20160930 Q3

Table of Contents





 

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

 

Form 10-Q

 

(Mark One)

QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2016

Or

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from             to             

Commission File Number 001-34899

 

Pacific Biosciences of California, Inc.

(Exact name of registrant as specified in its charter)

 

 



 

Delaware

16-1590339

(State or other jurisdiction of

incorporation or organization)

(I.R.S. Employer

Identification No.)



 

1380 Willow Road

Menlo Park, CA 94025

94025

(Address of principal executive offices)

(Zip Code)

(650) 521-8000

(Registrant’s telephone number, including area code)

 

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes    No  

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes      No  

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

 



 

 

 

Large accelerated filer

Accelerated filer   



 

 

 

Non-accelerated filer

(Do not check if a smaller reporting company)

Smaller reporting company



Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes      No  



Number of shares outstanding of the issuer’s common stock as of October 31, 2016:  92,646,752


 

Table of Contents

 

  

2

 


 

Table of Contents

 

TABLE OF CONTENTS







 



PAGE No.



 

PART I  - FINANCIAL INFORMATION

 



 

Item 1. Financial Statements (unaudited):

 



 

Condensed Consolidated Balance Sheets as of September 30, 2016 and December 31, 2015 



 

Condensed Consolidated Statements of Operations and Comprehensive Income (loss) for the Three- and Nine-Month Periods Ended September 30, 2016 and 2015 



 

Condensed Consolidated Statements of Cash Flows for the Nine-Month Periods Ended September 30, 2016 and 2015 



 

Notes to Condensed Consolidated Financial Statements 



 

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations 

17 



 

Item 3. Quantitative and Qualitative Disclosures About Market Risk 

25 



 

Item 4. Controls and Procedures 

25 



 

PART II. OTHER INFORMATION

 



 

Item 1. Legal Proceedings 

26 



 

Item 1A. Risk Factors 

26 



 

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds 

41 



 

Item 3. Default Upon Senior Securities 

41 



 

Item 4. Mine Safety Disclosures 

41 



 

Item 5. Other Information 

41 



 

Item 6. Exhibits 

41 



 



 

EXHIBIT INDEX 

43 







3

 


 

Table of Contents

 

PART I. FINANCIAL INFORMATION

Item 1.Financial Statements

PACIFIC BIOSCIENCES OF CALIFORNIA, INC.

Condensed Consolidated Balance Sheets

(Unaudited)





 

 

 

 

 

 



 

 

 

 

 

 



 

September 30,

 

December 31,

(in thousands except par value amounts)

 

2016

 

2015

Assets

 

 

 

 

 

 

Current assets

 

 

 

 

 

 

Cash and cash equivalents

 

$

22,794 

 

$

33,629 

Investments

 

 

64,539 

 

 

48,641 

Accounts receivable

 

 

11,761 

 

 

5,245 

Inventory

 

 

16,473 

 

 

10,955 

Prepaid expenses and other current assets

 

 

6,900 

 

 

12,071 

Total current assets

 

 

122,467 

 

 

110,541 

Property and equipment, net

 

 

14,003 

 

 

8,548 

Long-term restricted cash

 

 

4,500 

 

 

4,500 

Other long-term assets

 

 

9,665 

 

 

7,518 

Total assets

 

$

150,635 

 

$

131,107 



 

 

 

 

 

 

Liabilities and Stockholders' Equity

 

 

 

 

 

 

Current liabilities

 

 

 

 

 

 

Accounts payable

 

$

8,311 

 

$

4,749 

Accrued expenses

 

 

16,482 

 

 

15,551 

Deferred service revenue, current

 

 

6,436 

 

 

6,815 

Deferred contractual revenue, current

 

 

135 

 

 

10,822 

Other liabilities, current

 

 

742 

 

 

241 

Total current liabilities

 

 

32,106 

 

 

38,178 

Deferred service revenue, non-current

 

 

1,020 

 

 

1,143 

Deferred contractual revenue, non-current

 

 

1,212 

 

 

1,312 

Other liabilities, non-current

 

 

1,605 

 

 

1,386 

Notes payable

 

 

15,794 

 

 

14,948 

Financing derivative

 

 

218 

 

 

600 

Total liabilities

 

 

51,955 

 

 

57,567 



 

 

 

 

 

 

Commitments and contingencies

 

 

 

 

 

 



 

 

 

 

 

 

Stockholders’ equity

 

 

 

 

 

 

Preferred Stock, $0.001 par value:

 

 

 

 

 

 

Authorized 50,000 shares; No shares issued or outstanding

 

 

 —

 

 

 —

Common Stock, $0.001 par value:

 

 

 

 

 

 

Authorized 1,000,000 shares; Issued and outstanding 92,605 shares at September 30, 2016 and 79,983 shares at December 31, 2015

 

 

93 

 

 

80 

Additional paid-in capital

 

 

867,078 

 

 

786,636 

Accumulated other comprehensive income (loss)

 

 

23 

 

 

(7)

Accumulated deficit

 

 

(768,514)

 

 

(713,169)

Total stockholders’ equity

 

 

98,680 

 

 

73,540 

Total liabilities and stockholders’ equity

 

$

150,635 

 

$

131,107 

See accompanying notes to the condensed consolidated financial statements.

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PACIFIC BIOSCIENCES OF CALIFORNIA, INC.

