================================================================================ UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) [X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2006 OR [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD ________ TO ________. COMMISSION FILE NUMBER: 000-31745 THIRD WAVE TECHNOLOGIES, INC. (Exact name of Registrant as specified in its charter) DELAWARE 39-1791034 (State or other jurisdiction (I.R.S. Employer of incorporation or organization) Identification No.) 502 S. ROSA ROAD, MADISON, WI 53719 (Address of principal executive offices) (Zip Code) (888) 898-2357 (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 [X] No [ ] Indicate by check whether the Registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of "accelerated filer and large accelerated filer" in Rule 12b-2 of Exchange Act. (Check one): Large Accelerated Filer [ ] Accelerated Filer [X] Non-Accelerated Filer [ ] Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). [ ] Yes [X] No The number of shares outstanding of the registrant's Common Stock, $.001 par value, as of November 6, 2006, was 41,978,466. ================================================================================ THIRD WAVE TECHNOLOGIES, INC. QUARTERLY REPORT ON FORM 10-Q FOR THE QUARTER ENDED SEPTEMBER 30, 2006 TABLE OF CONTENTS PAGE NO. -------- PART I FINANCIAL INFORMATION......................................... Item 1. Consolidated Financial Statements......................... Consolidated Balance Sheets (Unaudited) as of September 30, 2006 and December 31, 2005.................................. Consolidated Statements of Operations (Unaudited) for the Three and Nine Months Ended September 30, 2006 and 2005..... Consolidated Statements of Cash Flows (Unaudited) for the Nine Months Ended September 30, 2006 and 2005............... Notes to Consolidated Financial Statements (Unaudited)......... Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations.................... Item 3. Quantitative and Qualitative Disclosures About Market Risk............................................ Item 4. Controls and Procedures................................... PART II OTHER INFORMATION............................................ Item 1. Legal Proceedings......................................... Item 2. Unregistered Sales of Equity Securities and Use of Proceeds............................................... Item 3. Defaults Upon Senior Securities........................... Item 4. Submission Of Matters To A Vote Of Security Holders....... Item 5. Other Information......................................... Item 6. Exhibits.................................................. SIGNATURES........................................................... EXHIBITS............................................................. 2 PART I - FINANCIAL INFORMATION ITEM 1. CONSOLIDATED FINANCIAL STATEMENTS THIRD WAVE TECHNOLOGIES, INC. Consolidated Balance Sheets (UNAUDITED) SEPTEMBER 30, 2006 DECEMBER 31, 2005 ------------------ ----------------- ASSETS Current assets: Cash and cash equivalents $ 31,226,265 $ 27,681,704 Short-term investments 1,770,000 11,035,000 Accounts receivable, net of allowance for doubtful accounts of $200,000 at September 30, 2006 and December 31, 2005, respectively 4,148,889 3,764,519 Inventories 3,419,297 2,248,183 Prepaid expenses and other 714,750 235,794 ------------- ------------- Total current assets 41,279,201 44,965,200 Equipment and leasehold improvements: Machinery and equipment 16,062,324 15,563,119 Leasehold improvements 2,362,831 2,346,938 ------------- ------------- 18,425,155 17,910,057 Less accumulated depreciation and amortization 14,337,214 13,192,617 ------------- ------------- 4,087,941 4,717,440 ------------- ------------- Restricted cash -- 805,184 Intangible assets, net of accumulated amortization 1,513,056 2,641,620 Indefinite-lived intangible assets 1,007,411 1,007,411 Goodwill 489,873 489,873 Capitalized license fees 2,929,386 2,797,046 Other assets 967,144 980,954 ------------- ------------- Total assets $ 52,274,012 $ 58,404,728 ============= ============= LIABILITIES AND SHAREHOLDERS' EQUITY Current liabilities: Accounts payable $ 6,291,211 $ 6,850,207 Accrued payroll and related liabilities 3,474,830 2,158,870 Other accrued liabilities 2,345,387 2,344,835 Deferred revenue 114,051 121,497 Capital lease obligations due within one year 132,468 114,693 Long-term debt due within one year 381,279 378,551 ------------- ------------- Total current liabilities 12,739,226 11,968,653 Long-term debt 354,766 639,564 Deferred revenue - long-term 63,593 145,382 Capital lease obligations - long-term 126,106 191,924 Other liabilities 4,900,640 5,384,904 Minority interest in subsidiary 597,728 -- Shareholders' equity: Participating preferred