##### Table of Contents



UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-Q
  þ
    
    Quarterly Report Pursuant to Section 13 or 15(d) of the Securities
Exchange Act of 1934
   o
    
    Transition Report Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934
  GEN-PROBE INCORPORATED
  Delaware
    
    33-0044608(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification Number)10210 Genetic Center Drive
    
    92121San Diego, CA
    
    (Zip Code)(Address of Principal ExecutiveOffices)
 (858) 410-8000
 þ o
 o o
  Large accelerated filer þ
    
    Accelerated filer o
    
    Non-accelerated filer o
    
    Smaller Reporting Company o(Do not check if a smaller reporting company)
 o þ




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##### 



GEN-PROBE INCORPORATED
 TABLE OF CONTENTS
FORM 10-Q
 PagePART I  FINANCIAL INFORMATIONItem 1. Consolidated Financial StatementsConsolidated Balance Sheets
    
    
    3Consolidated Statements of Income
    
    
    4Consolidated Statements of Cash Flows
    
    
    5Notes to Consolidated Financial Statements
    
    
    6Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    23Item 3. Quantitative and Qualitative Disclosures about Market Risk
    
    
    35Item 4. Controls and Procedures
    
    
    36PART II  OTHER INFORMATION
    
    
    37Item 1. Legal Proceedings
    
    
    37Item 1A. Risk Factors
    
    
    37Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    54Item 6. Exhibits
    
    
    55SIGNATURES
    
    
    56EX-10.103EX-10.104EX-10.105EX-31.1EX-31.2EX-32.1EX-32.2
  2




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##### Table of Contents



GEN-PROBE
INCORPORATED
 
 CONSOLIDATED BALANCE SHEETS
 September 30,
    
    
    December 31,2009
    
    
    2008(unaudited)ASSETSCurrent assets:Cash and cash equivalents, including restricted cash of $18 and $0 at
September 30, 2009
and December 31, 2008, respectively
    
    $
    156,739
    
    
    $
    60,122Marketable securities
    
    
    361,203
    
    
    
    371,276Trade accounts receivable, net of allowance for doubtful accounts of $740 and
$700 at September 30, 2009 and December 31, 2008, respectively
    
    
    44,629
    
    
    
    33,397Accounts receivable  other
    
    
    3,185
    
    
    
    2,900Inventories
    
    
    58,432
    
    
    
    54,406Deferred income tax
    
    
    8,827
    
    
    
    7,269Prepaid income tax
    
    
    8,809
    
    
    
    2,306Prepaid expenses
    
    
    17,956
    
    
    
    15,094Other current assets
    
    
    4,443
    
    
    
    6,135Total current assets
    
    
    664,223
    
    
    
    552,905Marketable securities, net of current portion
    
    
    6,677
    
    
    
    73,780Property, plant and equipment, net
    
    
    153,594
    
    
    
    141,922Capitalized software, net
    
    
    12,496
    
    
    
    13,409Goodwill
    
    
    91,114
    
    
    
    18,621Deferred income tax, net of current portion
    
    
    12,193
    
    
    
    12,286Purchased intangibles, net
    
    
    56,097
    
    
    
    298Licenses, manufacturing access fees and other assets, net
    
    
    63,255
    
    
    
    56,310Total assets
    
    $
    1,059,649
    
    
    $
    869,531LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable
    
    $
    18,035
    
    
    $
    16,050Accrued salaries and employee benefits
    
    
    27,815
    
    
    
    25,093Other accrued expenses
    
    
    11,194
    
    
    
    4,027Income tax payable
    
    
    853
    
    
    
    Short-term borrowings
    
    
    240,841
    
    
    
    Deferred income tax
    
    
    1,355
    
    
    
    Deferred revenue
    
    
    2,238
    
    
    
    1,278Total current liabilities
    
    
    302,331
    
    
    
    46,448Non-current income tax payable
    
    
    5,401
    
    
    
    4,773Deferred income tax, net of current portion
    
    
    14,387
    
    
    
    55Deferred revenue, net of current portion
    
    
    2,249
    
    
    
    2,333Other long-term liabilities
    
    
    3,357
    
    
    
    2,162Commitments and contingenciesStockholders equity:Preferred stock, $0.0001 par value per share; 20,000,000 shares authorized,
none
issued and outstanding
    
    
    
    
    
    
    Common stock, $0.0001 par value per share; 200,000,000 shares authorized,
48,925,449 and 52,920,971 shares issued and outstanding at September
30, 2009
and December 31, 2008, respectively
    
    
    5
    
    
    
    5Additional paid-in capital
    
    
    231,838
    
    
    
    382,544Accumulated other comprehensive income
    
    
    4,167
    
    
    
    3,055Retained earnings
    
    
    495,914
    
    
    
    428,156Total stockholders equity
    
    
    731,924
    
    
    
    813,760Total liabilities and stockholders equity
    
    $
    1,059,649
    
    
    $
    869,531
  3




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GEN-PROBE
INCORPORATED
 
 CONSOLIDATED STATEMENTS OF INCOME
 Three Months Ended
    
    
    Nine Months EndedSeptember 30,
    
    
    September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Revenues:Product sales
    
    $
    118,951
    
    
    $
    108,253
    
    
    $
    348,289
    
    
    $
    323,461Collaborative research revenue
    
    
    2,000
    
    
    
    11,343
    
    
    
    5,862
    
    
    
    18,453Royalty and license revenue
    
    
    1,753
    
    
    
    1,581
    
    
    
    5,281
    
    
    
    21,640Total revenues
    
    
    122,704
    
    
    
    121,177
    
    
    
    359,432
    
    
    
    363,554Operating expenses:Cost of product sales
(excluding
acquisition-related
intangibles amortization)
    
    
    36,345
    
    
    
    30,681
    
    
    
    107,939
    
    
    
    95,827Acquisition-related
intangibles amortization
    
    
    1,136
    
    
    
    
    
    
    
    2,250
    
    
    
    Research and development
    
    
    27,475
    
    
    
    24,507
    
    
    
    78,542
    
    
    
    76,941Marketing and sales
    
    
    13,477
    
    
    
    10,709
    
    
    
    38,547
    
    
    
    34,070General and administrative
    
    
    15,234
    
    
    
    12,908
    
    
    
    46,903
    
    
    
    38,516Total operating expenses
    
    
    93,667
    
    
    
    78,805
    
    
    
    274,181
    
    
    