Condensed Consolidated Statements of Operations and Comprehensive Income (Loss)

(Unaudited)









 

 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 

 



 

Three-Month Periods Ended September 30,

 

Nine-Month Periods Ended September 30,

(in thousands, except per share amounts)

 

2016

 

2015

 

2016

 

2015

Revenue:

 

 

 

 

 

 

 

 

 

 

 

 

Product revenue

 

$

18,050 

 

$

7,570 

 

$

44,016 

 

$

27,703 

Service and other revenue

 

 

3,472 

 

 

2,751 

 

 

10,188 

 

 

8,010 

Contractual revenue

 

 

3,596 

 

 

3,596 

 

 

10,788 

 

 

20,788 

Total revenue

 

 

25,118 

 

 

13,917 

 

 

64,992 

 

 

56,501 

Cost of revenue:

 

 

 

 

 

 

 

 

 

 

 

 

Cost of product revenue

 

 

9,273 

 

 

5,119 

 

 

23,268 

 

 

23,289 

Cost of service and other revenue

 

 

3,207 

 

 

2,247 

 

 

8,938 

 

 

6,228 

Total cost of revenue

 

 

12,480 

 

 

7,366 

 

 

32,206 

 

 

29,517 

Gross profit

 

 

12,638 

 

 

6,551 

 

 

32,786 

 

 

26,984 

Operating expense:

 

 

 

 

 

 

 

 

 

 

 

 

Research and development

 

 

17,479 

 

 

16,162 

 

 

51,362 

 

 

45,688 

Sales, general and administrative

 

 

11,894 

 

 

10,818 

 

 

34,794 

 

 

32,411 

Gain on lease amendments

 

 

 —

 

 

(23,043)

 

 

 —

 

 

(23,043)

Total operating expense

 

 

29,373 

 

 

3,937 

 

 

86,156 

 

 

55,056 

Operating income (loss)

 

 

(16,735)

 

 

2,614 

 

 

(53,370)

 

 

(28,072)

Interest expense

 

 

(821)

 

 

(741)

 

 

(2,395)

 

 

(2,153)

Other income (expense), net

 

 

62 

 

 

(52)

 

 

420 

 

 

(62)

Net income (loss)

 

 

(17,494)

 

 

1,821 

 

 

(55,345)

 

 

(30,287)

Other comprehensive loss:

 

 

 

 

 

 

 

 

 

 

 

 

Unrealized gain (loss) on investments

 

 

(29)

 

 

(6)

 

 

30 

 

 

(3)

Comprehensive income (loss)

 

$

(17,523)

 

$

1,815 

 

$

(55,315)

 

$

(30,290)



 

 

 

 

 

 

 

 

 

 

 

 

Net income (loss) per share:

 

 

 

 

 

 

 

 

 

 

 

 

Basic

 

$

(0.19)

 

$

0.02 

 

$

(0.63)

 

$

(0.41)

Diluted

 

$

(0.19)

 

$

0.02 

 

$

(0.63)

 

$

(0.41)



 

 

 

 

 

 

 

 

 

 

 

 

Weighted average shares outstanding used in calculating net income (loss) per share

Basic

 

 

92,110 

 

 

75,205 

 

 

87,969 

 

 

74,699 

Diluted

 

 

92,110 

 

 

80,479 

 

 

87,969 

 

 

74,699 



 

 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 

 



See accompanying notes to the condensed consolidated financial statements.



5

 


 

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PACIFIC BIOSCIENCES OF CALIFORNIA, INC.

Condensed Consolidated Statements of Cash Flows

(Unaudited)







 

 

 

 

 



 

 

 

 

 



Nine-Month Periods Ended September 30,

(in thousands)

2016

 

2015

Cash flows from operating activities

 

 

 

 

 

Net loss

$

(55,345)

 

$

(30,287)

Adjustments to reconcile net loss to net cash used in operating activities

 

 

 

 

 

Depreciation

 

2,822 

 

 

2,694 

Amortization of debt discount and financing costs

 

846 

 

 

699 

Stock-based compensation

 

14,726 

 

 

9,813 

Non-cash portion of gain on lease amendments

 

 —

 

 

(3,043)

Other items

 

(270)

 

 

21 

Changes in assets and liabilities

 

 

 

 

 

Accounts receivable

 

(6,516)

 

 

(758)

Inventory

 

(7,079)

 

 

(1,990)

Prepaid expenses and other assets

 

3,024 

 

 

(15,410)

Accounts payable

 

2,402 

 

 

364 

Accrued expenses

 

931 

 

 

1,523 

Deferred service revenue

 

(502)

 

 

303 

Deferred contractual revenue

 

(10,787)

 

 

(10,788)

Other liabilities

 

720 

 

 

(316)

Net cash used in operating activities

 

(55,028)

 

 

(47,175)

Cash flows from investing activities

 

 

 

 

 

Purchase of property and equipment

 

(5,556)

 

 

(2,131)

Disposal of property and equipment

 

10 

 

 

12 

Purchase of investments

 

(82,028)

 

 

(43,715)

Sales of investments

 

19,830 

 

 

8,317 

Maturities of investments

 

46,208 

 

 

68,553 

Net cash provided by (used in) investing activities

 

(21,536)

 

 

31,036 

Cash flows from financing activities

 

 

 

 

 

Proceeds from issuance of common stock from equity plans

 

7,529 

 

 

5,465 

Proceeds from issuance of common stock from at-the-market equity offering, net of issuance costs

 

58,200 

 

 

1,433 

Net cash provided by financing activities

 

65,729 

 

 

6,898 

Net decrease in cash and cash equivalents

 

(10,835)

 

 

(9,241)

Cash and cash equivalents at beginning of period

 

33,629 

 

 

36,449 

Cash and cash equivalents at end of period

$

22,794 

 

$

27,208 



 

 

 

 

 

Supplemental disclosure of non-cash investing and financing activities

 

 

 

 

 

Purchase of property and equipment through accounts payable

$

1,160 

 

$

(125)

Instruments that were transferred from inventory to property and equipment

$

1,561 

 

$

1,704 



See accompanying notes to the condensed consolidated financial statements.

