for potential excess, dated or obsolete status. Management evaluates the carrying value of inventories on a regular basis, taking into account such factors as historical and anticipated future sales compared to quantities on hand, the price we expect to obtain for products in their respective markets compared with historical cost and the remaining shelf life of goods on hand.
Raw materials inventories consist of raw materials used in the manufacture of our bulk drug material for Hylenex recombinant product. Work-in-process inventories consist of in-process Hylenex recombinant. Finished goods inventories consist of finished Hylenex recombinant product.
We expense costs relating to the purchase and production of pre-approval inventories for which the sole use is pre-approval products as research and development expense in the period incurred until such time as we believe future commercialization is probable and future economic benefit is expected to be realized. For products that have been approved by the regulatory bodies such as the U.S. Food and Drug Administration ("FDA"), inventories used in clinical trials are expensed at the time the inventories are packaged for the clinical trial. Prior to receiving approval from the FDA or comparable regulatory agencies in foreign countries, costs related to purchases of the API and the manufacturing of the product candidate is recorded as research and development expense. All direct manufacturing costs incurred after approval are capitalized as inventory.
Property and Equipment, Net
Property and equipment are recorded at cost, less accumulated depreciation and amortization. Equipment is depreciated using the straight-line method over their estimated useful lives of three years and leasehold improvements are amortized using the straight-line method over the estimated useful life of the asset or the lease term, whichever is shorter. Leased buildings under build-to-suit lease arrangements are capitalized and included in property and equipment when we are involved in the construction of the structural improvements or take construction risk prior to the commencement of the lease. Upon occupancy of facilities under the build-to-suit leases, we assess whether those arrangements qualify for sales recognition under the sale-leaseback accounting guidance. If we continue to be the deemed owner, the facilities would be accounted for as financing leases.
Impairment of Long-Lived Assets
We account for long-lived assets in accordance with authoritative guidance for impairment or disposal of long-lived assets. Long-lived assets are reviewed for events or changes in circumstances, which indicate that their carrying value may not be recoverable. For the years ended December 31, 2012 and 2011, there has been no impairment of the value of such assets.
Fair Value of Financial Instruments
We follow the authoritative guidance for fair value measurements and disclosures, which among other things, defines fair value, establishes a consistent framework for measuring fair value and expands disclosure for each major asset and liability category measured at fair value on either a recurring or nonrecurring basis. Fair value is defined as an exit price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or liability.
The framework for measuring fair value provides a hierarchy that prioritizes the inputs to valuation techniques used in measuring fair value as follows:
 
 
 
 
 
Level 1
  
Quoted prices (unadjusted) in active markets for identical assets or liabilities,
 
 
 
Level 2
  
Inputs other than quoted prices included within Level 1 that are either directly or indirectly observable, and
 
 
 