stock, Series A, $.001 par value, 10,000,000 shares authorized, no shares issued and outstanding -- -- Common stock, $.001 par value, 100,000,000 shares authorized, 41,801,305 shares issued, 41,583,305 shares outstanding at September 30, 2006 and 41,461,377 shares issued, 41,243,377 shares outstanding at December 31, 2005 41,801 41,461 Additional paid-in capital 206,821,976 199,097,187 Unearned stock compensation -- (114,892) Treasury stock - 218,000 shares acquired at an average price of $4.02 per share (877,159) (877,159) Foreign currency translation adjustment (112,032) 47,442 Accumulated deficit (172,382,633) (158,119,738) ------------- ------------- Total shareholders' equity 33,491,953 40,074,301 ------------- ------------- Total liabilities and shareholders' equity $ 52,274,012 $ 58,404,728 ============= ============= See accompanying notes to consolidated financial statements. 3 THIRD WAVE TECHNOLOGIES, INC. Consolidated Statements of Operations (Unaudited) THREE MONTHS ENDED NINE MONTHS ENDED SEPTEMBER 30, SEPTEMBER 30, ------------------------- --------------------------- 2006 2005 2006 2005 ----------- ----------- ------------ ------------ Revenues: Clinical product sales $ 5,368,470 $ 4,031,766 $ 15,136,818 $ 11,407,180 Research product sales 1,181,226 1,039,569 5,809,175 6,152,540 License and royalty revenue 51,827 89,763 106,353 272,609 Grant revenue -- 61,293 182,876 287,819 ----------- ----------- ------------ ------------ Total revenues 6,601,523 5,222,391 21,235,222 18,120,148 ----------- ----------- ------------ ------------ Operating expenses: Cost of goods sold Product cost of goods sold 1,549,928 1,108,385 4,229,464 3,960,294 Intangible and long-term asset amortization 687,178 468,035 2,068,563 1,427,625 ----------- ----------- ------------ ------------ 2,237,106 1,576,420 6,298,027 5,387,919 Research and development 3,451,043 2,063,762 8,785,640 6,569,300 Selling and marketing 2,713,646 3,662,014 8,634,435 10,208,077 General and administrative 3,536,620 2,922,659 11,482,926 8,490,318 Litigation 255,809 2,677,982 1,438,671 5,157,282 Impairment of equipment -- -- -- 202,707 Restructuring (180,000) -- (180,000) -- ----------- ----------- ------------ ------------ Total operating expense 12,014,224 12,902,837 36,459,699 36,015,603 ----------- ----------- ------------ ------------ Loss from operations (5,412,701) (7,680,446) (15,224,477) (17,895,455) Other income (expense): Interest income 368,727 459,704 1,115,637 1,200,042 Interest expense (55,251) (128,516) (161,433) (313,278) Other (118,845) (30,685) (98,949) (305,721) ----------- ----------- ------------ ------------ Total other income (expense) 194,631 300,503 855,255 581,043 ----------- ----------- ------------ ------------ Net loss before minority interest $(5,218,070) $(7,379,943) $(14,369,222) $(17,314,412) ----------- ----------- ------------ ------------ Minority interest $ 65,481 $ -- $ 106,327 $ -- ----------- ----------- ------------ ------------ Net loss $(5,152,589) $(7,379,943) $(14,262,895) $(17,314,412) =========== =========== ============ ============ Net loss per share - basic and diluted $ (0.12) $ (0.18) $ (0.34) $ (0.42) Weighted average shares outstanding Basic and diluted 41,515,143 41,073,652 41,427,973 41,094,740 See accompanying notes to consolidated financial statements. 4 THIRD WAVE TECHNOLOGIES, INC. Consolidated Statements of Cash Flows (Unaudited) NINE MONTHS ENDED SEPTEMBER 30, --------------------------- 2006 2005 ------------ ------------ OPERATING ACTIVITIES: Net loss $(14,262,895) $(17,314,412) Adjustments to reconcile net loss to net cash used in operating activities: Minority Interest in net loss of subsidiary (106,327) -- Depreciation and amortization 1,230,262 1,297,395 Amortization of intangible assets 1,128,564 1,128,564 Amortization of licensed technology 939,998 299,602 Noncash stock compensation 2,720,817 (354,827) Impairment charge and (gain) loss on disposal of equipment 28,564 208,731 Changes in operating assets and liabilities: Accounts Receivable (625,604) 2,084,109 Inventories (1,171,114) (997,692) Prepaid expenses and other assets (333,386) (266,647) Accounts payable (1,118,105) (349,913) Accrued expenses and other liabilities 971,293 1,542,341 Deferred revenue (89,235) 1,950 ------------ ------------ Net cash used in operating activities (10,687,168) (12,720,799) INVESTING ACTIVITIES: Purchases of equipment and leasehold improvements (570,668) (307,185) Proceeds on sale of equipment -- 197,287 Purchases of licensed technology (702,274) -- Maturity of short-term investments 11,035,000 11,070,000 Purchases of short-term investments (1,770,000) (11,835,000) Change in restricted cash balance 805,184 -- ------------ ------------ Net cash provided by (used in) investing activities 8,797,242 (874,898) FINANCING