 

6

 


 

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PACIFIC BIOSCIENCES OF CALIFORNIA, INC.

Notes to Condensed Consolidated Financial Statements

(Unaudited)

NOTE 1. OVERVIEW

Pacific Biosciences of California, Inc. (the “Company,” “we,” “us,” or “our”) designs, develops and manufactures sequencing systems to help scientists resolve genetically complex problems. Based on our novel Single Molecule, Real-Time (SMRT®) Sequencing technology, our products enable: de novo genome assembly to finish genomes in order to more fully identify, annotate and decipher genomic structures; full-length transcript analysis to improve annotations in reference genomes, characterize alternatively spliced isoforms in important gene families, and find novel genes; targeted sequencing to more comprehensively characterize genetic variations; and real-time kinetic information for epigenome characterization. Our technology provides high accuracy, ultra-long reads, uniform coverage, and is the only DNA sequencing technology that provides the ability to simultaneously detect epigenetic changes.  PacBio® sequencing systems, including consumables and software, provide a simple, fast, end-to-end workflow for SMRT Sequencing.

In September 2015, we announced that we had launched a new nucleic acid sequencing platform, the PacBio Sequel™ System, which will provide higher throughput, more scalability, a reduced footprint and lower sequencing project costs compared to the PacBio® RS II System, while maintaining the existing benefits of our SMRT Sequencing Technology.

The names “Pacific Biosciences,” “PacBio,” “SMRT,” “SMRTbell,” “Sequel” and our logo are our trademarks.



NOTE 2. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

In the opinion of management, our accompanying unaudited Condensed Consolidated Financial Statements (“Financial Statements”) have been prepared on a consistent basis with our December 31, 2015 audited Consolidated Financial Statements and include all adjustments, consisting of only normal recurring adjustments, necessary to fairly state the information set forth herein. The Financial Statements have been prepared in accordance with the rules and regulations of the Securities and Exchange Commission (“SEC”) and, as permitted by such rules and regulations, omit certain information and footnote disclosures necessary to present the statements in accordance with accounting principles generally accepted in the United States (“U.S. GAAP”). These Financial Statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2015. The results of operations for the nine-month period ended September 30,  2016 are not necessarily indicative of the results to be expected for the entire year or any future periods.

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires us to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes to the financial statements. Our estimates include, but are not limited to, the valuation of inventory, revenue valuation, the valuation of a financing derivative and long-term notes, the valuation and recognition of share-based compensation, the delivery period for collaboration agreements, the useful lives assigned to long-lived assets, and the computation provisions for income taxes. Actual results could differ materially from these estimates.  

Fair Value of Financial Instruments

Assets and liabilities measured at fair value on a recurring basis

The following table sets forth the fair value of our financial assets and liabilities measured on a recurring basis as of September 30, 2016 and December 31, 2015, respectively:







7

 


 

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 (in thousands)

September 30, 2016

 

December 31, 2015



Level 1

 

Level 2

 

Level 3

 

Total

 

Level 1

 

Level 2

 

Level 3

 

Total

Assets

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Cash and cash equivalents:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Cash and money market funds

$

10,850 

 

$

 —

 

$

 —

 

$

10,850 

 

$

22,034 

 

$

 —

 

$

 —

 

$

22,034 

Commercial paper

 

 —

 

 

11,944 

 

 

 —

 

 

11,944 

 

 

 —

 

 

8,595 

 

 

 —

 

 

8,595 

US government & agency securities

 

 —

 

 

 —

 

 

 —

 

 

 —

 

 

 —

 

 

3,000 

 

 

 —

 

 

3,000 

Total cash and cash equivalents

 

10,850 

 

 

11,944 

 

 

 —

 

 

22,794 

 

 

22,034 

 

 

11,595 

 

 

 —

 

 

33,629 

Investments:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Commercial paper

 

 —

 

 

26,486 

 

 

 —

 

 

26,486 

 

 

 —

 

 

15,903 

 

 

 —

 

 

15,903 

Corporate debt securities

 

 —

 

 

11,977 

 

 

 —

 

 

11,977 

 

 

 —

 

 

1,265 

 

 

 —

 

 

1,265 

US government & agency securities

 

 —

 

 

24,465 

 

 

 —

 

 

24,465 

 

 

 —

 

 

28,136 

 

 

 —

 

 

28,136 

Asset backed securities

 

 —

 

 

1,611 

 

 

 —

 

 

1,611 

 

 

 —

 

 

3,337 

 

 

 —

 

 

3,337 

Total investments

 

 —

 

 

64,539 

 

 

 —

 

 

64,539 

 

 

 —

 

 

48,641 

 

 

 —

 

 

48,641 

Long-term restricted cash:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Cash

 

4,500 

 

 

 —

 

 

 —

 

 

4,500 

 

 

4,500 

 

 

 —

 

 

 —

 

 

4,500 

Total assets measured at fair value

$

15,350 

 

$

76,483 

 

$

 —

 

$

91,833 

 

$

26,534 

 

$

60,236 

 

$

 —

 

$

86,770 



 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Liabilities

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Financing derivative

$

 —

 

$

 —

 

$

218 

 

$

218 

 

$

 —

 

$

 —

 

$

600 

 

$

600 

Total liabilities measured at fair value

$

 —

 

$

 —

 

$

218 

 

$

218 

 

$

 —

 

$

 —

 

$

600 

 

$

600 



We classify our cash deposits and money market funds within Level 1 of the fair value hierarchy because they are valued using bank balances or quoted market prices. We classify our investments as Level 2 instruments based on market pricing and other observable inputs. We did not classify any of our investments within Level 3 of the fair value hierarchy.