    245,354Income from operations
    
    
    29,037
    
    
    
    42,372
    
    
    
    85,251
    
    
    
    118,200Other income/(expense):Investment and interest income
    
    
    4,676
    
    
    
    4,167
    
    
    
    19,680
    
    
    
    12,274Interest expense
    
    
    (588
    )
    
    
    (1
    )
    
    
    (1,465
    )
    
    
    (3
    )Other income/(expense)
    
    
    210
    
    
    
    (1,929
    )
    
    
    (827
    )
    
    
    (647
    )Total other income, net
    
    
    4,298
    
    
    
    2,237
    
    
    
    17,388
    
    
    
    11,624Income before income tax
    
    
    33,335
    
    
    
    44,609
    
    
    
    102,639
    
    
    
    129,824Income tax expense
    
    
    11,139
    
    
    
    15,531
    
    
    
    34,881
    
    
    
    44,010Net income
    
    $
    22,196
    
    
    $
    29,078
    
    
    $
    67,758
    
    
    $
    85,814Net income per share:Basic
    
    $
    0.45
    
    
    $
    0.53
    
    
    $
    1.33
    
    
    $
    1.58Diluted
    
    $
    0.44
    
    
    $
    0.52
    
    
    $
    1.31
    
    
    $
    1.55Weighted average shares outstanding:Basic
    
    
    49,614
    
    
    
    54,363
    
    
    
    51,133
    
    
    
    54,174Diluted
    
    
    50,136
    
    
    
    55,552
    
    
    
    51,767
    
    
    
    55,357
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GEN-PROBE
INCORPORATED
 
 CONSOLIDATED STATEMENTS OF CASH FLOWS
 Nine Months EndedSeptember 30,2009
    
    
    2008Operating activitiesNet income
    
    $
    67,758
    
    
    $
    85,814Adjustments to reconcile net income to net cash provided by operating
activities:Depreciation and amortization
    
    
    29,468
    
    
    
    26,217Amortization of premiums on investments, net of accretion of discounts
    
    
    4,050
    
    
    
    5,118Stock-based compensation
    
    
    17,743
    
    
    
    15,012Stock-based compensation income tax benefits
    
    
    1,937
    
    
    
    3,025Excess tax benefit from stock-based compensation
    
    
    (1,186
    )
    
    
    (2,510
    )Deferred revenue
    
    
    (249
    )
    
    
    (3,399
    )Deferred income tax
    
    
    (1,318
    )
    
    
    (961
    )Gain on sale of investment in MPI
    
    
    
    
    
    
    (1,600
    )Impairment of intangible assets
    
    
    
    
    
    
    5,086Loss on disposal of property and equipment
    
    
    82
    
    
    
    38Changes in assets and liabilities:Trade and other accounts receivable
    
    
    (4,379
    )
    
    
    11,403Inventories
    
    
    2,325
    
    
    
    (4,270
    )Prepaid expenses
    
    
    (1,675
    )
    
    
    7,060Other current assets
    
    
    2,156
    
    
    
    (2,255
    )Goodwill
    
    
    856
    
    
    
    Other long-term assets
    
    
    (3,608
    )
    
    
    (510
    )Accounts payable
    
    
    (2,985
    )
    
    
    7,381Accrued salaries and employee benefits
    
    
    1
    
    
    
    4,922Other accrued expenses
    
    
    1,672
    
    
    
    96Income tax payable
    
    
    (6,655
    )
    
    
    2,926Other long-term liabilities
    
    
    733
    
    
    
    426Net cash provided by operating activities
    
    
    106,726
    
    
    
    159,019Investing activitiesProceeds from sales and maturities of marketable securities
    
    
    410,700
    
    
    
    94,103Purchases of marketable securities
    
    
    (338,976
    )
    
    
    (225,290
    )Purchases of property, plant and equipment
    
    
    (22,284
    )
    
    
    (30,530
    )Capitalization of software development costs
    
    
    (576
    )
    
    
    Purchases of intangible assets, including licenses and manufacturing access
fees
    
    
    (918
    )
    
    
    (1,868
    )Net cash paid for business combinations
    
    
    (123,713
    )
    
    
    Cash paid for investment in DiagnoCure and related license fees
    
    
    (5,500
    )
    
    
    Proceeds from sale of investment in MPI
    
    
    
    
    
    
    4,100Cash paid for Roche manufacturing access fees
    
    
    
    
    
    
    (10,000
    )Other assets
    
    
    (175
    )
    
    
    10Net cash used in investing activities
    
    
    (81,442
    )
    
    
    (169,475
    )Financing activitiesExcess tax benefit from stock-based compensation
    
    
    1,186
    
    
    
    2,510Repurchase and retirement of restricted stock for payment of taxes
    
    
    (923
    )
    
    
    (1,309
    )Repurchase and retirement of common stock
    
    
    (174,847
    )
    
    
    (9,992
    )Proceeds from issuance of common stock
    
    
    5,961
    
    
    
    17,848Short-term borrowings, net
    
    
    238,450
    
    
    
    Net cash provided by financing activities
    
    
    69,827
    
    
    
    9,057Effect of exchange rate changes on cash and cash equivalents
    
    
    1,506
    
    
    
    (198
    )Net increase (decrease) in cash and cash equivalents
    
    
    96,617
    
    
    
    (1,597
    )Cash and cash equivalents at the beginning of period
    
    
    60,122
    
    
    
    75,963Cash and cash equivalents at the end of period
    
    $
    156,739
    
    
    $
    74,366
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Notes to the Consolidated Financial Statements (unaudited)
 Note 1  Summary of significant accounting policies
 Basis of presentation
     Principles of consolidation
   Use of estimates
  Foreign currencies
  6




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Fair value of financial instruments
  Marketable securities
    Revenue recognition
     7




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Adoption of recent accounting pronouncements
 FASB ASC 105
  FASB ASC 855
  FASB ASC 320
  8




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FASB ASC 825
  FASB ASC 260
  FASB ASC 815
  FASB ASC 805
  FASB ASC 810
  9




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FASB ASC 808
  Note 2  Business combination
 Acquisition of Tepnel Life Sciences plc
     Total purchase price
    