ACTIVITIES: Proceeds from long-term debt -- 800,000 Payments on long-term debt (282,070) (126,040) Payments on capital lease obligations (106,702) (70,591) Proceeds from issuance of common stock, net 729,286 680,674 Proceeds from minority investment in subsidiary 5,093,973 -- Repurchase of common stock for treasury -- (877,159) ------------ ------------ Net cash provided by financing activities 5,434,487 406,884 ------------ ------------ Net increase (decrease) in cash and cash equivalents 3,544,561 (13,188,813) ------------ ------------ Cash and cash equivalents at beginning of period 27,681,704 55,619,981 ------------ ------------ Cash and cash equivalents at end of period $ 31,226,265 $ 42,431,168 ============ ============ Noncash investing and financing activities: During the nine months ended September 30, 2006 and 2005, the Company entered into capital lease obligations of $58,659 and $165,217, respectively. During the nine months ended September 30, 2006 the Company entered into a license agreement under which the Company will pay 1,000,000 Euros over two years. The estimated present value of the license is $1,122,338. See accompanying notes to consolidated financial statements. 5 THIRD WAVE TECHNOLOGIES, INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS September 30, 2006 (Unaudited) (1) Basis of Presentation The accompanying unaudited consolidated financial statements of Third Wave Technologies, Inc. have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. In the opinion of management, all adjustments, consisting of normal recurring adjustments, considered necessary for a fair presentation have been included. Interim results are not necessarily indicative of results that may be expected for the year ending December 31, 2006. The balance sheet at December 31, 2005 has been derived from the audited financial statements at that date but does not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. The accompanying unaudited consolidated financial statements should be read in conjunction with the audited financial statements and footnotes thereto included in our Form 10-K for the fiscal year ended December 31, 2005 filed with the Securities and Exchange Commission. (2) Net Loss Per Share In accordance with accounting principles generally accepted in the United States, basic net loss per share has been computed using the weighted-average number of shares of common stock outstanding during the respective periods. Diluted net loss per share takes into account the weighted average shares from options that could potentially dilute basic net income per share in the future. Shares associated with stock options are excluded for the three and nine months ended September 30, 2006 and 2005 because they are anti-dilutive. The following table presents the calculation of basic and diluted net loss per share: THREE MONTHS ENDED NINE MONTHS ENDED SEPTEMBER 30 SEPTEMBER 30 ------------------------- --------------------------- 2006 2005 2006 2005 ----------- ----------- ------------ ------------ Numerator: Net loss $(5,152,589) $(7,379,943) $(14,262,895) $(17,314,412) =========== =========== ============ ============ Denominator Weighted average shares outstanding - basic 41,515,143 41,073,652 41,427,973 41,094,740 Dilutive securities - stock options N/A N/A N/A N/A ----------- ----------- ------------ ------------ Weighted average shares outstanding - diluted 41,515,143 41,073,652 41,427,973 41,094,740 Basic net loss per share $ (0.12) $ (0.18) $ (0.34) $ (0.42) Dilutive net loss per share $ (0.12) $ (0.18) $ (0.34) $ (0.42) (3) Stock-Based Compensation The Company has Incentive Stock Option Plans for its employees and Nonqualified Stock Option Plans (collectively, the Plans) for employees and non-employees under which an aggregate of 13,213,183 stock options may be granted. Options under the Plans have a maximum life of ten years. Options vest at various intervals, as determined by the Board of Directors at the date of grant. At September 30, 2006, approximately 2.4 million shares were available for future grant under the plans. Stock Options The following table summarizes the stock option activity under the Plans for the nine months ended September 30, 2006: 6 WEIGHTED AVERAGE AGGREGATE NUMBER OF WEIGHTED AVERAGE CONTRACTUAL INTRINSIC SHARES EXERCISE PRICE LIFE VALUE ---------- ---------------- ----------- --------- Outstanding at December 31,2005 9,101,298 $4.34 Granted 909,250 2.99 Exercised (272,661) 2.05 Forfeited (1,489,072) 4.96 ---------- ----- Outstanding at September 30, 2006 8,248,815 $4.15 6.3 8,019,029 Options exercisable at September 30, 2006 5,688,164 $4.49 5.6 5,191,384 The weighted-average fair value of stock options granted in the nine months ended September 30, 2006 and 2005 was $1.90 and $3.05, respectively, using