Level 3
  
Unobservable inputs in which little or no market activity exists, therefore requiring an entity to develop its own assumptions about the assumptions that market participants would use in pricing.
Our financial instruments include cash and cash equivalents, accounts receivable, prepaid expenses, accounts payable, accrued expenses and long-term debt. Fair value estimates of these instruments are made at a specific point in time, based on relevant market information. These estimates may be subjective in nature and involve uncertainties and matters of significant judgment and therefore cannot be determined with precision. The carrying amount of cash and cash equivalents, accounts receivable, prepaid expenses, accounts payable and accrued expenses are generally considered to be representative of their respective fair values because of the short-term nature of those instruments. . Further, based on the borrowing rates currently available to us for loans with similar terms, we believe the fair value of long-term debt approximates its carrying value. Cash equivalents of approximately $98.4 million and $51.8 million at December 31, 2012 and 2011, respectively, are carried at fair value and are classified within Level 1 of the fair value hierarchy because they are valued based on quoted market prices for identical securities. We have no instruments that are classified within Level 2 and Level 3.
Deferred Rent
Rent expense is recorded on a straight-line basis over the initial term of the lease. The difference between rent expense accrued and amounts paid under lease agreements is recorded as deferred rent in the accompanying consolidated balance sheets.
Comprehensive Income/Loss
Comprehensive income (loss) is defined as the change in equity during a period from transactions and other events and circumstances from non-owner sources. Comprehensive loss was the same as our net loss for all periods presented.
Revenue Recognition
We generate revenues from product sales and collaborative agreements. Payments received under collaborative agreements may include nonrefundable fees at the inception of the agreements, license fees, milestone payments for specific achievements designated in the collaborative agreements, reimbursements of research and development services and supply of bulk rHuPH20, and/or royalties on sales of products resulting from collaborative arrangements.
We recognize revenues in accordance with the authoritative guidance for revenue recognition. We recognize revenue when all of the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the seller’s price to the buyer is fixed or determinable; and (4) collectibility is reasonably assured.
Product Sales, Net. Hylenex recombinant was approved for marketing by the FDA in December 2005. From 2005 through January 7, 2011, we granted Baxter the worldwide market rights for Hylenex recombinant under the terms of the amended and restated development and supply agreement with Baxter ("Hylenex Collaboration"). Baxter commercially launched Hylenex recombinant in October 2009. Effective January 7, 2011, we and Baxter mutually agreed to terminate the collaboration. During the second quarter of 2011, we submitted the data that the FDA had requested to support the reintroduction of Hylenex recombinant to the market. The FDA approved the submitted data and granted the reintroduction of Hylenex recombinant.
In December 2011, we reintroduced Hylenex recombinant to the market, shipped initial orders to our wholesaler customers and began promoting Hylenex recombinant through our sales force. We sell Hylenex recombinant in the United States to wholesale pharmaceutical distributors, who sell the product to hospitals and other end-user customers. The wholesale distributors take title to the product, bear the risk of loss of ownership and have economic substance to the inventory. Further, we have no significant obligations for future performance to generate pull-through sales; however, we allow the wholesale distributors to return product that is damaged or received in error. In addition, we allow for product to be returned beginning six months prior to and ending twelve months following product expiration.
Given our limited history of selling Hylenex recombinant and the lengthy return period, we currently cannot reliably estimate expected returns and chargebacks of Hylenex recombinant at the time the product is received by the wholesale distributors. Therefore, we do not recognize revenue upon delivery of Hylenex recombinant to the wholesale distributor until the point at which we can reliably estimate expected product returns and chargebacks from the wholesale distributors. Shipments of Hylenex recombinant are recorded as deferred revenue until evidence exists to confirm that pull-through sales to the hospitals or other end-user customers have occurred. We recognize revenue when the product is sold through from the distributors to the distributors’ customers. In addition, the costs of manufacturing Hylenex recombinant associated with the deferred revenue are recorded as deferred costs, which are included in inventory, until such time as the related deferred revenue is recognized. We estimate sell-through revenue and certain gross to net sales adjustments based on analysis of third-party information including information obtained from certain distributors with respect to their inventory levels and sell-through to the distributors’ customers. At the time we can reliably estimate product returns and chargebacks from the wholesale distributors, we will record a one-time increase in net product sales revenue related to the recognition of product sales revenue previously deferred.
We recognize product sales allowances as a reduction of product sales in the same period the related revenue is recognized. Product sales allowances are based on amounts owed or to be claimed on the related sales. These estimates take into consideration the terms of our agreements with wholesale distributors and hospitals and the levels of inventory within the distribution channels that may result in future discounts taken. We must make significant judgments in determining these allowances. If actual results differ from our estimates, we will be required to make adjustments to these allowances in the future, which could have an effect on product sales revenue in the period of adjustment. Our product sales allowances include:
Distribution Fees.    The distribution fees, based on contractually determined rates, arise from contractual agreements we have with certain wholesale distributors for distribution services they provide with respect to Hylenex recombinant. At the time the sale is made to the respective wholesale distributors, we record an allowance for distribution fees by reducing our accounts receivable and deferred revenue associated with such product sales.
Prompt Payment Discounts.    We offer cash discounts to certain wholesale distributors as an incentive to meet certain payment terms. We expect our customers will take advantage of this discount; therefore, at the time the sale is made to the respective wholesale distributors, we accrue the entire prompt payment discount, based on the gross amount of each invoice, by reducing our accounts receivable and deferred revenue associated with such product sales.
Chargebacks.    We provide discounts to end-user members of certain group purchasing organizations ("GPO") under collective purchasing contracts between us and the GPOs. We also provide discounts to certain hospitals, who are members of the GPOs with which we do not have contracts. The end-user members purchase products from the wholesale distributors at a contracted discounted price, and the wholesale distributors then charge back to us the difference between the current retail price and the price the end-users paid for the product. Given our lack of historical sales data, we recognize chargebacks in the same period the related product sales revenue is recognized and reduce our accounts receivable accordingly. We incur GPO fees for these transactions which are also recorded in the same period the related product sales revenue is recognized and are included in accrued expenses.
Product Returns.    The product returns reserve is based on management’s best estimate of the product sales recognized as revenue during the period that are anticipated to be returned. The product returns reserve is recorded as a reduction of product sales revenue in the same period the related product sales revenue is recognized and is included in accrued expenses.
For the years ended December 31, 2012 and 2011, we recorded product sales revenue of approximately $2.2 million and $35,000, respectively, related to Hylenex recombinant, net of estimated distribution fees, prompt payment discounts, chargebacks and product returns totaling approximately $1.1 million and $8,000, respectively. We have a deferred revenue balance of approximately $624,000 and $167,000 at December 31, 2012 and 2011, respectively, for Hylenex recombinant shipments, which is net of estimated distribution fees, prompt pay discounts and product returns. In addition, inventory at December 31, 2012 and 2011 included a deferred cost of product sales of approximately $178,000 and $31,000, respectively, associated with Hylenex recombinant shipments to wholesalers. At the time we can reliably estimate product returns and chargebacks from the wholesalers, we will record a one-time increase in net product sales revenue related to the recognition of product sales revenue previously deferred.
Revenues under Collaborative Agreements. We have license and collaboration agreements under which the collaborators obtained worldwide rights for the use of our proprietary rHuPH20 enzyme in the development and commercialization of the collaborators’ biologic compounds. The collaborative agreements contain multiple elements including nonrefundable payments at the inception of the arrangement, license fees, exclusivity fees, payments based on achievement of specified milestones designated in the collaborative agreements, annual maintenance fees, reimbursements of research and development services, payments for supply of rHuPH20 API for the collaborator and/or royalties on sales of products resulting from collaborative agreements. We analyze each element of our collaborative agreements and consider a variety of factors in determining the appropriate method of revenue recognition of each element.
Effective January 1, 2011, we adopted Accounting Standards Update ("ASU") No. 2009-13, Multiple-Deliverable Revenue Arrangements ("ASU 2009-13"). In order to account for the multiple-element arrangements, we identify the deliverables included within the agreement and evaluate which deliverables represent units of accounting. Analyzing the arrangement to identify deliverables requires the use of judgment, and each deliverable may be an obligation to deliver services, a right or license to use an asset, or another performance obligation. The deliverables under our collaborative agreements include (i) the license to our rHuPH20 technology, (ii) at the collaborator’s request, research and development services which are reimbursed at contractually determined rates, and (iii) at the collaborator’s request, supply of rHuPH20 API which is reimbursed at our cost plus a margin. A delivered item is considered a separate unit of accounting when the delivered item has value to the collaborator on a standalone basis based on the consideration of the relevant facts and circumstances for each arrangement. Factors considered in this determination include the research capabilities of the collaborator and the availability of research expertise in this field in the general marketplace.
Arrangement consideration is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”), of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence of selling price exists, we use our best estimate of the selling price for the deliverable. The amount of allocable arrangement consideration is limited to amounts that are not contingent upon the delivery of additional items or meeting other specified performance conditions. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. Changes in the allocation of the sales price between delivered and undelivered elements can impact revenue recognition but do not change the total revenue recognized under any agreement.
Nonrefundable upfront license fee payments are recognized upon delivery of the license if facts and circumstances dictate that the license has standalone value from the undelivered items, which generally include research and development services and the manufacture of rHuPH20 API, the relative selling price allocation of the license is equal to or exceeds the upfront license fee, persuasive evidence of an arrangement exists, our price to the collaborator is fixed or determinable and collectibility is reasonably assured. Upfront license fee payments are deferred if facts and circumstances dictate that the license does not have standalone value. The determination of the length of the period over which to defer revenue is subject to judgment and estimation and can have an impact on the amount of revenue recognized in a given period.
Prior to the adoption of ASU No. 2009-13 on January 1, 2011, in order for a delivered item to be accounted for separately from other deliverables in a multiple-element arrangement, the following three criteria had to be met: (i) the delivered item had standalone value to the customer, (ii) there was objective and reliable evidence of fair value of the undelivered items and (iii) if the arrangement included a general right of return relative to the delivered item, delivery or performance of the undelivered items was considered probable and substantially in the control of the vendor. For the collaborative agreements entered into prior to January 1, 2011, there was no objective and reliable evidence of fair value of the undelivered items. Thus, the delivered licenses did not meet all of the required criteria to be accounted for separately from undelivered items. Therefore, we recognize revenue on nonrefundable upfront payments and license fees from these collaborative agreements over the period of significant involvement under the related agreements.
The terms of our collaborative agreements provide for milestone payments upon achievement of certain development and regulatory events and/or specified sales volumes of commercialized products by the collaborator. Effective January 1, 2011, we adopted, on a prospective basis, ASU No. 2010-17, Revenue Recognition - Milestone Method (“Milestone Method”). Under the Milestone Method, we recognize consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:
1.
The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the entity’s performance to achieve the milestone,
2.
The consideration relates solely to past performance, and
3.
The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.
A milestone is defined as an event (i) that can only be achieved based in whole or in part on either the entity’s performance or on the occurrence of a specific outcome resulting from the entity’s performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved and (iii) that would result in additional payments being due to the vendor.
Prior to our adoption of the Milestone Method, we recognized milestone payments upon the achievement of specified milestones if: (1) the milestone was substantive in nature and the achievement of the milestone was not reasonably assured at the inception of the agreement, (2) the fees were nonrefundable and (3) our performance obligations after the milestone achievement would continue to be funded by our collaborator at a level comparable to the level before the milestone achievement.
Reimbursements of research and development services are recognized as revenue during the period in which the services are performed as long as there is persuasive evidence of an arrangement, the fee is fixed or determinable and collection of the related receivable is reasonably assured. Revenue from the manufacture of rHuPH20 API is recognized when the API has met all specifications required for the collaborator's acceptance and title and risk of loss have transferred to the collaborator. We do not directly control when any collaborator will request research and development services or supply of rHuPH20 API; therefore, we cannot predict when we will recognize revenues in connection with research and development services and supply of rHuPH20 API. Royalties to be received based on sales of licensed products by our collaborators will be recognized as earned.
The collaborative agreements typically provide the collaborators the right to terminate such agreement in whole or on a product-by-product or target-by-target basis at any time upon 30 to 90 days prior written notice to us. There are no performance, cancellation, termination or refund provisions in any of our collaborative agreements that contain material financial consequences to us.
Refer to Note 3, “Collaborative Agreements,” and Note 5, “Deferred Revenue,” for further discussion on our collaborative arrangements.
Cost of Product Sales
Cost of product sales consists primarily of raw materials, third-party manufacturing costs, fill and finish costs, freight costs, internal costs and manufacturing overhead associated with the production of Hylenex recombinant. Cost of product sales also consists of the write-down of excess, dated and obsolete inventories. As a result of the termination of the Baxter Hylenex Collaboration in January 2011, we recorded write-down of inventory obsolescence of $166,000 and $875,000 for Hylenex recombinant API for the years ended December 31, 2011 and 2010, respectively. There was no write-down of inventories for the year ended December 31, 2012.
Research and Development Expenses
Research and development expenses include salaries and benefits, facilities and other overhead expenses, external clinical trial expenses, research related manufacturing services, contract services and other outside expenses. Research and development expenses are charged to operations as incurred when these expenditures relate to our research and development efforts and have no alternative future uses. 
In accordance with certain research and development agreements, we are obligated to make certain upfront payments upon execution of the agreement. Advance payments, including nonrefundable amounts, for goods or services that will be used or rendered for future research and development activities are deferred and capitalized. Such amounts will be recognized as an expense as the related goods are delivered or the related services are performed or such time when we do not expect the goods to be delivered or services to be performed.
Milestone payments that we make in connection with in-licensed technology or product candidates are expensed as incurred when there is uncertainty in receiving future economic benefits from the licensed technology or product candidates. We consider the future economic benefits from the licensed technology or product candidates to be uncertain until such licensed technology or product candidates are approved for marketing by the regulatory bodies such as the FDA or when other significant risk factors are abated. Management has viewed future economic benefits for all of our licensed technology or product candidates to be uncertain and has expensed these amounts as incurred.
Clinical Trial Expenses
Payments in connection with our clinical trials are often made under contracts with multiple contract research organizations that conduct and manage clinical trials on our behalf. The financial terms of these agreements are subject to negotiation and vary from contract to contract and may result in uneven payment flows. Generally, these agreements set forth the scope of work to be performed at a fixed fee, unit price or on a time-and-material basis. Payments under these contracts depend on factors such as the successful enrollment or treatment of patients or the completion of other clinical trial milestones.
Expenses related to clinical trials are accrued based on our estimates and/or representations from service providers regarding work performed, including actual level of patient enrollment, completion of patient studies and progress of the clinical trials. Other incidental costs related to patient enrollment or treatment are accrued when reasonably certain. If the contracted amounts are modified (for instance, as a result of changes in the clinical trial protocol or scope of work to be performed), we modify our accruals accordingly on a prospective basis. Revisions in the scope of a contract are charged to expense in the period in which the facts that give rise to the revision become reasonably certain. Historically, we have had no material changes in clinical trial expense accruals that would have had a material impact on our consolidated results of operations or financial position.
Share-Based Compensation
We record compensation expense associated with stock options and other share-based awards in accordance with the authoritative guidance for stock-based compensation. The cost of employee services received in exchange for an award of an equity instrument is measured at the grant date, based on the estimated fair value of the award, and is recognized as expense on a straight-line basis, net of estimated forfeitures, over the requisite service period of the award. Share-based compensation expense recognized during the period is based on the value of the portion of share-based payment awards that is ultimately expected to vest during the period. Share-based compensation expense for an award with a performance condition is recognized when the achievement of such performance condition is determined to be probable. If the outcome of such performance condition is not determined to be probable or is not met, no compensation expense is recognized and any recognized compensation expense is reversed. As share-based compensation expense recognized is based on awards ultimately expected to vest, it has been reduced for estimated forfeitures. The guidance requires forfeitures to be estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Pre-vesting forfeitures were estimated to be approximately 10% for employees in the years ended December 31, 2012, 2011 and 2010 based on our historical experience for the years then ended.
Income Taxes
We provide for income taxes using the liability method. Under this method, deferred income tax assets and liabilities are determined based on the differences between the financial statement carrying amounts of existing assets and liabilities at each year end and their respective tax bases and are measured using enacted tax rates in effect for the year in which the differences are expected to affect taxable income. Deferred tax assets and other tax benefits are recorded when it is more likely than not that the position will be sustained upon audit. Valuation allowances have been established to reduce our net deferred tax assets to zero, as we believe that it is more likely than not that such assets will not be realized.
Other Income
Other income for the year ended December 31, 2010 consisted of one-time grants of approximately $978,000 received under the Qualifying Therapeutic Discovery Project program administered under section 48D of the Internal Revenue Code.
Net Loss Per Share
Basic net loss per common share is computed by dividing net loss for the period by the weighted average number of common shares outstanding during the period, without consideration for common stock equivalents. Stock options, unvested stock awards and restricted stock units are considered to be common equivalents and are only included in the calculation of diluted earnings per common share when their effect is dilutive. Because of our net loss, outstanding stock options, outstanding restricted stock units and unvested stock awards totaling 7,444,333, 6,365,667 and 8,095,365 were excluded from the calculation of diluted net loss per common share for the years ended December 31, 2012, 2011 and 2010, respectively, because their effect is anti-dilutive.
Segment Information
We operate our business in one segment, which includes all activities related to the research, development and commercialization of human enzymes that either transiently modify tissue under the skin to facilitate the delivery of injected drugs and fluids or to alter abnormal tissue structures for clinical benefit. This segment also includes revenues and expenses related to (1) research and development activities conducted under our collaborative agreements with third parties and (ii) product sales of Hylenex recombinant. The chief operating decision maker reviews the operating results on an aggregate basis and manages the operations as a single operating segment.
Adoption of Recent Accounting Pronouncements
Effective January 1, 2012, we adopted Financial Accounting Standards Board's (“FASB”) Accounting Standards Update (“ASU”) No. 2011-05, Comprehensive Income (Topic 220): Presentation of Comprehensive Income and ASU No. 2011-12, Comprehensive Income (Topic 220): Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in ASU No. 2011-5. In these updates, an entity has the option to present the total of comprehensive income, the components of net income, and the components of other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. In both choices, an entity is required to present each component of net income along with total net income, each component of other comprehensive income along with a total for other comprehensive income, and a total amount for comprehensive income. ASU No. 2011-05 eliminates the option to present the components of other comprehensive income as part of the statement of changes in stockholders' equity. The amendments in ASU No. 2011-05 do not change the items that must be reported in other comprehensive income or when an item of other comprehensive income must be reclassified to net income. The amendments in these updates are effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The adoption of ASU Nos. 2011-05 and 2011-12 did not have a material impact on our consolidated financial position or results of operations. We have presented comprehensive loss in our consolidated statements of comprehensive loss.
Effective January 1, 2012, we prospectively adopted FASB's ASU No. 2011-04, “Fair Value Measurement (Topic 820) - Amendments to Achieve Common Fair Value Measurement and Disclosure Requirements in U.S. GAAP and IFRS”. The amendments in ASU 2011-04 result in common fair value measurement and disclosure requirements in GAAP and International Financial Reporting Standards (“IFRS”). Consequently, the amendments change the wording used to describe many of the requirements in U.S. GAAP for measuring fair value and for disclosing information about fair value measurements. This pronouncement is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The adoption of ASU No. 2011-04 did not have a material effect on our consolidated financial position or results of operations.
Summary of Significant Accounting Policies Share-based compensation (Tables)
Disclosure of Share-based Compensation Arrangements by Share-based Payment Award [Table Text Block]
Total share-based compensation expense related to share-based awards for the years ended December 31, 2012, 2011 and 2010 was comprised of the following: 
 