    
    137,093Exchange rate differences
    
    
    (568
    )(1)Allocated purchase price
    
    $
    136,525Net working capital
    
    
    15,660Fixed assets
    
    
    11,352Goodwill
    
    
    70,997Deferred tax liabilities
    
    
    (15,599
    )Other intangible assets
    
    
    57,497Liabilities assumed
    
    
    (3,382
    )Allocated purchase price
    
    $
    136,525
 
 (1)
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Patents
    
    $
    294Software
    
    
    441Customer relationships
    
    
    45,439Trademarks / trade names
    
    
    11,323$
    57,497
   Years ending December 31,Remainder of 2009
    
    $
    1,1182010
    
    
    4,4702011
    
    
    4,4702012
    
    
    4,4702013
    
    
    4,470Thereafter
    
    
    37,380Total
    
    $
    56,379
   Goodwill balance as of December 31, 2008
    
    $
    18,621Additional goodwill recognized
    
    
    70,997Changes due to tax assets/liabilities
    
    
    698Changes due to foreign translation
    
    
    798Goodwill balance as of September 30, 2009
    
    $
    91,114
   Note
3  Spin-off of industrial testing assets to Roka Bioscience, Inc.
  11




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Note 4  Stock-based compensation
  Three Months Ended
    
    
    Nine Months EndedSeptember 30,
    
    
    September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Cost of product sales
    
    $
    753
    
    
    $
    591
    
    
    $
    2,356
    
    
    $
    1,778Research and development
    
    
    1,954
    
    
    
    1,744
    
    
    
    5,422
    
    
    
    4,445Marketing and sales
    
    
    943
    
    
    
    767
    
    
    
    2,481
    
    
    
    2,069General and administrative
    
    
    2,688
    
    
    
    2,682
    
    
    
    7,484
    
    
    
    6,720Total
    
    $
    6,338
    
    
    $
    5,784
    
    
    $
    17,743
    
    
    $
    15,012
  Three Months Ended
    
    
    Nine Months EndedSeptember 30,
    
    
    September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Stock Option PlansRisk-free interest rate
    
    
    2.2
    %
    
    
    3.1
    %
    
    
    2.0
    %
    
    
    3.0
    %Volatility
    
    
    35
    %
    
    
    33
    %
    
    
    35
    %
    
    
    33
    %Dividend yield
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Expected term (years)
    
    
    4.4
    
    
    
    4.2
    
    
    
    4.3
    
    
    
    4.2Resulting average fair value
    
    $
    12.29
    
    
    $
    18.90
    
    
    $
    12.64
    
    
    $
    18.64ESPPRisk-free interest rate
    
    
    2.3
    %
    
    
    3.3
    %
    
    
    1.8
    %
    
    
    3.3
    %Volatility
    
    
    34
    %
    
    
    34
    %
    
    
    40
    %
    
    
    34
    %Dividend yield
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Expected term (years)
    
    
    0.5
    
    
    
    0.5
    
    
    
    0.5
    
    
    
    0.5Resulting average fair value
    
    $
    10.65
    
    
    $
    12.07
    
    
    $
    11.42
    
    
    $
    13.22
 12




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Weighted
    
    
    UnrecognizedAverage
    
    
    Expense as ofRemaining
    
    
    September 30,Expense Life
    
    
    2009Awards
    
    (In years)
    
    
    (In thousands)Options
    
    
    1.3
    
    
    $
    32,910ESPP
    
    
    0.2
    
    
    
    266Restricted stock
    
    
    1.4
    
    
    
    10,098Deferred issuance restricted stock
    
    
    1.5
    
    
    
    2,241$
    45,515
 Note 5  Net income per share
   Three Months Ended
    
    
    Nine Months EndedSeptember 30,
    
    
    September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Net income
    
    $
    22,196
    
    
    $
    29,078
    
    
    $
    67,758
    
    
    $
    85,814Weighted average shares outstanding  Basic
    
    
    49,614
    
    
    
    54,363
    
    
    
    51,133
    
    
    
    54,174Effect of dilutive common stock options
outstanding
    
    
    522
    
    
    
    1,189
    
    
    
    634
    
    
    
    1,183Weighted average shares outstanding  Diluted
    
    
    50,136
    
    
    
    55,552
    
    
    
    51,767
    
    
    
    55,357Net income per share:Basic
    
    $
    0.45
    
    
    $
    0.53
    
    
    $
    1.33
    
    
    $
    1.58Diluted
    
    $
    0.44
    
    
    $
    0.52
    
    
    $
    1.31
    
    
    $
    1.55
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Note 6  Fair value measurements
  
    
    Level 1  Quoted prices for identical instruments in active markets.
    
    Level 2  Quoted prices for similar instruments in active markets; quoted prices for
identical or similar instruments in markets that are not active; and model-derived
valuations in which all significant inputs and significant value drivers are observable in
active markets.
    
    Level 3  Valuations derived from valuation techniques in which one or more significant
inputs or significant value drivers are unobservable.
   Assets and liabilities measured at fair value on a recurring basis
   Fair Value Measurements at September 30, 2009Quoted prices in
    
    
    
    
    
    
    Significant
    
    
    Total carryingactive markets for
    
    
    Significant other
    
    
    unobservable
    
    
    value in theidentical assets
    
    
    observable inputs
    
    
    inputs
    
    
    consolidated(Level 1)
    
    
    (Level 2)
    
    
    (Level 3)
    
    
    balance sheetAssets:Cash equivalents
    
    $
    
    
    
    $
    111,822
    
    
    $
    
    
    
    $
    111,822Marketable securities
    
    
    
    
    
    
    367,880
    
    
    
    
    
    
    
    367,880Deferred compensation plan assets
    
    
    
    
    
    
    5,390
    
    
    
    
    
    
    
    5,390Total assets at fair value
    
    
    
    
    
    
    485,092
    
    
    
    
    
    
    
    485,092Liabilities:Deferred compensation plan liabilities
    
    
    
    
    
    
    5,660
    
    
    
    
    
    
    
    5,660Total liabilities at fair value
    
    $
    
    
    
    $
    5,660
    
    
    $
    
    
    
    $
    5,660
 Assets and liabilities measured at fair value on a non-recurring basis
  14




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Equity investment in public company
  Equity investments in private companies
      15




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Note 7  Balance sheet information
  Inventories
 September 30,
    
    
    December 31,2009
    
    
    2008Raw materials and supplies
    
    $
    9,827
    
    
    $
    8,529Work in process
    
    
    24,245
    
    
    
    24,945Finished goods
    
    
    24,360
    
    
    