the Black-Scholes option-pricing model. The calculations were made assuming a dividend yield of 0%, a weighted-average expected option life of five years and a weighted-average risk-free interest rate of 4.83%, and 4.28% in 2006 and 2005, respectively. The volatility factor used in the Black-Scholes model for 2006 and 2005 was 74% and 81%, respectively. The expected life of stock options is estimated based on historical experience. The expected volatility is estimated based on historical financial data for the Company. The interest rates were based on the U.S. Treasury constant maturity interest rate whose term is consistent with the expected life of the stock options. As of September 30, 2006, there was approximately $4.5 million of total unrecognized compensation cost related to the stock options granted under the plans. The intrinsic value of the shares exercised in the nine months ended September 30, 2006 and 2005 was $0.4 million and $0.6 million, respectively. Restricted Stock Units The Company's stock plan also permits the granting of restricted stock units to eligible employees and non-employee directors. Restricted stock units are payable in shares of Company stock upon vesting. The restricted stock units vest at various intervals as determined by the Board of Directors at the date of grant. The following table presents a summary of the Company's nonvested restricted stock units granted to employees as of September 30, 2006. NINE MONTHS ENDED SEPTEMBER 30, 2006 ---------------------------- NUMBER OF WEIGHTED AVERAGE SHARES FAIR VALUE --------- ---------------- Nonvested shares of restricted stock units at December 31, 2005 -- $ -- Granted 112,530 2.84 Vested -- -- Forfeited (3,451) 2.84 ------- ----- Nonvested shares of restricted stock units at September 30, 2006 109,079 $2.84 ======= ===== As of September 30, 2006, there was approximately $0.3 million of total unrecognized compensation cost related to the nonvested restricted stock units granted under the plan. The expense is expected to be recognized over the vesting period. Compensation expense related to restricted stock units was approximately $28,000 in the nine months ended September 30, 2006. As of September 30, 2006, there were 109,079 restricted stock units outstanding. Employee Stock Purchase Plan The Company also has an Employee Stock Purchase Plan (Purchase Plan) under which an aggregate of 1,256,800 common shares may be issued. All employees are eligible to participate in the Purchase Plan. Eligible employees may make contributions through payroll deductions of up to 10% of their compensation. The price of common stock purchased under the Purchase Plan is 85% of the lower of the fair market value of the common stock at the beginning or end of the offering period. There were 67,267 and 57,428 shares sold to employees in the nine months ended September 30, 2006, and 2005, respectively. At September 30, 2006, approximately 364,000 shares were available for issuance under the Purchase Plan. Review of Stock Option Grants and Procedures In October 2006, the Company's audit committee concluded a voluntary investigation of the Company's historical stock option granting practices and related accounting. This investigation, which was conducted with the assistance of outside legal counsel, covered the timing, pricing and authorization of all the Company's stock option grants made since the Company's initial public offering in February 2001. Based on this review, the Company determined that it used incorrect measurement dates with respect to the accounting for certain previously granted stock options, primarily during the years 2002 through 2004. The audit committee concluded that deficiencies in the grant process were the result of administrative errors and misunderstanding of applicable accounting rules, and were not attributable to fraud or intentional misconduct. 7 Based upon the Company's determination that certain of its historic stock option grants had intrinsic value on the grant date, the Company had unrecorded non-cash stock compensation expense. The Company has concluded that the additional unrecorded non-cash stock compensation expense is not material to its financial statements in any of the periods to which such charges would have related, and therefore will not revise its historic financial statements. The Company recorded an additional non-cash stock-based compensation charge totaling $176,000 in the quarter ended September 30, 2006, representing the effect of the adjustment resulting from the non-cash charges discussed above that relate to 2006. Additionally, the Company expects to record a reclassification between accumulated deficit and additional paid in capital, within the equity section of the consolidated balance sheet to be included