 
Year Ended December 31,
 
 
2012
 
2011
 
2010
Research and development
 
$
4,190,938

 
$
2,815,362

 
$
2,517,172

Selling, general and administrative
 
4,157,649

 
2,754,537

 
2,349,153

Share-based compensation expense
 
$
8,348,587

 
$
5,569,899

 
$
4,866,325

Net share-based compensation expense, per basic and diluted share
 
$
0.08

 
$
0.05

 
$
0.05

Share-based compensation expense from:
 

 

 

Stock options
 
$
4,722,629

 
$
3,230,822

 
$
4,022,790

Restricted stock awards and restricted stock units
 
3,625,958

 
2,339,077

 
843,535

 
 
$
8,348,587

 
$
5,569,899

 
$
4,866,325

Certain Balance Sheet Items (Tables)
Inventories consist of the following:
 
 
December 31,
2012
 
December 31,
2011
Raw materials
 
$
1,127,061

 
$
201,822

Work-in-process
 
792,257

 
290,647

Finished goods
 
751,378

 
74,794

 
 
$
2,670,696

 
$
567,263

Property and equipment consists of the following:
 
 
December 31,
2012
 
December 31,
2011
Research equipment
 
$
6,360,004

 
$
5,231,763

Computer and office equipment
 
1,432,975

 
1,266,041

Leasehold improvements
 
1,138,110

 
1,019,147

Building (1)
 
1,450,000

 

 
 
10,381,089

 
7,516,951

Accumulated depreciation and amortization
 
(6,680,627
)
 
(5,745,903
)
 
 
$
3,700,462

 
$
1,771,048

________________________
(1)
Represents capitalized building under a build-to-suit lease arrangement where we are considered the owner (for accounting purposes only) during the construction period.
Accrued expenses consist of the following:
 
 
December 31,
2012
 
December 31,
2011
Accrued outsourced research and development expenses
 
$
2,223,242

 
$
1,910,273

Accrued compensation and payroll taxes
 
4,053,590

 
3,223,936

Other accrued expenses
 
1,506,615

 
481,365

 
 
$
7,783,447

 
$
5,615,574

Deferred Revenue (Tables)
Summary of Deferred revenue
Deferred revenue consists of the following:
 
 
December 31,
2012
 
December 31,
2011
Collaborative agreements
 
$
43,222,473

 
$
40,716,806

Product sales
 
623,510

 
167,184

Total deferred revenue
 
43,845,983

 
40,883,990

Less current portion
 
8,891,017

 
4,129,407

Deferred revenue, net of current portion
 
$
34,954,966

 
$
36,754,583

Long-Term Debt, Net (Tables)
Schedule of future maturities and interest payments
Future maturities and interest payments under the term loan as of December 31, 2012, are as follows:
2013
 
$
2,076,250

2014
 
10,461,382

2015
 
11,206,507

2016
 
11,206,507

2017
 
3,483,876

Total minimum payments
 
38,434,522

Less amount representing interest
 
(8,434,522
)
Gross balance of long-term debt
 
30,000,000

Less unamortized debt discount
 
(338,320
)
Present value of long-term debt
 
29,661,680

Less current portion of long-term debt, less discount
 

Long-term debt, less current portion and discount
 
$
29,661,680

Equity Incentive Plans (Tables)
A summary of our stock option award activity as of and for the years ended December 31, 2012, 2011 and 2010 is as follows: 