    20,932$
    58,432
    
    
    $
    54,406
 Property, plant and equipment, net
 September 30,
    
    
    December 31,2009
    
    
    2008Land
    
    $
    19,268
    
    
    $
    18,804Building
    
    
    85,632
    
    
    
    80,426Machinery and equipment
    
    
    175,734
    
    
    
    153,211Building improvements
    
    
    38,238
    
    
    
    34,592Furniture and fixtures
    
    
    17,616
    
    
    
    16,270Construction in-progress
    
    
    207
    
    
    
    19Property, plant and equipment, at cost
    
    
    336,696
    
    
    
    303,322Less accumulated depreciation and amortization
    
    
    (183,101
    )
    
    
    (161,400
    )Property, plant and equipment, net
    
    $
    153,594
    
    
    $
    141,922
 Purchased intangible assets, net
 September 30,
    
    
    December 31,2009
    
    
    2008Purchased intangible assets, at cost
    
    
    91,922
    
    
    
    33,636Less accumulated amortization
    
    
    (35,825
    )
    
    
    (33,338
    )Purchased intangible assets, net
    
    $
    56,097
    
    
    $
    298
 16




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Licenses, manufacturing access fees and other assets, net
 September 30,
    
    
    December 31,2009
    
    
    2008Patents
    
    $
    14,690
    
    
    $
    13,962Licenses and manufacturing access fees
    
    
    59,845
    
    
    
    58,707Investment in Qualigen
    
    
    5,404
    
    
    
    5,404Investment in DiagnoCure
    
    
    5,000
    
    
    
    Investment in Roka
    
    
    725
    
    
    
    Other assets
    
    
    7,219
    
    
    
    3,611Licenses and manufacturing access fees and other assets, at cost
    
    
    92,883
    
    
    
    81,684Less accumulated amortization
    
    
    (29,628
    )
    
    
    (25,374
    )Licenses and manufacturing access fees and other assets, net
    
    $
    63,255
    
    
    $
    56,310
 Other accrued expenses
 September 30,
    
    
    December 31,2009
    
    
    2008Royalties
    
    $
    3,396
    
    
    $
    985Professional fees
    
    
    3,426
    
    
    
    1,494Warranty
    
    
    381
    
    
    
    923Other
    
    
    3,991
    
    
    
    625Other accrued expenses
    
    $
    11,194
    
    
    $
    4,027
 Note 8  Marketable securities
   Amortized
    
    
    Gross Unrealized
    
    
    Gross Unrealized
    
    
    EstimatedCost
    
    
    Gains
    
    
    Losses
    
    
    Fair Value$
    365,051
    
    
    $
    2,836
    
    
    $
    (7
    )
    
    $
    367,880
  Less than 12 Months
    
    
    More than 12 MonthsEstimated Fair Value
    
    
    Unrealized Losses
    
    
    Estimated Fair Value
    
    
    Unrealized Losses$
    4,576
    
    
    $
    (4
    )
    
    $
    3,105
    
    
    $
    (3
    )
 17




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##### Table of Contents



September 30,
    
    
    December 31,2009
    
    
    2008Current
    
    $
    361,203
    
    
    $
    371,276Non-current
    
    
    6,677
    
    
    
    73,780Total marketable securities
    
    $
    367,880
    
    
    $
    445,056
   Three Months Ended        September 30,
    
    
    Nine Months Ended            September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Proceeds from sale of marketable securities
    
    $
    100,771
    
    
    $
    10,652
    
    
    $
    371,714
    
    
    $
    39,920Gross realized gains
    
    $
    2,470
    
    
    $
    34
    
    
    $
    10,985
    
    
    $
    440Gross realized losses
    
    
    (12
    )
    
    
    (31
    )
    
    
    (467
    )
    
    
    (53
    )Net realized gains
    
    $
    2,458
    
    
    $
    3
    
    
    $
    10,518
    
    
    $
    387
 Note 9  Short-term borrowings
   18




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##### Table of Contents



Note 10  Income tax
  Note 11  Stockholders equity
  Balance at December 31, 2008
    
    $
    813,760Net income
    
    
    67,758Other comprehensive income, net
    
    
    1,112Proceeds from the issuance of common stock
    
    
    3,884Proceeds from the issuance of common stock through ESPP
    
    
    2,077Proceeds from the issuance of common stock to board members
    
    
    134Repurchase and retirement of common stock
    
    
    (174,847
    )Repurchase and retirement of restricted stock for payment of taxes
    
    
    (923
    )Stock-based compensation
    
    
    17,783Excess tax benefit from stock-based compensation
    
    
    1,186Balance at September 30, 2009
    
    $
    731,924
 Comprehensive income
  19




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##### Table of Contents



Three Months Ended
    
    
    Nine Months EndedSeptember 30,
    
    
    September 30,2009
    
    
    2008
    
    
    2009
    
    
    2008Net income, as reported
    
    $
    22,196
    
    
    $
    29,078
    
    
    $
    67,758
    
    
    $
    85,814Other comprehensive (loss) income:Foreign currency translation adjustment
    
    
    (846
    )
    
    
    (162
    )
    
    
    2,513
    
    
    
    (78
    )Change in net unrealized gain (loss) on
available-for-sale
securities during the period
    
    
    2,384
    
    
    
    (948
    )
    
    
    5,436
    
    
    
    (2,223
    )Reclassification adjustments:Net realized gains on available-for-sale securities
    
    
    (1,598
    )
    
    
    (2
    )
    
    
    (6,837
    )
    
    
    (252
    )Total other comprehensive (loss) income, net
    
    
    (60
    )
    
    
    (1,112
    )
    
    
    1,112
    
    
    
    (2,553
    )Comprehensive income
    
    $
    22,136
    
    
    $
    27,966
    
    
    $
    68,870
    
    
    $
    83,261
 Stock options
  WeightedAverageRemaining
    
    
    AggregateNumber of
    
    
    Weighted Average
    
    
    Contractual
    
    
    IntrinsicShares
    
    
    Exercise Price
    
    
    Life (Years)
    
    
    ValueOutstanding at December 31, 2008
    
    
    5,657
    
    
    $
    44.12Granted
    
    
    764
    
    
    
    39.97Exercised
    
    
    (221
    )
    
    
    17.60Cancelled
    
    
    (126
    )
    
    
    52.66Outstanding at September 30, 2009
    
    
    6,074
    
    
    $
    44.39
    
    
    
    4.6
    
    
    $
    26,399Exercisable at September 30, 2009
    
    
    4,073
    
    
    $
    41.18
    
    
    