During the nine-month periods ended September 30, 2016 and 2015, there were no impairments of our investments.

The estimated fair value of the Financing Derivative liability (as defined in Note 6 Notes Payable) was determined using Level 3 inputs, or significant unobservable inputs. Refer to Note 6 Notes Payable for a detailed description and valuation approach. Changes to the estimated fair value of the Financing Derivative are recorded in “Other income (expense), net” in the condensed consolidated statements of operations and comprehensive income (loss).  

The following table provides the changes in the estimated fair value of the Financing Derivative during the nine-month period ended September 30, 2016 (in thousands):





 

 



 

 

Financing Derivative

Amount

Balance as of December 31, 2015

$

600 

Gain on change in estimated fair value

 

(382)

Balance as of September 30, 2016

$

218 



During the nine-month period ended September 30, 2016 there were no transfers between Level 1, Level 2, or Level 3 assets or liabilities reported at fair value on a recurring basis and the valuation techniques used did not change compared to our established practice.

Financial assets and liabilities not measured at fair value on a recurring basis

The carrying amount of our accounts receivable, prepaid expenses, other current assets, accounts payable, accrued expenses and other liabilities, current,  approximate fair value due to their short maturities. The carrying value of our other liabilities, non-current, approximates fair value due to the time to maturity and prevailing market rates.

We determined the estimated fair value of the Notes (as defined in Note 6 Notes Payable) using Level 3 inputs, or significant unobservable inputs. The estimated fair value of the Notes was determined by comparing the difference between the estimated fair value of the Notes with and without the Financing Derivative by calculating the respective present values from future cash flows using a  weighted average market yield of 11.4% and 13.5% at September 30, 2016 and December 31, 2015, respectively. 







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The estimated fair value and carrying value of the Notes are as follows (in thousands):







 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 



September 30, 2016

 

December 31, 2015



Fair Value

 

Carrying Value

 

Fair Value

 

Carrying Value

Notes payable

$

19,381 

 

$

15,794 

 

$

18,037 

 

$

14,948 



Net Income (loss) per Share

Basic net income (loss) per share and diluted net income (loss) per share are presented in conformity with ASC 260 Earnings per Share, for all periods presented. Basic net income (loss) per share is computed by dividing net income (loss) by the weighted average number of shares of common stock outstanding during the period. Diluted net income (loss) per share is computed using the weighted average number of shares of common stock outstanding and potential shares assuming the dilutive effect of outstanding stock options, warrants and common stock issuable pursuant to our employee stock purchase plan, or ESPP, using the treasury stock method.

The following table presents the calculation of weighted average number of shares of common stock used in the computations of basic and diluted net income (loss) per share amounts presented in the accompanying condensed consolidated statements of operations and comprehensive income (loss) (in thousands, except per share amounts):







 

 

 

 

 

 

 

 

 

 

 

 

 



 

Three-Month Periods Ended

 

Nine-Month Periods Ended

 



 

September 30,

 

September 30,

 



 

2016

 

2015

 

2016

 

2015

 



 

 

 

 

 

 

 

 

 

 

 

 

 

Net income (loss)

 

$

(17,494)

 

$

1,821 

 

$

(55,345)

 

$

(30,287)

 



 

 

 

 

 

 

 

 

 

 

 

 

 

Basic

 

 

 

 

 

 

 

 

 

 

 

 

 

Weighted average number of shares used in computing basic net income (loss) per share

 

 

92,110 

 

 

75,205 

 

 

87,969 

 

 

74,699 

 

Basic net income (loss) per share

 

$

(0.19)

 

$

0.02 

 

$

(0.63)

 

$

(0.41)

 



 

 

 

 

 

 

 

 

 

 

 

 

 

Diluted

 

 

 

 

 

 

 

 

 

 

 

 

 

Weighted average number of shares used in computing basic net income (loss) per share

 

 

92,110 

  

 

75,205 

 

 

87,969 

  

 

74,699 

 

Add: weighted average stock options

 

 

 —

 

 

2,733 

 

 

 —

 

 

 —

 

Add: weighted average warrants

 

 

 —

 

 

2,541 

 

 

 —

 

 

 —

 

Weighted average number of shares used in computing diluted net income (loss) per share

 

 

92,110 

 

 

80,479 

 

 

87,969 

 

 

74,699 

 

Diluted net income (loss) per share

 

$

(0.19)

 

$

0.02 

 

$

(0.63)

 

$

(0.41)

 



The following outstanding common stock options and warrants to purchase common stock were excluded from the computation of diluted net income(loss) per share for the periods presented because including them would have had an anti-dilutive effect (in thousands):





 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 



 

Three Months Ended

 

Nine Months Ended

 



 

September 30,

 

September 30,

 

 



 

2016

 

2015

 

2016

 

2015

 

 

Options to purchase common stock

 

22,635 

 

11,959 

 

22,635 

 

18,469 

 

 

Warrants to purchase common stock

 

 —

 

 —

 

 —

 

5,500 

 

 



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Recent Accounting Pronouncements



Recently Adopted Accounting Standards

In July 2015, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU) No. 2015-11, Simplifying the Measurement of Inventory, which simplifies the subsequent measurement of inventory by replacing the lower of cost or market test with a lower of cost and net realizable value test. ASU 2015-11 is effective for annual report periods beginning after December 15, 2016 and is effective for us in the first quarter of 2017. We have elected to early adopt ASU 2015-11 effective beginning with the three-month period ended March 31, 2016, as permitted by the standard. The early adoption of this update did not have a material impact on our condensed consolidated financial statements.