in its Form 10-K for the fiscal year ending December 31, 2006, of approximately $731,000. This reclassification represents the effect of the adjustment resulting from the non-cash charges discussed above that related to fiscal 2005 and prior years. Neither the current period charge nor the reclassification affect the Company's cash position. There were no significant income tax effects relating to this adjustment for the Company. Prior to January 1, 2006, we used the intrinsic value method prescribed in Accounting Principles Board Opinion No. 25, "Accounting for Stock Issued to Employees", and related interpretations, in accounting for stock options granted under our Plans. Generally, no compensation cost was required to be recognized for options granted to employees because the options had an exercise price equal to the market value per share of the underlying common stock on the date of grant. Prior to 2006, the Purchase Plan was considered noncompensatory under APB Opinion No. 25 and, therefore, no expense was recorded for the 15% discount. Prior to January 1, 2006, options granted to non-employee consultants were accounted for in accordance with SFAS No. 123 and Emerging Issues Task Force (EITF) Issue No. 96-18, "Accounting for Equity Instruments That Are Issued to Other Than Employees for Acquiring, or in Conjunction with Selling, Goods or Services," and therefore were measured based upon their fair value as calculated using the Black-Scholes option pricing model. The fair value of options granted to non-employees was periodically remeasured as the underlying options vested. On January 1, 2006, the Company adopted SFAS No. 123 (revised 2004), "Share-Based Payment", which is a revision of SFAS No. 123. SFAS No. 123(R) permits public companies to adopt its requirements using one of two methods: (1) a "modified prospective" method in which compensation cost is recognized beginning with the effective date (a) based on the requirements of SFAS No. 123(R) for all-share based payments granted after the effective date and (b) based on the requirements of SFAS No. 123 for all awards granted to employees prior to the effective date of SFAS No. 123(R) that remain unvested on the effective date; or (2) a "modified retrospective" method which includes the requirements of the modified prospective method described above, but also permits entities to restate based on the amounts previously recognized under SFAS No. 123 for purposes of pro forma disclosures either (a) all prior periods presented or (b) prior interim periods of the year of adoption. The Company has adopted the modified prospective approach. As prescribed in the modified prospective approach, prior periods have not been restated to reflect the effects of implementing FAS 123(R). For the three and nine month periods ended September 30, 2005, the pro forma stock option expense, net loss and net loss per share are as follows: THREE MONTHS NINE MONTHS ------------ ------------ Net loss, as reported $(7,379,943) $(17,314,412) Add: Stock-based compensation, as reported 422,357 (354,827) Add: Stock-based compensation, using fair value method (1,217,295) (3,557,025) Add: Stock-based compensation, related to the employee stock purchase plan determined under SFAS No. 123 0 (95,847) ----------- ------------ Pro forma net loss $(8,147,881) $(21,322,111) =========== ============ Net loss per share, basic and diluted, as reported $ (0.18) $ (0.42) Pro forma net loss per share, basic and diluted $ (0.20) $ (0.52) The stock-based compensation expense attributable to SFAS No. 123(R) for the three months and nine months ended September 30, 2006 was $0.6 million and $2.0 million, respectively. 8 (4) Inventories Inventories are carried at the lower of cost or market using the first-in, first-out (FIFO) method for determining cost. Inventories consist of the following: SEPTEMBER 30, DECEMBER 31, 2006 2005 ------------- ------------ Raw materials $2,344,098 $1,486,166 Finished goods 1,521,610 1,271,101 Work in process 383,589 165,916 Reserve for excess and obsolete inventory (830,000) (675,000) ---------- ---------- Total inventories $3,419,297 $2,248,183 ========== ========== (5) Stock Compensation Included in operating expenses are the following stock compensation charges, net of reversals related to terminated employees: THREE MONTHS ENDED NINE MONTHS ENDED SEPTEMBER 30, SEPTEMBER 30, ------------------- ---------------------- 2006 2005 2006 2005 -------- -------- ---------- --------- Cost of goods sold $ 43,636 $ 40,143 $ 105,945 $ 27,163 Research and development 155,982 1,969 476,892 (499,113) Selling and marketing 183,728 33,150 565,234 45,557 General and administrative 551,821 347,095 1,572,746 71,566 -------- -------- ---------- --------- Total stock compensation $935,167 $422,357 $2,720,817 $(354,827) -------- -------- ---------- --------- (6) Comprehensive Loss The components of comprehensive loss are as follows: THREE MONTHS ENDED NINE MONTHS ENDED SEPTEMBER 30, SEPTEMBER 30, ------------------------- --------------------------- 2006 2005 2006 2005 ----------- ----------- ------------ ------------ Net loss $(5,152,589) $(7,379,943) $(14,262,895) $(17,314,412) Other comprehensive income (loss): Foreign currency translation adjustments (114,167) 4,625 (159,474) 9,187 ----------- ----------- ------------ ------------ Comprehensive loss $(5,266,756) $(7,375,318) $(14,422,369) $(17,305,225) =========== =========== ============ ============ 9 (7) Amortizable Intangible Assets Amortizable intangible assets consist of the following: SEPTEMBER 30, 2006 DECEMBER 31, 2005 -------------------------- -------------------------- GROSS GROSS CARRYING ACCUMULATED CARRYING ACCUMULATED AMOUNT AMORTIZATION AMOUNT AMORTIZATION ----------- ------------ ----------- ------------ Costs of settling patent litigation $10,533,248 $ 9,020,192 $10,533,248 $ 7,891,628 Reacquired marketing and distribution rights 2,211,111 2,211,111 2,211,111 2,211,111 Customer agreements 38,000 38,000 38,000 38,000 ----------- ----------- ----------- ----------- Total $12,782,359 $11,269,303 $12,782,359 $10,140,739 =========== =========== =========== =========== (8) Restructuring and Impairment of Long Lived Assets During the third quarter of 2002, we announced a restructuring plan designed to simplify product development and manufacturing operations and reduce operating expenses. The restructuring charges recorded were determined based upon plans submitted by the Company's management and approved by the Board of Directors using information available at the time. The restructuring charge included $2.5 million for the consolidation of facilities, $500,000 for prepayment penalties mainly under capital lease arrangements, an impairment charge of $7.2 million for abandoned leasehold improvements and equipment to be sold and $900,000 of other costs related to the restructuring. The Company also recorded a $1.1 million charge within cost of goods sold related to inventory that was considered obsolete based upon the restructuring plan. The facilities charge contained estimates based on the Company's potential to sublease a portion of its corporate office. The Company has offered the corporate office space for sublease, but has been unable to sublease the space. Accordingly, the Company decreased its estimate of the amount of sublease income it expects to receive. The estimated lease and operating expenses were also reduced, based on a portion of the office space being utilized and revisions to the building lease. The following table shows the changes in the restructuring accrual since December 31, 2005. The restructuring accrual was reduced in the quarter ended September 30, 2006 due to an amendment to the building lease that resulted in lower lease payments over the original remaining life of the lease. The remaining restructuring balance of $0.7 million is for rent payments on a non-cancelable lease, net of estimated sublease income, which will continue to be paid over the lease term through 2011. The current portion of the accrual is included in other accrued liabilities on the balance sheets and the remainder is included in other long-term liabilities. Accrued restructuring balance at December 31, 2005 $ 957,563 Payments made (117,767) Adjustment (180,000) ========= Accrued restructuring balance at September 30, 2006 $ 659,796 ========= (9) Other Long-term Liabilities Other long-term liabilities consist of the long-term portion of the following items: SEPTEMBER 30, 2006 DECEMBER 31, 2005 ------------------ ----------------- License payments $1,291,896 $1,430,942 Long-term Incentive Plan 1,667,289 1,312,841 Restructuring 536,488 775,174 Rent 1,138,909 1,159,094 Other 266,058 706,853 ---------- ---------- $4,900,640 $5,384,904 ========== ========== (10) Shareholders' Equity The Board of Directors had authorized a program for the repurchase by the Company of up to 5% of its outstanding common stock. Third Wave has repurchased 218,000 shares of common stock as of December 31, 2005 for $877,159. The program expired on December 31, 2005. 