 
Shares
Underlying
Stock Options

Weighted
Average Exercise
Price per Share

Weighted Average
Remaining
Contractual  Term (yrs)
 
Aggregate
Intrinsic
Value
Outstanding at January 1, 2010
 
7,804,266

 
$3.73
 
 
 
 
Granted
 
1,332,714

 
$5.94
 
 
 
 
Exercised
 
(479,093
)
 
$3.88
 
 
 
 
Canceled/forfeited
 
(682,522
)
 
$6.29
 
 
 
 
Outstanding at December 31, 2010
 
7,975,365

 
$3.87
 
 
 
 
Granted
 
1,624,768

 
$7.79
 
 
 
 
Exercised
 
(3,137,056
)
 
$1.71
 
 
 
 
Canceled/forfeited
 
(593,293
)
 
$6.72
 
 
 
 
Outstanding at December 31, 2011
 
5,869,784

 
$5.82
 
 
 
 
Granted
 
1,215,442

 
$9.90
 
 
 
 
Exercised
 
(444,637
)
 
$4.56
 
 
 
 
Canceled/forfeited
 
(260,722
)
 
$8.34
 
 
 
 
Outstanding at December 31, 2012
 
6,379,867

 
$6.59
 
6.5
 

$7.4
 million
Vested and expected to vest at December 31, 2012
 
6,086,988

 
$6.49
 
6.3
 

$7.4
 million
Exercisable at December 31, 2012
 
3,958,125

 
$5.34
 
5.1
 

$6.8
 million
Assumptions used in the Black-Scholes model were as follows:
 
 
Year Ended December 31,
 
 
2012

2011

2010
Expected volatility
 
64.0-69.2%


64.0-65.1%


65.8-70.8%

Average expected term (in years)
 
5.6


5.8


5.7

Risk-free interest rate
 
0.80-1.15%


1.14-2.55%


1.39-2.80%

Expected dividend yield
 
0
%

0
%

0
%
The following table summarizes our restricted stock award activity during the years ended December 31, 2012, 2011 and 2010:

 
Number of
Shares

Weighted  Average
Grant Date
Fair Value
Unvested at January 1, 2010
 
120,000

 
$
5.81

Granted
 
120,000

 
$
7.67

Vested
 
(120,000
)
 
$
5.81

Forfeited
 

 
$

Unvested at December 31, 2010
 
120,000

 
$
7.67

Granted
 
353,508

 
$
6.51

Vested
 
(120,000
)
 
$
7.67

Forfeited
 
(5,625
)
 
$
6.67

Unvested at December 31, 2011
 
347,883

 
$
6.51

Granted
 
380,158

 
$
10.29

Vested
 
(339,758
)
 
$
6.51

Forfeited
 
(5,963
)
 
$
10.81

Unvested at December 31, 2012
 
382,320

 
$
10.21

The following table summarizes our restricted stock unit activity during the years ended December 31, 2012 and 2011:

 
Number of
Shares

Weighted
Average
Purchase  Price

Weighted
Average  Remaining
Contractual Term (yrs)
 
Aggregate
Intrinsic
Value
Unvested at January 1, 2011
 

 
$

 
 
 
 
Granted
 
163,000

 
$

 
 
 
 
Vested
 
(15,000
)
 
$

 
 
 
 
Forfeited
 

 
$

 
 
 
 
Unvested at December 31, 2011
 
148,000

 
$

 
 
 
 
Granted
 
682,146

 
$

 
 
 
 
Vested
 
(128,000
)
 
$

 
 
 
 
Forfeited
 
(20,000
)
 
$

 
 
 
 
Unvested at December 31, 2012
 
682,146

 
$

 
2.03
 

$4.6
 million
Expected to vest at December 31, 2012
 
556,377

 
$

 
1.84
 

$3.7
 million
Commitments and Contingencies (Tables)
Schedule of future minimum rental payments for operating leases
Approximate annual future minimum operating lease payments as of December 31, 2012 are as follows: 
Year:
 
Operating
Leases
2013
 
$
1,865,000

2014
 
2,052,000

2015
 
2,049,000

2016
 
2,073,000

2017
 
2,126,000

Thereafter
 
80,000

Total minimum lease payments
 
$
10,245,000

Income Taxes (Tables)
Significant components of our net deferred tax assets at December 31, 2012 and 2011 are shown below. A valuation allowance of $128.4 million and $107.5 million has been established to offset the net deferred tax assets as of December 31, 2012 and 2011, respectively, as realization of such assets is uncertain.

 
2012

2011
Deferred tax assets:
 



Net operating loss carryforwards
 
$
86,732,000

 
$
69,912,000

Deferred revenue
 
17,345,000

 
15,338,000

Research and development credits
 
20,286,000

 
19,270,000

Share-based compensation
 
2,975,000

 
2,122,000

Depreciation
 
179,000

 
76,000

Other, net
 
926,000

 
771,000

Total deferred tax assets
 
128,443,000

 
107,489,000

Valuation allowance for deferred tax assets
 
(128,443,000
)
 
(107,489,000
)
Net deferred tax assets
 
$

 
$

The provision for income taxes on earnings subject to income taxes differs from the statutory federal income tax rate at December 31, 2012, 2011 and 2010, due to the following:

 
2012

2011

2010
Federal income tax at 34%
 
$
(18,208,000
)
 
$
(6,722,000
)
 
$
(18,102,000
)
State income tax, net of federal benefit
 
(3,023,000
)
 
(1,153,000
)
 
(3,106,000
)
Increase in valuation allowance
 
20,954,000

 
9,935,000

 
22,469,000

Tax effect on non-deductible expenses and other
 
1,293,000

 
1,671,000

 
2,118,000

Research and development credits
 
(1,016,000
)
 
(3,731,000
)
 
(3,379,000
)

 
$

 
$

 
$

Summary of Unaudited Quarterly Financial Information (Tables)
Schedule of quarterly financial information
The following is a summary of our unaudited quarterly results for the years ended December 31, 2012 and 2011:
 
 
Quarter Ended
2012 (Unaudited):
 
March 31,
 
June 30,
 
September 30,
 
December 31,
Total revenues (a)
 
$
7,440,179

 
$
7,757,175

 
$
5,334,323

 
$
21,793,549

Total operating expenses
 
$
22,580,577

 
$
21,805,273

 
$
25,364,160

 
$
26,200,662

Net loss
 
$
(15,119,181
)
 
$
(14,021,119
)
 
$
(20,005,846
)
 
$
(4,405,856
)
Net loss per share, basic and diluted
 
$
(0.14
)
 
$
(0.13
)
 
$
(0.18
)
 
$
(0.04
)
Shares used in computing net loss per share, basic and diluted
 
107,589,514

 
112,063,665

 
112,305,002

 
112,323,056

 
 
Quarter Ended
2011 (Unaudited):
 
March 31,
 
June 30,
 
September 30,
 
December 31,
Total revenues (b)
 
$
7,543,894

 
$
23,188,948

 
$
22,942,428

 
$
2,411,166

Total operating expenses
 
$
17,203,480

 
$
20,093,017

 
$
17,789,595

 
$
20,839,285

Net income (loss)
 
$
(9,635,717
)
 
$
3,116,288

 
$
5,165,193

 
$
(18,415,615
)
Net income (loss) per share, basic and diluted
 
$
(0.10
)
 
$
0.03

 
$
0.05

 
$
(0.18
)
Shares used in computing net income (loss) per share:
 
 
 
 
 
 
 
 
Basic
 
100,927,402

 
102,671,410

 
103,223,352

 
103,406,407

Diluted
 
100,927,402

 
104,393,835

 
105,009,189

 
103,406,407

 
 
(a)
Revenues for the quarter ended December 31, 2012 included $9.5 million in revenue under collaborative agreements from the Pfizer Collaboration.
(b)
Revenues for the quarter ended June 30, 2011 included revenue under collaborative agreements totaling $18.0 million from the ViroPharma and Intrexon Collaborations. Revenues for the quarter ended September 30, 2011 included revenue from collaborative agreements totaling $17.9 million related to recognition of unamortized deferred prepaid product-based payments and unamortized deferred upfront payment pursuant to the termination of the Hylenex Collaboration with Baxter in July 2011.
Summary of Significant Accounting Policies (Concentrations of Credit Risk, Sources of Supply and Significant Customers) (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Concentration Risk
 
 
 
Allowance for Doubtful Accounts Receivable
$ 0 
$ 0 
 
Roche and Pfizer |
Accounts Receivable |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
86.00% 
 
 
Roche, Baxter and ViroPharma |
Accounts Receivable |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
 
82.00% 
 
Roche |
Sales |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
45.00% 
19.00% 
52.00% 
Baxter |
Sales |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
17.00% 
42.00% 
42.00% 
ViroPharma |
Sales |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
 