    4.0
    
    
    $
    24,626
 Restricted Stock
  WeightedAverageGrant-Number of
    
    
    Date FairShares
    
    
    ValueUnvested at December 31, 2008
    
    
    294
    
    
    $
    57.51Granted
    
    
    56
    
    
    
    40.63Vested and exercised
    
    
    (90
    )
    
    
    56.76Forfeited
    
    
    (8
    )
    
    
    53.07Unvested at September 30, 2009
    
    
    252
    
    
    $
    54.15
 Stock Repurchase Program
  20




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##### Table of Contents



Note 12  Contingencies
  Digene Corporation
    Becton, Dickinson and Company
  Quidel Corporation
  Note 13  Derivative financial instruments
   Three Months Ended
    
    
    Nine Months EndedLocation of gain/(loss)
    
    September 30,
    
    
    September 30,Derivatives not designated as hedging instruments under SFAS No. 133:
    
    recognized in income
    
    2009
    
    
    2008
    
    
    2009
    
    
    2008Foreign currency
forward contracts
    
    Other income/(expense)
    
    
    
    
    
    
    
    
    
    
    (635
    )
    
    
    
  21




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##### Table of Contents



Note 14  Subsequent events
 Acquisition of Prodesse, Inc.
  Quidel Corporation
  Becton, Dickinson and Company
  22




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##### Table of Contents



Item 2. Managements Discussion and Analysis of Financial Condition and Results of Operations
   Overview
    Recent Events
 Financial Results
  23




---



##### Table of Contents



Acquisition of Prodesse, Inc.
  Spin-off of Industrial Testing Assets to Roka Bioscience, Inc.
  Stock Repurchase Program
  24




---



##### Table of Contents



Critical accounting policies and estimates
   Marketable securities
    Adoption of recent accounting pronouncements
 FASB ASC 105
  FASB ASC 855
  25




---



##### Table of Contents



FASB ASC 320
  FASB ASC 825
  FASB ASC 260
  FASB ASC 815
  FASB ASC 805
  FASB ASC 810
  26




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##### Table of Contents



FASB ASC 808
  Results of Operations
 Product sales
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeClinical diagnostics
    
    $
    69.6
    
    
    $
    55.6
    
    
    $
    14.0
    
    
    
    25
    %
    
    $
    196.6
    
    
    $
    165.3
    
    
    $
    31.3
    
    
    
    19
    %Blood screening
    
    
    45.4
    
    
    
    52.7
    
    
    
    (7.3
    )
    
    
    (14
    )%
    
    
    144.1
    
    
    
    158.2
    
    
    
    (14.1
    )
    
    
    (9
    )%Research products and services
    
    
    4.0
    
    
    
    
    
    
    
    4.0
    
    
    
    N/M
    
    
    
    7.6
    
    
    
    
    
    
    
    7.6
    
    
    
    N/MProduct sales
    
    $
    119.0
    
    
    $
    108.3
    
    
    $
    10.7
    
    
    
    10
    %
    
    $
    348.3
    
    
    $
    323.5
    
    
    $
    24.8
    
    
    
    8
    %As a percent of total revenues
    
    
    97
    %
    
    
    89
    %
    
    
    
    
    
    
    
    
    
    
    97
    %
    
    
    89
    %
    Diagnostic product sales
    27




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##### Table of Contents



Blood screening related sales
   Research products and services
  Collaborative research revenue
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeCollaborative research revenue
    
    $
    2.0
    
    
    $
    11.3
    
    
    $
    (9.3
    )
    
    
    (82
    )%
    
    $
    5.9
    
    
    $
    18.5
    
    
    $
    (12.6
    )
    
    
    (68
    )%As a percent of total revenues
    
    
    2
    %
    
    
    9
    %
    
    
    
    
    
    
    
    
    
    
    2
    %
    
    
    5
    %
      28




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##### Table of Contents



Royalty and license revenue
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeRoyalty and license revenue
    
    $
    1.7
    
    
    $
    1.6
    
    
    $
    0.1
    
    
    
    6
    %
    
    $
    5.3
    
    
    $
    21.6
    
    
    $
    (16.3
    )
    
    
    (75
    )%As a percent of total revenues
    
    
    1
    %
    
    
    1
    %
    
    
    
    
    
    
    
    
    
    
    1
    %
    
    
    6
    %
    Cost of product sales
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeCost of product sales
    
    $
    36.4
    
    
    $
    30.7
    
    
    $
    5.7
    
    
    
    19
    %
    
    $
    107.9
    
    
    $
    95.8
    
    
    $
    12.1
    
    
    
    13
    %Gross profit margin
as a percent of
product sales
    
    
    69
    %
    
    
    72
    %
    
    
    
    
    
    
    
    
    
    
    69
    %
    
    
    70
    %
     29




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##### Table of Contents




    
    lower overall gross margin percentages for the recently acquired Tepnel business;
    
    an increase in cost of product sales related to changes in production volumes; and
    
    an increase in the amortization of intellectual property associated with the
commercialization of our CE-marked APTIMA HPV assay; which were partially offset by
    
    an increase in APTIMA sales.
    Acquisition-related intangibles amortization
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeAcquisition-related
intangibles amortization
    
    $
    1.1
    
    
    $
    
    
    
    $
    1.1
    
    
    
    N/M
    
    
    $
    2.3
    
    
    $
    
    
    
    $
    2.3
    
    
    
    N/MAs a percent of total revenues
    
    
    1
    %
    
    
    0
    %
    
    
    
    
    
    
    
    
    
    
    1
    %
    
    
    0
    %
  30




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##### Table of Contents



Research and development
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeResearch and development
    
    $
    27.5
    
    
    $
    24.5
    
    
    $
    3.0
    
    
    
    12
    %
    
    $
    78.5
    
    
    $
    77.0
    
    
    $
    1.5
    
    
    
    2
    %As a percent of total
revenues
    
    
    22
    %
    
    
    20
    %
    
    
    
    
    
    
    
    
    
    
    22
    %
    
    
    21
    %
     Marketing and sales
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeMarketing and sales
    
    $
    13.5
    
    
    $
    10.7
    
    
    $
    2.8
    
    
    
    26
    %
    
    $
    38.6
    
    
    $
    34.1
    
    
    $
    4.5
    
    
    
    13
    %As a percent of
total revenues
    
    
    11
    %
    
    
    9
    %
    
    
    
    
    
    
    