Recently Issued Accounting Standards

In March 2016, the FASB issued ASU 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting, which amends the current stock compensation guidance. The amendments simplify the accounting for the taxes related to stock based compensation, including adjustments to how excess tax benefits and a company's payments for tax withholdings should be classified. The standard is effective for fiscal periods beginning after December 15, 2016, with early adoption permitted. We are currently evaluating the impact of the adoption of this standard on our consolidated financial statements.

In February 2016, the FASB issued ASU 2016-02, Leases. The guidance in ASU 2016-02 supersedes the lease recognition requirements in ASC Topic 840, Leases. ASU 2016-02 requires an entity to recognize assets and liabilities arising from a lease for both financing and operating leases, along with additional qualitative and quantitative disclosures. ASU 2016-02 is effective for fiscal years beginning after December 15, 2018, with early adoption permitted. We are currently evaluating the impact of the adoption of this standard on our consolidated financial statements.

In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers,  requiring an entity to recognize the amount of revenue to which it expects to be entitled for the transfer of promised goods or services to customers. The updated standard will replace most existing revenue recognition guidance in U.S. GAAP when it becomes effective and permits the use of either the retrospective or the cumulative effect transition method. ASU 2014-09 is effective for periods beginning after December 15, 2017, 2017, with early adoption permitted but not earlier than the original effective date. Accordingly, the updated standard is effective for us in the first quarter of 2018. We are currently evaluating the new guidance to determine the impact it may have to our condensed consolidated financial statements.



NOTE 3. CONTRACTUAL REVENUE

During September 2013, we entered into a Development, Commercialization and License Agreement (the “Roche Agreement”) with F. Hoffman-La Roche Ltd (“Roche”), pursuant to which we account for, and recognize as revenue, the up-front payment received thereunder using the proportional performance method over the periods in which the delivery of elements pursuant to the Roche Agreement occurs. We recognize revenue under the Roche Agreement using a straight-line convention over the service periods of the deliverables as this method approximates our performance of services pursuant to the agreement. Out of the $35.0 million upfront cash payment received, quarterly amortization of $1.7 million has been recognized as contractual revenue from the fourth quarter of 2013 to the fourth quarter of 2014. Beginning in the three-month period ended March 31, 2015, we revised the estimated development period related to our contractual revenue amortization based on increasing certainty of the development time on a prospective approach and quarterly amortization of $3.6 million has been recognized as contractual revenue for each of the four quarters of 2015 and for the each of the first three quarters of 2016. As of September 30, 2016, the total deferred contractual revenue balance was $1.3 million, relating to the amount allocated to the deliverable of our participation on the joint steering committee and will be fully amortized by the third quarter of 2026. 

Further, the Roche Agreement provided for additional payments totaling up to $40.0 million upon the achievement of certain development milestones. Consideration from development milestones is recognized in the period in which a milestone is achieved only if the milestone is considered substantive in its entirety. We achieved the first development milestone under the Roche Agreement and recognized the related $10.0 million as contractual revenue during the year ended December 31, 2014. We achieved the second and third (final) development milestones under the Roche Agreement and recognized the related $10.0 million and $20.0 million as contractual revenue during the three-month periods ended June 30, 2015 and December 31, 2015, respectively.

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NOTE 4. CASH, CASH EQUIVALENTS AND INVESTMENTS

The following tables summarize our cash, cash equivalents and investments as of September 30, 2016 and December 31, 2015 (in thousands):





 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 



September 30, 2016



 

 

Gross

 

Gross

 

 



Amortized

 

unrealized

 

unrealized

 

Fair



cost

 

gains

 

losses

 

value

Cash and cash equivalents:

 

 

 

 

 

 

 

 

 

 

 

Cash and money market funds

$

10,850 

 

$

 —

 

$

 —

 

$

10,850 

Commercial paper

 

11,943 

 

 

 

 

 —

 

 

11,944 

Total cash and cash equivalents

 

22,793 

 

 

 

 

 —

 

 

22,794 

Investments:

 

 

 

 

 

 

 

 

 

 

 

Commercial paper

 

26,479 

 

 

 

 

(1)

 

 

26,486 

Corporate debt securities

 

11,980 

 

 

 

 

(5)

 

 

11,977 

Asset backed securities

 

1,611 

 

 

 —

 

 

 —

 

 

1,611 

US government & agency securities

 

24,447 

 

 

20 

 

 

(2)

 

 

24,465 

Total investments

 

64,517 

 

 

30 

 

 

(8)

 

 

64,539 

Total cash, cash equivalents and investments

$

87,310 

 

$

31 

 

$

(8)

 

$

87,333 



 

 

 

 

 

 

 

 

 

 

 

Long-term restricted cash:

 

 

 

 

 

 

 

 

 

 

 

Cash

 

4,500 

 

 

 —

 

 

 —

 

 