22.00% 
 
Pfizer |
Sales |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
22.00% 
 
 
Intrexon |
Sales |
Customer Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
 
16.00% 
 
Domestic |
Geographic Concentration Risk
 
 
 
Concentration Risk
 
 
 
Revenue, net
22,700,000 
44,900,000 
6,000,000 
Foreign Countries
 
 
 
Concentration Risk
 
 
 
Long-Lived assets in foreign countries
Foreign Countries |
Geographic Concentration Risk
 
 
 
Concentration Risk
 
 
 
Revenue, net
19,600,000 
11,200,000 
7,600,000 
Switzerland |
Geographic Concentration Risk
 
 
 
Concentration Risk
 
 
 
Revenue, net
$ 18,900,000 
$ 10,400,000 
$ 7,200,000 
Bulk formulation |
Third Party Manufacturer |
Accounts Payable |
Supplier Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
20.00% 
59.00% 
 
Fill and Finish |
Third Party Manufacturer |
Accounts Payable |
Supplier Concentration Risk
 
 
 
Concentration Risk
 
 
 
Concentration risk, percentage
8.00% 
3.70% 
 
Summary of Significant Accounting Policies Accounts Receivable, Net (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Accounts Receivable, Net [Abstract]
 
 
Allowance for Doubtful Accounts Receivable
$ 0 
$ 0 
Summary of Significant Accounting Policies (Share Based Payments) (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Share-based compensation expense related to share-based awards
 
 
 
Share-based compensation expense
$ 8,348,587 
$ 5,569,899 
$ 4,866,325 
Share-based compensation expense per basic and diluted share
$ 0.08 
$ 0.05 
$ 0.05 
Share-based Compensation, Additional Disclosures
 
 
 
Pre-vesting forfeitures percent
10.00% 
10.00% 
10.00% 
Share-based compensation, tax benefit
Stock options
 
 
 
Share-based compensation expense related to share-based awards
 
 
 
Share-based compensation expense
4,722,629 
3,230,822 
4,022,790 
Restricted stock awards and restricted stock units [Member]
 
 
 
Share-based compensation expense related to share-based awards
 
 
 
Share-based compensation expense
3,625,958 
2,339,077 
843,535 
Research and development
 
 
 
Share-based compensation expense related to share-based awards
 
 
 
Share-based compensation expense
4,190,938 
2,815,362 
2,517,172 
Selling, general and administrative
 
 
 
Share-based compensation expense related to share-based awards
 
 
 
Share-based compensation expense
$ 4,157,649 
$ 2,754,537 
$ 2,349,153 
Summary of Significant Accounting Policies (Net Loss Per Share) (Details)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Accounting Policies [Abstract]
 
 
 
Antidilutive securities excluded from the calculation of diluted net loss per common share
7,444,333 
6,365,667 
8,095,365 
Summary of Significant Accounting Policies (Details Textual) (USD $)
12 Months Ended
Dec. 31, 2012
Segment
Dec. 31, 2011
Dec. 31, 2010
Summary of Significant Accounting Policies (Additional Textual)
 
 
 
Estimated useful life of equipment
3 years 
 
 
Impairment of long lived assets
$ 0 
$ 0 
 
Write-down for inventory obsolescence
166,000 
875,000 
Product sales, net
2,887,442 
1,836,102 
895,518 
Deferred revenue
43,845,983 
40,883,990 
 
Revenue from one-time grants
 
 
978,000 
Number of operating segments
 
 
Hylenex Recombinant [Member]
 
 
 
Summary of Significant Accounting Policies (Additional Textual)
 
 
 
Product sales, net
2,200,000 
35,000 
 
Distribution fees, prompt payment discounts and product returns
1,100,000 
8,000 
 
Deferred revenue
624,000 
167,000 
 
Deferred costs
178,000 
31,000 
 
Cash Equivalents [Member] |
Level 1
 
 
 
Summary of Significant Accounting Policies (Textual)
 
 
 
Cash Equivalents, Fair Value Disclosure
98,400,000 
51,800,000 
 
Instruments [Member] |
Level 2
 
 
 
Summary of Significant Accounting Policies (Textual)
 
 
 
Instruments, Fair Value Disclosure
 
Instruments [Member] |
Level 3
 
 
 
Summary of Significant Accounting Policies (Textual)
 
 
 
Instruments, Fair Value Disclosure
$ 0 
$ 0 
 
Collaborative Agreements (Details) (USD $)
12 Months Ended 3 Months Ended 12 Months Ended
Dec. 31, 2012
Dec. 31, 2012
Roche Collaboration [Member]
Compound
Dec. 31, 2011
Roche Collaboration [Member]
Dec. 31, 2010
Roche Collaboration [Member]
Dec. 31, 2012
Gammagard Collaboration [Member]
Dec. 31, 2011
Gammagard Collaboration [Member]
Dec. 31, 2010
Gammagard Collaboration [Member]
Dec. 31, 2012
Pfizer Collaboration [Member]
Dec. 31, 2012
Pfizer Collaboration [Member]
Compound
Dec. 31, 2012
ViroPharma Collaboration [Member]
Dec. 31, 2011
ViroPharma Collaboration [Member]
Dec. 31, 2012
Intrexon Collaboration [Member]
Dec. 31, 2011
Intrexon Collaboration [Member]
Collaborative Agreements (Textual) [Abstract]
 
 
 
 
 
 
 
 
 
 
 
 
 
Number of product combinations licensed to develop
 
13 
 
 
 
 
 
 
 
 
 
 
Number of targets elected
 
 
 
 
 
 
 
 
 
 
 
Number of additional target, optional
 
 
 
 
 
 
 
 
 
 
 
 
Total to date proceeds received from partner under license and collaborative agreement
 
$ 61,750,000 
 
 
$ 13,000,000 
 
 
 
 
$ 13,000,000 
 
$ 10,000,000 
 
Nonrefundable upfront license fee payment
 
20,000,000 
 
 
10,000,000 
 
 
9,500,000 
9,500,000 
9,000,000 
 
9,000,000 
 
Amount received from Roche for additional exclusive targets and annual license maintenance fees
 
20,750,000 
 
 
 
 
 
 
 
 
 
 
 
Clinical development milestone payments received under collaborative agreement
 
13,000,000 
 
 
 
 
 
 
 
3,000,000 
 
 
 
Regulatory milestone payments received under collaborative agreement
 
8,000,000 
 
 
3,000,000 
 
 
 
 
 
 
 
 
Royalty receivable, Duration
 
10 years 
 
 
10 years 
 
 
 
10 years 
10 years 
 
10 years 
 
Milestone payments recognized as revenues
 
8,000,000 
5,000,000 
3,000,000 
9,500,000 
9,500,000 
 
9,000,000 
 
9,000,000 
Time period to provide prior notice to terminate collaborative agreements
 
 
 
 
 
 
 
 
30 days 
90 days 
 
90 days 
 
Allocation of license fee received to license fee deliverable under agreement
 
 
 
 
 
 
 
 
9,500,000 
9,000,000 
 
9,000,000 
 
Recognized payment of revenues under collaborative agreements
 
 
 
 
 
 
 
 
 
3,000,000 
 
Additional Maximum Proceeds Receivable from License and Collaborative Agreements Upon Achievement of Clinical Development Milestones
58,500,000 
 
 
 
 
 
 
 
 
 
 
 
 
Additional Maximum Proceeds Receivable From Achievement of Regulatory Milestones
$ 84,000,000 
 
 
 
 
 
 
 
 
 
 
 
 
Certain Balance Sheet Items Inventories (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Summary of Inventories
 
 
Raw materials
$ 1,127,061 
$ 201,822 
Work-in-process
792,257 
290,647 
Finished goods
751,378 
74,794 
Inventories
$ 2,670,696 
$ 567,263 
Certain Balance Sheet Items Property and Equipment, Net (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Summary of property and equipment
 
 
Property and equipment, gross
$ 10,381,089 
$ 7,516,951 
Building
1,450,000 1
Accumulated depreciation and amortization
(6,680,627)
(5,745,903)
Property, Plant and Equipment, Net
3,700,462 
1,771,048 
Research Equipment [Member]
 
 
Summary of property and equipment
 
 
Property and equipment, gross
6,360,004 
5,231,763 
Computer and Office Equipment [Member]
 
 
Summary of property and equipment
 
 
Property and equipment, gross
1,432,975 
1,266,041 
Leasehold Improvements [Member]
 
 
Summary of property and equipment
 
 
Property and equipment, gross
$ 1,138,110 
$ 1,019,147 
Certain Balance Sheet Items Property and Equipment, Net (Textual) (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Property and Equipment, Net (Textual) [Abstract]
 