10 (11) New Accounting Pronouncements On December 16, 2004, the Financial Accounting Standards Board (FASB) issued SFAS No. 123 (revised 2004), "Share-Based Payment," which is a revision of SFAS No. 123. SFAS No. 123(R) supersedes APB Opinion No. 25 and amends SFAS No. 95, "Statement of Cash Flows." Generally, the approach in SFAS No. 123(R) is similar to the approach described in SFAS No. 123. However, SFAS No. 123(R) requires all share-based payments to employees, including grants of employee stock options, to be recognized in the income statement based on their fair values. Pro forma disclosure is no longer an alternative. The Company adopted SFAS No. 123(R) on January 1, 2006. SFAS No. 123(R) permits public companies to adopt its requirements using one of two methods: (1) a "modified prospective" method in which compensation cost is recognized beginning with the effective date (a) based on the requirements of SFAS No. 123(R) for all-share based payments granted after the effective date and (b) based on the requirements of SFAS No. 123 for all awards granted to employees prior to the effective date of SFAS No. 123(R) that remain unvested on the effective date; or (2) a "modified retrospective" method which includes the requirements of the modified prospective method described above, but also permits entities to restate based on the amounts previously recognized under SFAS No. 123 for purposes of pro forma disclosures either (a) all prior periods presented or (b) prior interim periods of the year of adoption. The Company adopted the modified prospective approach. In September 2006, the FASB issued FIN No. 48, "Accounting for Uncertainty in Income Taxes," which clarifies the accounting for uncertainty in income taxes recognized in an enterprise's financial statements in accordance with SFAS No. 109, "Accounting for Income Taxes." This interpretation prescribes a recognition threshold and measurement attribute for the financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return. This interpretation also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure, and transition. FIN No. 48 is effective for fiscal years beginning after December 15, 2006. The adoption of Interpretation No. 48 is not expected to have any significant effect on the Company's consolidated financial position or results of operations. In September 2006, the Securities and Exchange Commission ("SEC) issued Staff Accounting Bulletin ("SAB") No. 108, "Considering the Effects of Prior Year Misstatements when Quantifying Misstatements in Current Year Financial Statements." SAB 108 provides guidance on the consideration of effects of the prior year misstatements in quantifying current year misstatements for the purpose of a materiality assessment. The SEC staff believes registrants must quantify errors using both a balance sheet and income statement approach and evaluate whether either approach results in quantifying a misstatement that, when all relevant quantitative and qualitative factors are considered, is material. SAB 108 is effective for the first annual period ending after November 15, 2006 with early application encouraged. The Company adopted SAB 108 in the quarter ended September 30, 2006. The adoption of this guidance has not had a material impact on the Company's consolidated financial statements. In May 2005, the FASB issued SFAS No. 154, "Accounting Changes and Error Corrections - a replacement of Accounting Principles Board Opinion ("APB") No. 20 and SFAS No. 3," which changes the requirements for the accounting for, and reporting of, a change in accounting principle. SFAS No. 154 is effective for accounting changes and correction of errors made in fiscal years beginning after December 15, 2005; however, the statement does not change the transition provisions of any existing accounting pronouncements. The adoption of this guidance has not had a material impact on the Company's consolidated financial statements. (12) Reclassifications Certain reclassifications have been made to the 2005 financial statements to conform to the 2006 presentation. 11 THIRD WAVE TECHNOLOGIES, INC. ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS This Management's Discussion and Analysis of Financial Condition and Results of Operations as of September 30, 2006 and for the three and nine months ended September 30, 2006 and 2005 should be read in conjunction with our Form 10-K for the fiscal year ended December 31, 2005 filed with the Securities and Exchange Commission. In this Form 10-Q, the terms "we," "us," "our," "Company," and "Third Wave" each refer to Third Wave Technologies, Inc. The following discussion of our financial condition and results of our operations should be read in conjunction with our Financial Statements, including the Notes thereto, included elsewhere in this Form 10-Q. OVERVIEW Third Wave Technologies, Inc. develops and markets molecular diagnostic reagents for a variety of DNA and RNA analysis applications to meet the needs of our customers. The Company offers a number of products based on its Invader(R) chemistry for clinical testing. Third Wave offers in vitro diagnostic kits and analyte specific, general purpose, and research use only reagents for nucleic acid analysis. We believe our proprietary Invader(R) chemistry, a novel, molecular chemistry, is