4,500 

Total long-term restricted cash

$

4,500 

 

$

 —

 

$

 —

 

$

4,500 



 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 



December 31, 2015



 

 

Gross

 

Gross

 

 



Amortized

 

unrealized

 

unrealized

 

Fair



cost

 

gains

 

losses

 

value

Cash and cash equivalents:

 

 

 

 

 

 

 

 

 

 

 

Cash and money market funds

$

22,034 

 

$

 —

 

$

 —

 

$

22,034 

Commercial paper

 

8,595 

 

 

 —

 

 

 —

 

 

8,595 

US government & agency securities

 

3,000 

 

 

 —

 

 

 —

 

 

3,000 

Total cash and cash equivalents

 

33,629 

 

 

 —

 

 

 —

 

 

33,629 

Investments:

 

 

 

 

 

 

 

 

 

 

 

Commercial paper

 

15,903 

 

 

 

 

(2)

 

 

15,903 

Corporate debt securities

 

1,266 

 

 

 —

 

 

(1)

 

 

1,265 

Asset backed securities

 

3,337 

 

 

 —

 

 

 —

 

 

3,337 

US government & agency securities

 

28,142 

 

 

 

 

(10)

 

 

28,136 

Total investments

 

48,648 

 

 

 

 

(13)

 

 

48,641 

Total cash, cash equivalents and investments

$

82,277 

 

$

 

$

(13)

 

$

82,270 



 

 

 

 

 

 

 

 

 

 

 

Long-term restricted cash:

 

 

 

 

 

 

 

 

 

 

 

Cash

 

4,500 

 

 

 —

 

 

 —

 

 

4,500 

Total long-term restricted cash

$

4,500 

 

$

 —

 

$

 —

 

$

4,500 

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The following table summarizes the contractual maturities of our cash equivalents and available-for-sale investments, excluding money market funds, as of September 30, 2016:







 

 



 

 

(in thousands)

Fair Value

Due in one year or less

$

76,483 



Actual maturities may differ from contractual maturities because issuers may have the right to call or prepay obligations without call or prepayment penalties. 



NOTE 5.  INVENTORY



As of September 30, 2016 and December 31, 2015,  our inventory consisted of the following components:





 

 

 

 

 



 

 

 

 

 



September 30,

 

December 31,

(in thousands)

2016

 

2015

Purchased materials

$

4,458 

 

$

4,041 

Work in process

 

8,341 

 

 

3,576 

Finished goods

 

3,674 

 

 

3,338 

Inventory

$

16,473 

 

$

10,955 













NOTE 6. NOTES PAYABLE

Pursuant to a Facility Agreement (the “Facility Agreement”) we entered into with entities affiliated with Deerfield Management Company, L.P. (collectively, “Deerfield”) during February 2013, we issued promissory notes in the aggregate principal amount of $20.5 million (the “Notes”). The Notes bear simple interest at a rate of 8.75% per annum, payable quarterly in arrears commencing on April 1, 2013.

In connection with the execution of the Facility Agreement, we issued warrants to purchase an aggregate of 5,500,000 shares of common stock immediately exercisable at an exercise price per share initially equal to $2.63 (the “Warrants”). As of September 30, 2016,  no warrants remained outstanding. Please see Note 8 Stockholders’ Equity for the warrant-related activities during the nine-month period ended September 30, 2016.

In addition, the Facility Agreement requires us to maintain consolidated cash and cash equivalents on the last day of each calendar quarter of not less than $2.0 million. As security for our repayment of our obligations under the Facility Agreement, we granted to Deerfield a security interest in substantially all of our property.

The Facility Agreement has a maximum term of seven years from inception.  Subsequent to the date of the Facility Agreement, at the election of the holders of Notes representing a majority of the aggregate principal amount of the outstanding Notes, the Notes holders may elect to receive 25% of the net proceeds from any financing that includes an equity component, including without limitation, the sale or issuance of our common stock, options, warrants or other securities convertible or exchangeable for shares of our common stock, as payment of the Notes. This right is subject to certain exceptions set forth in the Facility Agreement.  The Notes holders have the option to require us to repay the Notes if we complete a Major Transaction (as defined in the Facility Agreement), including a change of control or a sale of all or substantially all of our assets. Additionally, the principal balance of the Facility Agreement may become immediately due and payable upon an Event of Default (as defined in the Facility Agreement), in which case the Notes holders would have the right to require us to repay 100% of the principal amount of the loan, plus any accrued and unpaid interest thereon. The Facility Agreement does not provide for a prepayment of the Notes at our option.

Financing Derivative

A number of features embedded in the Notes to the Facility Agreement met the requirements to be accounted for as a  derivative, including the indemnification of certain withholding taxes and the acceleration of debt upon (i) a qualified financing, (ii) an Event of Default, (iii) a Major Transaction, and (iv) the exercise of the warrant via offset to debt principal. These features represent a single derivative (the “Financing Derivative”) that was bifurcated from the debt instrument and accounted for as a liability at fair value, with changes in fair value between reporting periods recorded in other income (expense), net.

The estimated fair value of the Financing Derivative was determined by comparing the difference between the fair value of the Notes with and without the Financing Derivative by calculating the respective present values from future cash flows using 11.4% and 

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13.5% weighted average market yield at September 30, 2016 and December 31, 2015, respectively.  The estimated fair value of the Financing Derivative as of September 30, 2016 and December 31, 2015 was $0.2 million and $0.6 million, respectively.