 
 
Depreciation and amortization
$ 1,079,424 
$ 1,095,823 
$ 1,507,925 
Certain Balance Sheet Items Accrued Expenses (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Accrued Expenses
 
 
Accrued outsourced research and development expenses
$ 2,223,242 
$ 1,910,273 
Accrued compensation and payroll taxes
4,053,590 
3,223,936 
Accrued other liabilities
1,506,615 
481,365 
Accrued expenses
$ 7,783,447 
$ 5,615,574 
Deferred Revenue (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Summary of Deferred revenue
 
 
Total deferred revenue
$ 43,845,983 
$ 40,883,990 
Less current portion
8,891,017 
4,129,407 
Deferred revenue, net of current portion
34,954,966 
36,754,583 
Collaborative agreements [Member]
 
 
Summary of Deferred revenue
 
 
Total deferred revenue
43,222,473 
40,716,806 
Product sales [Member]
 
 
Summary of Deferred revenue
 
 
Total deferred revenue
$ 623,510 
$ 167,184 
Deferred Revenue (Details Textual) (USD $)
12 Months Ended 73 Months Ended 12 Months Ended 12 Months Ended 36 Months Ended 12 Months Ended
Dec. 31, 2012
Roche Collaboration [Member]
Dec. 31, 2011
Roche Collaboration [Member]
Dec. 31, 2010
Roche Collaboration [Member]
Dec. 31, 2012
Roche Collaboration [Member]
Dec. 31, 2006
Roche Collaboration [Member]
Dec. 31, 2012
Gammagard Collaboration [Member]
Dec. 31, 2011
Gammagard Collaboration [Member]
Dec. 31, 2010
Gammagard Collaboration [Member]
Sep. 30, 2007
Gammagard Collaboration [Member]
Dec. 31, 2011
Hylenex Collaboration [Member]
Dec. 31, 2010
Hylenex Collaboration [Member]
Dec. 31, 2009
Hylenex Collaboration [Member]
Dec. 31, 2012
Hylenex Collaboration [Member]
Feb. 28, 2007
Hylenex Collaboration [Member]
Dec. 31, 2012
Roche Collaboration [Member]
Manufacturing Arrangement [Member]
Dec. 31, 2011
Roche Collaboration [Member]
Manufacturing Arrangement [Member]
Deferred Revenue (Textual) [Abstract]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Nonrefundable upfront payment
 
 
 
 
$ 20,000,000 
 
 
 
$ 10,000,000 
 
 
 
 
$ 10,000,000 
 
 
Deferred revenue, additions
 
 
 
20,750,000 
 
 
 
 
 
 
 
10,000,000 
 
 
7,000,000 
 
Deferred revenue remaining, upfront fees, license fees, maintenance fees
30,400,000 
31,700,000 
 
30,400,000 
 
7,100,000 
7,600,000 
 
 
991,000 
 
 
5,600,000 
Deferred revenue, revenue recognized
2,000,000 
2,000,000 
2,000,000 
 
 
483,000 
483,000 
521,000 
 
991,000 
 
 
 
 
1,400,000 
 
Recognized revenues relating to prepaid product-based payments
 
 
 
 
 
 
 
 
 
9,300,000 
332,000 
 
 
 
 
 
Recognized revenues related to upfront payment
 
 
 
 
 
 
 
 
 
$ 7,800,000 
$ 503,000 
 
 
 
 
 
Long-Term Debt, Net (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Debt Disclosure [Abstract]
 
 
2013
$ 2,076,250 
 
2014
10,461,382 
 
2015
11,206,507 
 
2016
11,206,507 
 
2017
3,483,876 
 
Total minimum payments
38,434,522 
 
Less amount representing interest
(8,434,522)
 
Gross balance of long-term debt
30,000,000 
 
Less unamortized debt discount
(338,320)
 
Present value of long-term debt
29,661,680 
Less current portion of long-term debt, less discount
 
Long-term debt, less current portion and discount
$ 29,661,680 
 
Long-Term Debt, Net (Details Textual) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Debt Instrument [Line Items]
 
 
 
Long-term debt, gross
$ 30,000,000 
 
 
Proceeds from issuance of long-term debt, net
29,660,600 
Interest expense
28,000 
 
 
Secured Single Draw Term Loan [Member] |
Loan Agreement [Member]
 
 
 
Debt Instrument [Line Items]
 
 
 
Face amount of term loan facility
30,000,000 
 
 
Maturity date of term loan facility
Jan. 01, 2017 
 
 
Long-term debt, gross
30,000,000 
 
 
Fixed interest rate on term loan
7.55% 
 
 
Period for which principal and interest payments are to be made
36 months 
 
 
Final payment required on term loan
2,550,000 
 
 
Proceeds from issuance of long-term debt, net
$ 29,660,600 
 
 
Secured Single Draw Term Loan [Member] |
Loan Agreement [Member] |
Minimum [Member]
 
 
 
Debt Instrument [Line Items]
 
 
 
Percentage of pre payment fee on term loan
1.00% 
 
 
Secured Single Draw Term Loan [Member] |
Loan Agreement [Member] |
Maximum [Member]
 
 
 
Debt Instrument [Line Items]
 
 
 
Percentage of pre payment fee on term loan
3.00% 
 
 
Stockholders' Equity (Details) (USD $)
1 Months Ended 12 Months Ended
Feb. 29, 2012
Sep. 30, 2010
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Stockholders' Equity (Textual) [Abstract]
 
 
 
 
 
Options exercised, shares
 
 
444,637 
3,137,056 
479,093 
Issuance of common stock, exercise of options net, shares
 
 
 
3,045,540 
 
Net proceeds from stock options exercised
 
 
$ 1,680,173 
$ 4,748,612 
$ 1,858,333 
Shares issued related to restricted stock awards, net of any shares forfeited
 
 
374,195 
347,883 
120,000 
Underwritten public offering and issued shares
7,820,000 
8,300,000 
 
 
 
Shares sold to underwriter pursuant to the full exercise of an over-allotment option granted to the underwriter
1,020,000 
 
 
 
 
Public offering price per share
$ 10.61 
$ 7.50 
 
 
 
Net proceeds from common stock issued
81,500,000 
60,000,000 
81,476,845 
59,965,059 
Purchase of common stock by affiliates
1,360,000 
 
 
 
 
Purchase of common stock by affiliates amount
14,400,000 
 
 
 
 
Option issued to underwriter
 
1,245,000 
 
 
 
Option issued to underwriter, price per share
 
$ 7.25 
 
 
 
Sale of shares required for options to underwriters to be exercisable
 
8,300,000 
 
 
 
Stock options
 
 
 
 
 
Stockholders' Equity (Textual) [Abstract]
 
 
 
 
 
Net proceeds from stock options exercised
 
 
2,000,000 
 
 
Restricted Stock Units (RSUs)
 
 
 
 
 
Stockholders' Equity (Textual) [Abstract]
 
 
 
 
 
Number of shares of common stock issued related to RSUs, net of RSUs surrendered as payment for withholding taxes
 
 
81,070 
15,000 
 
Number of RSUs surrendered to pay for minimum withholding taxes
 
 
46,930 
 
 
Amount of withholding taxes associated with RSUs vested during the period
 
 
$ 347,000 
 
 
Equity Incentive Plans (Details) Options (USD $)
In Millions, except Share data, unless otherwise specified
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
 
 
 
Outstanding, Number, At Beginning
5,869,784 
7,975,365 
7,804,266 
Granted
1,215,442 
1,624,768 
1,332,714 
Exercised
(444,637)
(3,137,056)
(479,093)
Cancelled/forfeited
(260,722)
(593,293)
(682,522)
Outstanding, Number, At End
6,379,867 
5,869,784 
7,975,365 
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]
 
 
 
Options, outstanding, weighted average exercise price, at beginning
$ 5.82 
$ 3.87 
$ 3.73 
Options, grants in period, weighted average exercise price
$ 9.90 
$ 7.79 
$ 5.94 
Options, exercises in period, weighted average exercise price
$ 4.56 
$ 1.71 
$ 3.88 
Options, forfeitures and expirations in period, weighted average exercise price
$ 8.34 
$ 6.72 
$ 6.29 
Options, outstanding, weighted average exercise price, at end
$ 6.59 
$ 5.82 
$ 3.87 
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
 
 
 
Options, outstanding, weighted average remaining contractual term
6 years 6 months 
 
 
Options, outstanding, intrinsic value
$ 7.4 
 
 
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested and Expected to Vest [Abstract]
 
 
 
Options, vested and expected to vest, outstanding, number
6,086,988 
 
 
Options, vested and expected to vest, outstanding, weighted average exercise price
$ 6.49 
 