    
    
    
    11
    %
    
    
    9
    %
   General and administrative
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeGeneral and administrative
    
    $
    15.2
    
    
    $
    12.9
    
    
    $
    2.3
    
    
    
    18
    %
    
    $
    46.9
    
    
    $
    38.5
    
    
    $
    8.4
    
    
    
    22
    %As a percent of total
revenues
    
    
    12
    %
    
    
    11
    %
    
    
    
    
    
    
    
    
    
    
    13
    %
    
    
    11
    %
   31




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Total other income, net
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeInvestment
and interest income
    
    $
    4.7
    
    
    $
    4.1
    
    
    $
    0.6
    
    
    
    15
    %
    
    $
    19.7
    
    
    $
    12.3
    
    
    $
    7.4
    
    
    
    60
    %Interest expense
    
    
    (0.6
    )
    
    
    
    
    
    
    (0.6
    )
    
    
    N/M
    
    
    
    (1.5
    )
    
    
    
    
    
    
    (1.5
    )
    
    
    N/MOther income / (expense)
    
    
    0.2
    
    
    
    (1.9
    )
    
    
    2.1
    
    
    
    N/M
    
    
    
    (0.8
    )
    
    
    (0.7
    )
    
    
    (0.1
    )
    
    
    14
    %Total other income, net
    
    $
    4.3
    
    
    $
    2.2
    
    
    $
    2.1
    
    
    
    95
    %
    
    $
    17.4
    
    
    $
    11.6
    
    
    $
    5.8
    
    
    
    50
    %
  Income tax expense
 (Dollars in millions)
    
    Three Months Ended September 30,
    
    
    Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change
    
    
    % Change
    
    
    2009
    
    
    2008
    
    
    $ Change
    
    
    % ChangeIncome tax expense
    
    $
    11.1
    
    
    $
    15.5
    
    
    $
    (4.4
    )
    
    
    (28
    )%
    
    $
    34.9
    
    
    $
    44.0
    
    
    $
    (9.1
    )
    
    
    (21
    )%As a percent of
income before tax
    
    
    33
    %
    
    
    35
    %
    
    
    
    
    
    
    
    
    
    
    34
    %
    
    
    34
    %
   Liquidity and capital resources
 September 30,
    
    
    December 31,2009
    
    
    2008(In thousands)Cash, cash equivalents and current marketable securities
    
    $
    517,942
    
    
    $
    431,398Working capital
    
    
    361,892
    
    
    
    506,457Current ratio
    
    
    2.2
    
    
    
    11.9
    32




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##### Table of Contents



Nine Months Ended September 30,2009
    
    
    2008
    
    
    $ Change(In thousands)Cash provided by (used in):Operating activities
    
    $
    106,726
    
    
    $
    159,019
    
    
    $
    (52,293
    )Investing activities
    
    
    (81,442
    )
    
    
    (169,475
    )
    
    
    88,033Financing activities
    
    
    69,827
    
    
    
    9,057
    
    
    
    60,770Purchases of property, plant and equipment
(included in investing activities above)
    
    
    (22,284
    )
    
    
    (30,530
    )
    
    
    (8,246
    )
       33




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##### Table of Contents



Contractual obligations and commercial commitments
  Less than
    
    
    
    
    
    
    
    
    
    
    More ThanTotal
    
    
    1 Year
    
    
    1-3 Years
    
    
    3-5 Years
    
    
    5 YearsMaterial purchase commitments (1)
    
    $
    26,214
    
    
    $
    10,474
    
    
    $
    15,740
    
    
    $
    
    
    
    $
    Operating leases (2)
    
    
    5,027
    
    
    
    1,022
    
    
    
    1,728
    
    
    
    1,739
    
    
    
    538Collaborative commitments (3)
    
    
    5,764
    
    
    
    100
    
    
    
    3,497
    
    
    
    750
    
    
    
    1,417Minimum royalty commitments (4)
    
    
    9,505
    
    
    
    960
    
    
    
    3,545
    
    
    
    3,090
    
    
    
    1,910Deferred employee compensation (5)
    
    
    3,374
    
    
    
    895
    
    
    
    1,093
    
    
    
    929
    
    
    
    457Capital leases (6)
    
    
    746
    
    
    
    343
    
    
    
    349
    
    
    
    55
    
    
    
    Total(7)
    
    $
    50,631
    
    
    $
    13,794
    
    
    $
    25,951
    
    
    $
    6,563
    
    
    $
    4,322
 
 (1)
    
    Amounts represent our minimum purchase commitments from key vendors for the TIGRIS,
Panther and Luminex instruments, as well as raw materials used in manufacturing. Of the $26.2
million total, $19.3 million is expected to be used to purchase TIGRIS instruments, of which
we anticipate that approximately $11.9 million of instruments will be sold to Novartis. Not
included in the $26.2 million is $6.6 million expected to be used to purchase pre-production
and production instruments, and associated tooling, pursuant to our development agreement with
Stratec Biomedical Systems AG, or Stratec, for the Panther instrument, as well as potential
minimum purchase commitments under our supply agreement with Stratec. Our obligations under
the supply agreement are contingent on successful completion of all activities under the
development agreement with Stratec.(2)
    
    Reflects obligations for facilities and vehicles under operating leases in place as
of September 30, 2009. Future minimum lease payments are included in the table above.(3)
    
    In addition to the minimum payments due under our collaborative agreements, we may
be required to pay up to $12.2 million in milestone payments, plus royalties on net sales of
any products using specified technology. We may also be required to pay up to $5.2 million in
future development costs in the form of milestone payments.(4)
    
    Amounts represent our minimum royalties due on the net sales of products
incorporating licensed technology and subject to a minimum annual royalty payment. During the
three and nine months ended September 30, 2009, we recorded $2.0 million and $5.8 million,
respectively, in royalty costs related to our various license agreements.(5)
    
    We have liabilities for deferred employee compensation which totaled $5.7 million at
September 30, 2009. Under our deferred compensation plan, participants may elect in-service
distributions on specified future dates, or a distribution upon retirement. Of the $5.7
million, $2.3 million is payable upon employee retirement and as such was not included in the
table above as we cannot reasonably predict when a retirement event may occur. Total
liabilities for deferred employee compensation are partially offset by deferred compensation
assets, which totaled $5.4 million at September 30, 2009.(6)
    
    Reflects obligations on capital leases in place as of September 30, 2009. Interest
amounts were not material, therefore, capital lease obligations were shown net of interest
expense in the table above.(7)
    