Notes

We initially recorded the Notes and Warrants at $14.1 million and $6.4 million, respectively, based upon the relative fair value allocation of the $20.5 million of proceeds. The carrying value of the Notes at the inception of the debt was $12.8 million, resulting in an original issue discount of $7.7 million. As of September 30, 2016 and December 31, 2015,  a  debt discount of $4.6 million and $5.4 million, respectively, remained to be amortized through February 2020, the maturity of the Notes.



NOTE 7.  COMMITMENTS AND CONTINGENCIES

Leases

In December 2009 we entered into a lease agreement for a manufacturing and office facility in Menlo Park. In order for the facility to meet our needs and operating requirements, substantial tenant improvements, including improvements to the structural elements and principal operating systems of the facility, were necessary. The lessor provided a tenant improvement allowance of $1.8 million to apply towards the necessary improvements and we remained obligated for additional amounts over the afforded allowance. Due to our involvement in and the nature of the renovations made to the facility and our obligations to fund the costs of renovations exceeding the incentives afforded to us, we account for the facility as if we are the owner. Accordingly, we recorded $3.0 million of building and leasehold improvement assets, reflecting the $1.2 million fair value of the facility prior to commencing renovations and the $1.8 million of landlord incentives within property and equipment, net and a corresponding liability recorded to facility financing obligation.

As a result of the lease amendment agreement described below, future rent expense associated with our existing Menlo Park facility leases was reduced to zero. The remaining long-term facility financing obligations associated with these leases, presented as “Other liabilities, non-current” on the condensed consolidated balance sheets at September 30, 2016 and December 31, 2015, were $1.6 million and $1.4 million, respectively. 

Lease Amendment Agreement

On July 23, 2015, we entered into a Lease Amendment Agreement (the “Lease Amendment Agreement”) with Peninsula Innovation Partners, LLC (the “Existing Landlord”), which amends the terms and conditions of certain of our existing Menlo Park facility real property leases. The Lease Amendment Agreement provides for, among other things, amendments of the term for certain of the existing leases, the termination of all renewal, expansion and extension rights contained in any of the existing leases with the Existing Landlord (including our options to extend the terms for certain of the existing leases for two consecutive five-year periods), as well as rent abatement for a specified period of time. As consideration for our agreement to amend the existing leases pursuant to the Lease Amendment Agreement, and subject to the terms and conditions contained therein, we became eligible to receive up to four payments of $5.0 million each from the Existing Landlord over time (the “Landlord Payments”), and rent abatement for the remainder of the lease. In the event that we breach any of the leases and fail to cure such breach within the time permitted, the Existing Landlord would have no obligation to make the final $5.0 million payment. On September 1, 2015, the permitting process related to an architectural approval and a change of use permit with respect to our new premises at 1315 O’Brien Drive, Menlo Park, California (the “O’Brien Premises”) was completed, which satisfied the contingencies under the Lease Amendment Agreement. As a result, we recorded $23.0 million in “Gain on lease amendments” in the consolidated statements of operations and comprehensive loss for the three-month period ended September 30, 2015, reflecting that our rent payments were reduced to zero for the remaining term of our existing Menlo Park facility real property leases, the aggregate of $20.0 million in Landlord Payments became receivable and any associated financing obligation was revalued. Of the $20.0 million in Landlord Payments, the first $5.0 million Landlord Payment was received in September 2015,  the second $5.0 million Landlord Payment was received in February 2016 and the third $5.0 million Landlord Payment was received in August 2016.  

In June 2016 we entered into a Second Lease Amendment Agreement with the Existing Landlord that modified the payment schedule for the final $5.0 million,  such that $2.6 million became a short term receivable and was recorded in “Prepaid Expenses and Other Current Assets” and $2.4 million was recorded in “Other Long-term Assets” in the condensed consolidated balance sheets as of September 30, 2016.  We do not believe that there are any remaining performance obligations relating to the remaining Landlord Payments.

O’Brien Lease Agreement

On July 22, 2015, we entered into a new lease agreement (the “O’Brien Lease”) with respect to the O’Brien Premises. The term of the O’Brien Lease is one hundred thirty-two (132) months, commencing on the date that is the later of April 15, 2016 or the date on which the O’Brien Premises landlord has substantially completed certain shell improvements and tenant improvements. Based on the currently agreed construction schedule, the O’Brien Lease is expected to commence in the fourth quarter of 2016. Base monthly rent will be abated for the first six (6) months of the lease term and thereafter will be $540,000 per month during the first year of the lease

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term, with specified annual increases thereafter until reaching $711,000 per month during the last twelve (12) months of the lease term. We were required to pay $2,160,000 in prepaid rent which will be applied to the monthly rent installments due for the first to fourth months after the rent abatement period. We were required to establish a deposit of $4.5 million in the form of a letter of credit in October 2015; and, as such, $4.5 million was recorded in “Long-term restricted cash” in the condensed consolidated balance sheet as of both September 30, 2016 and December 31, 2015.  The landlord is obligated to construct certain shell improvements at the landlord’s cost and expense and provide us with improvement allowances in the amount of $12.6 million.

Under the O’Brien Lease, we expect to pay approximately $80 million in rent and $24 million in operating expenses over the expected lease term. In addition to the lease payments, we are also required to reimburse the landlord for certain improvement costs in excess of the tenant improvement allowances provided. These improvement costs, along with the costs associated with the anticipated move to the O’Brien Premises, are expected to be substantial in nature. These future expenditures are expected to be partially offset by the $5.0 million of future Landlord Payments from our Existing Landlord as described above. 