 
Options, vested and expected to vest, outstanding, weighted average remaining contractual term
6 years 3 months 18 days 
 
 
Options, vested and expected to vest, outstanding, aggregate intrinsic value
7.4 
 
 
Options, vested and expected to vest, exercisable, number
3,958,125 
 
 
Options, vested and expected to vest, exercisable, weighted average exercise price
$ 5.34 
 
 
Options, vested and expected to vest, exercisable, weighted average remaining contractual term
5 years 1 month 6 days 
 
 
Options, vested and expected to vest, exercisable, aggregate intrinsic value
$ 6.8 
 
 
Equity Incentive Plans (Details) Black-Scholes Assumptions
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Share-based Compensation
 
 
 
Average expected term
5 years 7 months 6 days 
5 years 9 months 18 days 
5 years 8 months 12 days 
Risk free interest rate, minimum
0.80% 
1.14% 
1.39% 
Risk free interest rate, maximum
1.15% 
2.55% 
2.80% 
Expected dividend rate
0.00% 
0.00% 
0.00% 
Minimum [Member]
 
 
 
Share-based Compensation
 
 
 
Expected volatility rate
64.00% 
64.00% 
65.80% 
Maximum [Member]
 
 
 
Share-based Compensation
 
 
 
Expected volatility rate
69.20% 
65.10% 
70.80% 
Equity Incentive Plans (Details) Restricted Stock Awards (Restricted Stock, USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Restricted Stock
 
 
 
Share-based Compensation - restricted stock awards
 
 
 
Unvested, Number, At Beginning
347,883 
120,000 
120,000 
Granted
380,158 
353,508 
120,000 
Vested
(339,758)
(120,000)
(120,000)
Forfeited
(5,963)
(5,625)
Unvested, Number, At end
382,320 
347,883 
120,000 
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Roll Forward]
 
 
 
Nonvested, weighted average grant date fair value, at beginning
$ 6.51 
$ 7.67 
$ 5.81 
Granted, weighted average grant date fair value
$ 10.29 
$ 6.51 
$ 7.67 
Vested, weighted average grant date fair value
$ 6.51 
$ 7.67 
$ 5.81 
Forfeitures, weighted average grant date fair value
$ 10.81 
$ 6.67 
$ 0 
Nonvested, weighted average grant date fair value, at end
$ 10.21 
$ 6.51 
$ 7.67 
Equity Incentive Plans (Details) Restricted Stock Units (Restricted Stock Units (RSUs), USD $)
In Millions, except Share data, unless otherwise specified
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Restricted Stock Units (RSUs)
 
 
Share-based Compensation - restricted stock units
 
 
Unvested, Number, At Beginning
148,000 
Granted
682,146 
163,000 
Exercised
(128,000)
(15,000)
Forfeited
(20,000)
Unvested, Number, At end
682,146 
148,000 
Share Based Compensation Arrangement By Share Based Payment Award Equity Instrument Other Than Options Vested And Expected To Vest [Abstract]
 
 
Expected to vest, outstanding, number
556,377 
 
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options,WeightedAverage Purchase Price [Roll Forward]
 
 
Unvested, weighted average purchase price at beginning
$ 0 
$ 0 
Granted, weighted average purchase price
$ 0 
$ 0 
Exercised, weighted average purchase price
$ 0 
$ 0 
Forfeited, weighted average purchase price
$ 0 
$ 0 
Unvested, weighted average purchase price at end
$ 0 
$ 0 
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Additional Disclosures [Abstract]
 
 
Vested and expected to be vested, weighted average purchase price
$ 0 
 
Unvested, weighted average remaining contractual terms
2 years 0 months 11 days 
 
Unvested, aggregate intrinsic value
$ 4.6 
 
Expected to vest, weighted average remaining contractual terms
1 year 10 months 2 days 
 
Expected to vest, outstanding, aggregate intrinsic value
$ 3.7 
 
Equity Incentive Plans (Details - Textuals) (USD $)
12 Months Ended
Dec. 31, 2012
plan
Dec. 31, 2011
Dec. 31, 2010
Share-based Compensation
 
 
 
Number of equity incentive plans
 
 
Shares reserved for future issuance
2,730,059 
 
 
Future dividend payments expected for dividend yield assumption
$ 0 
 
 
Share based compensation expenses recognized
8,348,587 
5,569,899 
4,866,325 
Outstanding awards [Member]
 
 
 
Share-based Compensation
 
 
 
Options outstanding, number
7,062,013 
 
 
Stock options
 
 
 
Share-based Compensation
 
 
 
Weighted average grant-date fair values
$ 5.63 
$ 4.57 
$ 3.69 
Total unrecognized compensation costs related to non-vested stock option awards
9,000,000 
 
 
Period over which the unrecognized compensation costs will be recognized
2 years 8 months 12 days 
 
 
Intrinsic value of options exercised
2,900,000 
16,600,000 
1,800,000 
Cash received from stock option exercises
2,000,000 
4,700,000 
1,900,000 
Share based compensation expenses recognized
4,722,629 
3,230,822 
4,022,790 
Stock options |
Minimum [Member]
 
 
 
Share-based Compensation
 
 
 
Exercise price as a percent of fair value
100.00% 
 
 
Stock options |
Maximum [Member]
 
 
 
Share-based Compensation
 
 
 
Options, outstanding, initial contractual term
10 years 
 
 
Restricted Stock
 
 
 
Share-based Compensation
 
 
 
Period over which the unrecognized compensation costs will be recognized
2 years 2 months 12 days 
 
 
Total fair value of restricted stock awards vested
2,200,000 
900,000 
700,000 
Share based compensation expenses recognized
2,100,000 
1,700,000 
800,000 
Unrecognized share based compensation costs
2,000,000 
 
 
Shares granted
380,158 
353,508 
120,000 
Granted, weighted average grant date fair value
$ 10.29 
$ 6.51 
$ 7.67 
Restricted Stock Units (RSUs)
 
 
 
Share-based Compensation
 
 
 
Period over which the unrecognized compensation costs will be recognized
3 years 10 months 24 days 
 
 
Total fair value of restricted stock awards vested
900,000 
100,000 
 
Share based compensation expenses recognized
1,500,000 
700,000 
 
Unrecognized share based compensation costs
4,200,000 
 
 
Shares granted
682,146 
163,000 
 
Granted, weighted average grant date fair value
$ 10.61 
$ 6.71 
 
2011 Stock Plan [Member]
 
 
 
Share-based Compensation
 
 
 
Number of shares authorized
6,000,000 
 
 
2011 Stock Plan [Member] |
Restricted Stock
 
 
 
Share-based Compensation
 
 
 
Restricted stock unit purchase price
$ 0 
$ 0 
 
2011 Stock Plan [Member] |
Restricted Stock Units (RSUs)
 
 
 
Share-based Compensation
 
 
 
Shares granted
682,146 
163,000 
Cliff Vesting, First Anniversary [Member] |
Stock options
 
 
 
Share-based Compensation
 
 
 
Percent of shares vested on the first anniversary of the date of grant
25.00% 
 
 
Percentage Vesting [Member] |
2011 Stock Plan [Member] |
Restricted Stock Units (RSUs)
 
 
 
Share-based Compensation
 
 
 
Shares granted
 
148,000 
 
Monthly Vesting, after One Year [Member] |
Stock options
 
 
 
Share-based Compensation
 
 
 
Percent of shares vested on the first anniversary of the date of grant
2.08% 
 
 
Commitments and Contingencies Operating Lease (Details) (USD $)
Dec. 31, 2012
Commitments and Contingencies Disclosure [Abstract]
 
2013
$ 1,865,000 
2014
2,052,000 
2015
2,049,000 
2016
2,073,000 
2017
2,126,000 
Thereafter
80,000 
Total minimum lease payments
$ 10,245,000 
Commitments and Contingencies Operating Lease - Textual (Details) (USD $)
1 Months Ended 1 Months Ended 1 Months Ended 12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Jan. 31, 2013
BMR - 11388 [Member]
Jun. 30, 2011
BMR - 11388 [Member]
Dec. 31, 2012
BMR - 11388 [Member]
Dec. 31, 2011
BMR - 11388 [Member]
Jul. 31, 2007
11404 Sublease [Member]
Dec. 31, 2012
11404 Sublease [Member]
Dec. 31, 2011
11404 Sublease [Member]
Apr. 30, 2009
11408 Sublease [Member]
Jun. 30, 2011
11404/11408 Lease [Member]
Oct. 31, 2012
11436 Property [Member]
Dec. 31, 2012
11436 Property [Member]
Dec. 31, 2012
Office Equipment [Member]
Dec. 31, 2011
Office Equipment [Member]
Dec. 31, 2010
Office Equipment [Member]
Dec. 31, 2012
Office and Research Facility [Member]
sqft
Operating Leased Assets [Line Items]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Aggregate leased office and research space (in square feet)
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
76,000 
Monthly rental payment
 