    Does not include amounts relating to our obligations under our collaboration with
Novartis, pursuant to which both parties have obligations to each other. We are obligated to
manufacture and supply blood screening assays to Novartis, and Novartis is obligated to
purchase all of the assay quantities specified on a 90-day demand forecast, due 90 days prior
to the date Novartis intends to take delivery, and certain quantities specified on a rolling
12-month forecast.   34




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Available Information
  
 Item 3. Quantitative and Qualitative Disclosures about Market Risk
 Interest Rate Risk
  Foreign Currency Exchange Risk
   35




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##### Table of Contents



U.S. dollars
    
    $
    35,549Euros
    
    
    4,881British pounds
    
    
    3,336Canadian dollars
    
    
    1,329Danish kroner
    
    
    163Czech koruna
    
    
    111Total gross trade accounts receivable
    
    $
    45,369
   
 Item 4. Controls and Procedures
     36




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##### Table of Contents



PART II  OTHER INFORMATION
 
 Item 1. Legal Proceedings
  
 Item 1A. Risk Factors
  Our quarterly revenue and operating results may vary significantly in future periods and our stock
price may decline.*
  37




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##### Table of Contents



Our financial performance may be adversely affected by current global economic conditions.
  We are dependent on Novartis and other third parties for the distribution of some of our products.
If any of our distributors terminates its relationship with us or fails to adequately perform, our
product sales will suffer.
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If we cannot maintain our current corporate collaborations and enter into new corporate
collaborations, our product development could be delayed. In particular, any failure by us to
maintain our collaboration with Novartis with respect to blood screening would have a material
adverse effect on our business.
     We may acquire other businesses or form collaborations, strategic alliances and joint ventures
that could decrease our profitability, result in dilution to stockholders or cause us to incur
debt or significant expense, and acquired companies or technologies could be difficult to
integrate and could disrupt our business.*
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
    
    the anticipated financial performance and estimated cost savings and other synergies as
a result of the acquisitions;
    
    the inability to retain or replace key employees of any acquired businesses or hire
enough qualified personnel to staff any new or expanded operations;
    
    the impairment of relationships with key customers of acquired businesses due to
changes in management and ownership of the acquired businesses;
    
    the exposure to federal, state, local and foreign tax liabilities in connection with
any acquisition or the integration of any acquired businesses;
    
    the exposure to unknown liabilities;
    
    higher than expected acquisition and integration costs that could cause our quarterly
and annual operating results to fluctuate;
    
    increased amortization expenses if an acquisition includes significant intangible
assets;
    
    combining the operations and personnel of acquired businesses with our own, which could
be difficult and costly;
    
    the risk of entering new markets; and
    
    integrating, or completing the development and application of, any acquired
technologies and personnel with diverse business and cultural backgrounds, which could
disrupt our business and divert our managements time and attention.
  Our future success will depend in part upon our ability to enhance existing products and to
develop, introduce and commercialize new products.*
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We face intense competition, and our failure to compete effectively could decrease our revenues
and harm our profitability and results of operations.*
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Failure to manufacture our products in accordance with product specifications could result in
increased costs, lost revenues, customer dissatisfaction or voluntary product recalls, any of
which could harm our profitability and commercial reputation.
  Disruptions in the supply of raw materials and consumable goods or issues associated with the
quality thereof from our single source suppliers, including Roche Molecular Biochemicals, which is
an affiliate of one of our primary competitors, could result in a significant disruption in sales
and profitability.*
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We have only one third-party manufacturer for each of our instrument product lines, which exposes
us to increased risks associated with production delays, delivery schedules, manufacturing
capability, quality control, quality assurance and costs.
    We and our customers are subject to various governmental regulations, and we may incur significant
expenses to comply with, and experience delays in our product commercialization as a result of,
these regulations.*
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Trichomonas vaginalis Trichomonas Trichomonas ®
   Trichomonas vaginalis.
   Our products are subject to recalls even after receiving FDA approval or clearance.
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Our gross profit margin percentage on the sale of blood screening assays will decrease upon the
implementation of smaller pool size testing.
   Because we depend on a small number of customers for a significant portion of our total revenues,
the loss of any of these customers or any cancellation or delay of a large purchase by any of
these customers could significantly reduce our revenues.
  Intellectual property rights on which we rely to protect the technologies underlying our products
may be inadequate to prevent third parties from using our technologies or developing competing
products.
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The diagnostic products industry has a history of patent and other intellectual property
litigation, and we have been and may continue to be involved in costly intellectual property
lawsuits.*
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Health care reform initiatives could adversely affect our business, profitability and stock price.
  Our indebtedness could adversely affect our financial health .
   
    
    increase our vulnerability to general adverse economic and industry conditions;
    
    have a material adverse effect on our business and financial condition if we are unable
to service our indebtedness or refinance such indebtedness;
    
    limit our flexibility in planning for, or reacting to, changes in our business and the
industry in which we operate;
    
    place us at a disadvantage compared to our competitors that have less indebtedness; and
    
    expose us to higher interest expense in the event of increases in interest rates
because indebtedness under our credit facility bears interest at a variable rate.
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We may be subject to future product liability claims that may exceed the scope and amount of our
insurance coverage, which would expose us to liability for uninsured claims.
  We are exposed to risks associated with acquisitions and other long-lived and intangible assets
that may become impaired and result in an impairment charge.*
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Future changes in financial accounting standards or practices, or existing taxation rules or
practices, may cause adverse unexpected revenue or expense fluctuations and affect our reported
results of operations.
  We expect to continue to incur significant research and development expenses, which may reduce our
profitability.
  Our marketable securities are subject to market and investment risks which may result in a loss of
value.
  We may not have financing for future capital requirements, which may prevent us from addressing
gaps in our product offerings or improving our technology.
   If we or our contract manufacturers are unable to manufacture our products in sufficient
quantities, on a timely basis, at acceptable costs and in compliance with regulatory requirements,
our ability to sell our products will be harmed.
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Our sales to international markets are subject to additional risks.
   