Legal

On November 2, 2016, we filed a complaint against Oxford Nanopore Technologies Ltd., Oxford Nanopore Technologies, Inc. and Metrichor, Ltd. (together, “ONT”) with the U.S. International Trade Commission for patent infringement. We are seeking injunctive relief with respect to several ONT products, including ONT’s MinION and PromethION devices. The complaint is based on our U.S. Patent No. 9,404,146, entitled “Compositions and methods for nucleic acid sequencing” which covers novel methods for sequencing single nucleic acid molecules using linked double-stranded nucleic acid templates, providing improved sequencing accuracy. We are seeking, among other things, an exclusion order permanently barring entry of infringing ONT products into the United States, and a cease and desist order preventing ONT from advertising and selling infringing products in the United States.  The estimated financial effect associated with this complaint cannot be made as of this 10-Q filing time.

From time to time, we may also be involved in a variety of other claims, lawsuits, investigations and proceedings relating to securities laws, product liability, patent infringement, contract disputes, employment and other matters that arise in the normal course of our business. In addition, third parties may, from time to time, assert claims against us in the form of letters and other communications. We record a provision for contingent losses when it is both probable that a liability has been incurred and the amount of the loss can be reasonably estimated. We currently do not believe that the ultimate outcome of any of the matters described above is probable or reasonably estimable, or that these matters will have a material adverse effect on our business; however, the results of litigation and claims are inherently unpredictable. Regardless of the outcome, litigation can have an adverse impact on us because of litigation and settlement costs, diversion of management resources and other factors.



NOTE 8. STOCKHOLDERS’ EQUITY

Equity Offering

During the three-month period ended March 31, 2016, we issued 3.1 million shares of our common stock at an average price of $8.80 per share through our “at-the-market” offering, resulting in net proceeds of $26.5 million. During the three-month period ended June 30, 2016, we issued 3.4 million shares of our common stock at an average price of $9.56 per share through our “at-the-market” offering, resulting in net proceeds of $31.7 million. During the three-month period ended September 30, 2016, no shares of common stock were issued through our “at-the-market” offering. In total, for the nine-month period ended September 30, 2016, we issued 6.5 million shares of our common stock through our “at-the-market” offering, resulting in net proceeds of $58.2 million.

As of September 30, 2016, no shares of common stock remained available for future sales through our “at-the-market” offering.

Warrants

In connection with the execution of the Facility Agreement, we issued immediately exercisable warrants to purchase 5,500,000 shares of common stock at an exercise price per share initially equal to $2.63, all of which were outstanding at December 31, 2015. The number of shares of common stock into which the warrants are exercisable and the exercise price will be adjusted to reflect any stock splits, payment of stock dividends, recapitalizations, reclassifications or other similar adjustments in the number of outstanding shares of common stock. The exercise price may also be adjusted to reflect certain dividends or other distributions, including distributions of stock or other securities, property or options by way of a dividend, spin off, reclassification, corporate rearrangement or similar transaction.  

During the three months ended March 31, 2016, warrants to purchase 3,818,000 shares of common stock were net exercised, resulting in the issuance of approximately 3.0 million shares. During the three months ended June 30, 2016, warrants to purchase the remaining 1,682,000 shares of common stock were net exercised, resulting in the issuance of approximately 1.2 million shares in the first week of July 2016. The cashless net exercises of the warrants did not result in any additional funds being collected by us.

As of September 30, 2016, no warrants remained outstanding.

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Equity Plans

As of September 30, 2016, we had three active equity compensation plans: the 2010 Equity Incentive Plan, the 2010 Outside Director Equity Incentive Plan, and the 2010 Employee Stock Purchase Plan (“ESPP”).

The following table summarizes stock option activity for all our stock option plans for the nine-month period ended September 30, 2016 (in thousands, except per share amounts):





 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 



 

 

Stock Options Outstanding



 

 

 

 

 

 

 

Weighted



Shares available

 

Number

 

 

 

 

average



for grant

 

of options

 

Exercise price

 

exercise price

Balances, December 31, 2015

5,814 

 

19,468 

 

$

0.70 – 16.00

 

$

5.69 

Additional shares reserved 

4,799 

 

 —

 

 

 

 

 

 

Options granted

(4,137)

 

4,137 

 

 

7.87 – 12.85

 

 

8.72 

Options exercised

—  

 

(672)

 

 

0.70 – 8.90

 

 

3.44 

Options canceled

298 

 

(298)

 

 

1.16 – 16.0

 

 

7.11 

Balances, September 30, 2016

6,774 

 

22,635 

 

$

1.16 – 16.00

 

$

6.29 





Shares issued under our ESPP totaled 1,259,239 and 1,080,913 shares during the nine-month periods ended September 30, 2016 and 2015, respectively. As of September 30, 2016, 738,063 shares of our common stock remain available for issuance under our ESPP.

Stock-Based Compensation



Total stock-based compensation expense consists of the following (in thousands):





 

 

 

 

 

 

 

 

 

 

 

 



 

 

 

 

 

 

 

 

 

 

 

 



Three-Month Periods Ended September 30,

 

Nine-Month Periods Ended September 30,

 



2016

 

2015

 

2016

 

2015

 

Cost of revenue

$

549 

 

$

337 

 

$

1,610 

 

$

926 

 

Research and development

 

2,141 

 

 

1,245 

 

 

6,182 

 

 

3,735 

 

Sales, general and administrative

 

2,417 

 

 

1,656 

 

 

6,934 

 

 

5,152 

 

Total stock-based compensation expense

$

5,107