 
$ 65,000 
$ 38,000 
 
 
$ 54,000 
 
 
$ 21,000 
$ 71,000 
$ 24,300 
 
 
 
 
 
Percent of annual increase in base rent
 
 
 
2.50% 
 
 
4.00% 
 
 
3.00% 
2.50% 
3.00% 
 
 
 
 
 
Cash incentive received
 
 
 
98,000 
 
 
 
 
 
 
 
 
 
 
 
 
 
Allowance for Tenant Improvement
 
 
 
300,000 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lease Incentive Receivable
 
 
 
744,000 
1,100,000 
854,000 
492,000 
4,000 
149,000 
 
 
158,000 
 
 
 
 
 
Building fair value asset
1,450,000 1
 
 
 
 
 
 
 
 
 
 
1,500,000 
 
 
 
 
Total rent expense
 
 
 
 
 
 
 
 
 
 
 
 
 
$ 1,600,000 
$ 1,500,000 
$ 1,500,000 
 
Commitments and Contingencies Other Commitments - Textual (Details) (USD $)
Dec. 31, 2012
Cook Commercial Supply Agreement [Member]
 
Purchase Obligation By Agreement [Line Items]
 
Minimum purchase obligation
$ 7,700,000 
March 2010 Avid Amendment [Member]
 
Purchase Obligation By Agreement [Line Items]
 
Minimum purchase obligation
217,000 
Avid Commercial Supply Agreement [Member]
 
Purchase Obligation By Agreement [Line Items]
 
Minimum purchase obligation
7,700,000 
Baxter Manufacturing and Supply Agreement [Member]
 
Purchase Obligation By Agreement [Line Items]
 
Minimum purchase obligation
9,500,000 
Third Party Manufacturer Agreement [Member]
 
Purchase Obligation By Agreement [Line Items]
 
Minimum purchase obligation
$ 0 
Income Taxes (Components of net deferred tax assets) (Details) (USD $)
Dec. 31, 2012
Dec. 31, 2011
Components of net deferred tax assets
 
 
Net operating loss carryforwards
$ 86,732,000 
$ 69,912,000 
Deferred revenue
17,345,000 
15,338,000 
Research and development credits
20,286,000 
19,270,000 
Share-based compensation
2,975,000 
2,122,000 
Depreciation
179,000 
76,000 
Other, net
926,000 
771,000 
Total deferred tax assets
128,443,000 
107,489,000 
Valuation allowance for deferred tax assets
(128,443,000)
(107,489,000)
Net deferred tax assets
$ 0 
$ 0 
Income Taxes (Schedule of income tax reconciliation) (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Income Tax Expense (Benefit), Continuing Operations, Income Tax Reconciliation [Abstract]
 
 
 
Federal income tax at 34%
$ (18,208,000)
$ (6,722,000)
$ (18,102,000)
State income tax, net of federal benefit
(3,023,000)
(1,153,000)
(3,106,000)
Increase in valuation allowance
20,954,000 
9,935,000 
22,469,000 
Tax effect on non-deductible expenses and other
1,293,000 
1,671,000 
2,118,000 
Research and development credits
(1,016,000)
(3,731,000)
(3,379,000)
Provision for income taxes
$ 0 
$ 0 
$ 0 
Federal income tax rate
34.00% 
34.00% 
34.00% 
Income Taxes (Operating Loss Carryforwards - Textual) (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Operating Loss Carryforwards [Line Items]
 
 
 
Net operating loss carryforwards
$ 27,900,000 
 
 
Income tax interest and penalty
Federal [Member]
 
 
 
Operating Loss Carryforwards [Line Items]
 
 
 
Net operating loss carryforwards
245,300,000 
 
 
Operating loss carryforwards, begin to expire
2018 
 
 
California [Member]
 
 
 
Operating Loss Carryforwards [Line Items]
 
 
 
Net operating loss carryforwards
$ 247,000,000 
 
 
Operating loss carryforwards, begin to expire
2013 
 
 
Income Taxes (Tax Credit Carryforward - Textual) (Details) (Research Tax Credit Carryforward [Member], USD $)
In Millions, unless otherwise specified
12 Months Ended
Dec. 31, 2012
Federal [Member]
 
Tax Credit Carryforward [Line Items]
 
Tax credit carryforwards
$ 14.3 
Tax credit carry forward, begin to expire
Dec. 31, 2024 
California [Member]
 
Tax Credit Carryforward [Line Items]
 
Tax credit carryforwards
$ 9.0 
Employee Savings Plan (Details) (USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Employee Savings Plan [Abstract]
 
 
 
Voluntary contribution by employer in the ESP
$ 508,000 
$ 355,000 
$ 433,000 
Restructuring Expense (Details) (USD $)
1 Months Ended 12 Months Ended
Oct. 31, 2010
Dec. 31, 2010
Restructuring Cost and Reserve [Line Items]
 
 
Reduction in workforce, period percent
25.00% 
 
Severance pay and benefits expenses in connection with the reorganization
$ 1,300,000 
 
Other restructuring charges
 
Cash payments for restructuring charges
 
1,200,000 
Research and Development Expense [Member]
 
 
Restructuring Cost and Reserve [Line Items]
 
 
Severance pay and benefits expenses in connection with the reorganization
1,200,000 
 
Selling, General and Administrative Expenses [Member]
 
 
Restructuring Cost and Reserve [Line Items]
 
 
Severance pay and benefits expenses in connection with the reorganization
$ 76,000 
 
Related Party Transactions (Details) (Affiliated Entity [Member], USD $)
12 Months Ended
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Intrexon
 
 
 
Related Party Transaction [Line Items]
 
 
 
Revenue from Related Parties
$ 1,000,000 
$ 9,000,000 
 
BC Sorrento [Member]
 
 
 
Related Party Transaction [Line Items]
 
 
 
Amount paid to related party
$ 0 
$ 0 
$ 982,000 
Summary of Unaudited Quarterly Financial Information (Details) (USD $)
3 Months Ended 12 Months Ended
Dec. 31, 2012
Sep. 30, 2012
Jun. 30, 2012
Mar. 31, 2012
Dec. 31, 2011
Sep. 30, 2011
Jun. 30, 2011
Mar. 31, 2011
Dec. 31, 2012
Dec. 31, 2011
Dec. 31, 2010
Quarterly Financial Information Disclosure [Abstract]
 
 
 
 
 
 
 
 
 
 
 
Total revenues
$ 21,793,549 1
$ 5,334,323 1
$ 7,757,175 1
$ 7,440,179 1
$ 2,411,166 2
$ 22,942,428 2
$ 23,188,948 2
$ 7,543,894 2
$ 42,325,226 
$ 56,086,436 
$ 13,624,115 
Total operating expenses
26,200,662 
25,364,160 
21,805,273 
22,580,577 
20,839,285 
17,789,595 
20,093,017 
17,203,480 
95,950,672 
75,925,377 
67,881,747 
Net Income (Loss)
$ (4,405,856)
$ (20,005,846)
$ (14,021,119)
$ (15,119,181)
$ (18,415,615)
$ 5,165,193 
$ 3,116,288 
$ (9,635,717)
$ (53,552,002)
$ (19,769,851)
$ (53,241,650)
Net income (loss) per share, basic and diluted
$ (0.04)
$ (0.18)
$ (0.13)
$ (0.14)
$ (0.18)
$ 0.05 
$ 0.03 
$ (0.10)
$ (0.48)
$ (0.19)
$ (0.56)
Shares used in computing net loss per share, basic and diluted
112,323,056 
112,305,002 
112,063,665 
107,589,514 
 
 
 
 
111,077,105 
102,566,089 
94,357,695 
Shares used in computing net income (loss) per share: Basic
 
 
 
 
103,406,407 
103,223,352 
102,671,410 
100,927,402 
 
 
 
Shares used in computing net income (loss) per share: Diluted
 
 
 
 
103,406,407 
105,009,189 
104,393,835 
100,927,402 
 
 
 
Summary of Unaudited Quarterly Financial Information (Details Textual) (USD $)
3 Months Ended 12 Months Ended 3 Months Ended
Dec. 31, 2012
Pfizer Collaboration [Member]
Dec. 31, 2012
Pfizer Collaboration [Member]
Jun. 30, 2011
Viropharma and Interxon [Member]
Sep. 30, 2011
Baxter
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
 
 
 
 
Revenue under collabrative agreements
$ 9,500,000 
$ 9,500,000 
$ 18,000,000 
$ 17,900,000