    
    the imposition of government controls;
    
    export license requirements;
    
    economic and political instability;
    
    price controls;
    
    trade restrictions and tariffs;
    
    differing local product preferences and product requirements; and
    
    changes in foreign medical reimbursement and coverage policies and programs.
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If third-party payors do not reimburse our customers for the use of our clinical diagnostic
products or if they reduce reimbursement levels, our ability to sell our products will be harmed.
    We are dependent on technologies we license, and if we fail to maintain our licenses or license
new technologies and rights to particular nucleic acid sequences for targeted diseases in the
future, we may be limited in our ability to develop new products.*
    If we fail to attract, hire and retain qualified personnel, we may not be able to design, develop,
market or sell our products or successfully manage our business.
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If a natural or man-made disaster strikes our manufacturing facilities, we will be unable to
manufacture our products for a substantial amount of time and our sales will decline.
  If we use biological and hazardous materials in a manner that causes injury or violates laws, we
may be liable for damages.
  The anti-takeover provisions of our certificate of incorporation and bylaws, and provisions of
Delaware law, could delay or prevent a change of control that our stockholders may favor.
  
    
    divide our board of directors into three classes, with members of each class to be
elected for staggered three-year terms;
    
    limit the right of stockholders to remove directors;
    
    regulate how stockholders may present proposals or nominate directors for election at
annual meetings of stockholders; and
    
    authorize our board of directors to issue preferred stock in one or more series,
without stockholder approval.
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If we do not effectively manage our growth, it could affect our ability to pursue opportunities
and expand our business.
  Information technology systems implementation issues could disrupt our internal operations and
adversely affect our financial results.
  Our forecasts and other forward-looking statements are based upon various assumptions that are
subject to significant uncertainties that may result in our failure to achieve our forecasted
results.
  Compliance with changing corporate governance and public disclosure regulations may result in
additional expenses.
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Item 2. Unregistered Sales of Equity Securities and Use of Proceeds
 Total Number
    
    
    Approximateof Shares
    
    
    Dollar ValuePurchased as
    
    
    of Shares thatPart of
    
    
    May Yet BePublicly
    
    
    PurchasedTotal      Number
    
    
    Average
    
    
    Announced
    
    
    Under theof Shares
    
    
    Price Paid
    
    
    Plans or
    
    
    Plans orPurchased
    
    
    Per Share
    
    
    Programs
    
    
    ProgramsJuly 1-31, 2009
    
    
    246,100
    
    
    $
    40.60
    
    
    
    246,100
    
    
    $
    59,462,128August 1-31, 2009
    
    
    1,583,053
    
    
    
    38.00
    
    
    
    1,560,100
    
    
    $
    182,785September 1-30, 2009
    
    
    61
    
    
    
    37.74
    
    
    
    
    
    
    $
    182,785Total(1) (2)
    
    
    1,829,214
    
    
    
    38.35
    
    
    
    1,806,200
 
 (1)
    
    In August 2008, our Board of Directors authorized the repurchase of up to $250.0
million of our common stock over the two years following adoption of the program, through
negotiated or open market transactions. There is no minimum or maximum number of shares to be
repurchased under the program. This program was completed in August 2009.(2)
    
    During the third quarter of 2009, we repurchased and retired 23,014 shares of our
common stock, at an average price of $38.51, withheld by us to satisfy employee tax
obligations upon vesting of restricted stock granted under our 2003 Incentive Award Plan. We
may make similar repurchases in the future to satisfy employee tax obligations upon vesting of
restricted stock. As of September 30, 2009, we had an aggregate of 207,517 shares of
restricted stock and 60,000 shares of deferred issuance restricted stock awards outstanding. 54




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Item 6. Exhibits
 ExhibitNumber
    
    Description2.1(1)
    
    Recommended Cash Offer for Tepnel Life Sciences plc.2.2(2)
    
    Implementation Agreement dated as of January 30, 2009 by and between Gen-Probe
Incorporated and Tepnel Life Sciences plc.3.1(3)
    
    Form of Amended and Restated Certificate of Incorporation of Gen-Probe Incorporated.3.2(4)
    
    Certificate of Amendment of Amended and Restated Certificate of Incorporation of
Gen-Probe Incorporated.3.3(5)
    
    Amended and Restated Bylaws of Gen-Probe Incorporated.3.4(6)
    
    Certificate of Elimination of Series A Junior Participating Preferred Stock of
Gen-Probe Incorporated.4.1(3)
    
    Specimen common stock certificate.10.103**
    
    Restated Agreement dated as of July 24, 2009 by and between Gen-Probe Incorporated
and Novartis Vaccines and Diagnostics, Inc.10.104
    
    Nonexclusive License Agreement Under Vysis Collins Patents effective as of June
22, 1999 by and between Gen-Probe Incorporated and Vysis, Inc.10.105
    
    Development, License and Supply Agreement entered into as of October 16, 2000 by
and between Gen-Probe Incorporated and KMC Systems, Inc.31.1
    
    Certification dated November 5, 2009, of Principal Executive Officer required
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002.31.2
    
    Certification dated November 5, 2009, of Principal Financial Officer required
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002.32.1
    
    Certification dated November 5, 2009, of Principal Executive Officer required
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.32.2
    
    Certification dated November 5, 2009, of Principal Financial Officer required
pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.
 
 
    
    Filed herewith.**
    
    Gen-Probe has requested confidential treatment with respect to certain portions of this
exhibit.(1)
    
    Incorporated by reference to Gen-Probes Current Report on Form 8-K filed with the
SEC on January 30, 2009.(2)
    
    Incorporated by reference to Gen-Probes Current Report on Form 8-K filed with the
SEC on February 5, 2009.(3)
    
    Incorporated by reference to Gen-Probes Amendment No. 2 to Registration Statement
on Form 10 filed with the SEC on August 14, 2002.(4)
    
    Incorporated by reference to Gen-Probes Quarterly Report on Form 10-Q for the
quarterly period ended September 30, 2004 filed with the SEC on August 9, 2004.(5)
    
    Incorporated by reference to Gen-Probes Current Report on Form 8-K filed with the
SEC on February 18, 2009.(6)
    
    Incorporated by reference to Gen-Probes Annual Report on Form 10-K for the year
ended December 31, 2006 filed with the SEC on February 23, 2007. 55




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SIGNATURES
  GEN-PROBE INCORPORATEDDATE: November 5, 2009
    
    By:
    
    /s/ Carl W. Hull

Carl W. HullPresident, Chief Executive Officer and Director(Principal Executive Officer)DATE: November 5, 2009
    
    By:
    
    /s/ Herm Rosenman

Herm RosenmanSenior Vice President  Finance and ChiefFinancial Officer (Principal Financial Officer andPrincipal Accounting Officer)
 56