easier to use, cost-effective, and enables higher testing throughput. These and other advantages conferred by our chemistry enable us to provide clinicians and researchers with superior molecular solutions. Approximately 160 clinical laboratory customers are using Third Wave's molecular diagnostic reagents. Other customers include pharmaceutical and biotechnology companies, academic research centers and major health care providers. Our customer base is dominated by a small number of large clinical testing labs. We regularly experience pricing and other competitive pressures in these accounts. If for any reason, we are unable to maintain or renew our contracts, particularly our contracts with key customers, or if, for any reason, we are unable to maintain current pricing levels and/or volumes with our customers, or are unable to manufacture the required product, our revenues and business may suffer materially. Third Wave has received clearance from the U.S. Food and Drug Administration (FDA) for its Invader(R) UGT1A1 Molecular Assay. The Invader(R) UGT1A1 Molecular Assay is used to identify patients who may be at increased risk of adverse reaction to the chemotherapy Camptosar(R) (irinotecan) by detecting and identifying specific mutations in the UGT1A1 gene that have been associated with that risk. Camptosar(R), marketed in the United States by Pfizer, Inc., is used to treat colorectal cancer and has been relabeled to include dosing recommendations based on a patient's genetic profile. We also market a growing number of products, including analyte specific reagents (ASRs). These ASRs allow certified clinical reference laboratories to create assays that test for infectious disease (e.g., hepatitis C virus), inherited disorders (e.g., Factor V Leiden), and a host of other markers associated with genetic predispositions and other diseases. The FDA is currently reviewing draft guidance for the regulation of ASRs. If the FDA issues guidance or takes other actions that limit ASRs generally or limits Third Wave's ASRs specifically, such guidance or actions could materially affect our business. The Company has developed or plans to develop a menu of molecular diagnostic products for clinical applications that include genetic testing, pharmacogenetics, and women's health. The Company also has a number of other Invader(R) products for research, agricultural and other applications. Currently, one of our key strategic initiatives is the commercialization of our Human Papillomavirus (HPV) offering. To bring this product to market we will need to receive premarket approval, known as a PMA, from the FDA. Seeking a PMA for our HPV offering (and for any other product offerings) will be costly and there can be no assurance that we will receive FDA approval or that other difficulties will not delay or prevent the successful commercialization of our HPV offering. If we are unable to successfully commercialize our HPV offering, our business and prospects may be materially adversely affected. Additionally, we anticipate significant competition in the HPV market as additional large competitors have announced plans to enter the market in the near future. This competition may have a significant impact on the success of our commercialization of our HPV offering. Our financial results may vary significantly from quarter to quarter due to fluctuations in the demand for our products, timing of new product introductions and deliveries made during the quarter, the timing of research, development and grant revenues, and increases in spending, including expenses related to our product development submissions for FDA clearances or approvals and intellectual property litigation. 12 CRITICAL ACCOUNTING POLICIES Management's discussion and analysis of our financial condition and results of operations are based upon our consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. We review the accounting policies we use in reporting our financial results on a regular basis. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis, we evaluate our estimates, including those related to accounts receivable, inventories, equipment and leasehold improvements and intangible assets. We base our estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Results may differ from these estimates due to actual outcomes being different from those on which we based our assumptions. These estimates and judgments are reviewed by management on an ongoing basis, and by the Audit Committee at the end of each quarter prior to the public release of our financial results. We believe the following critical accounting policies affect our more significant judgments and estimates used in the preparation of our consolidated financial statements. REVENUE RECOGNITION Revenue from product sales is recognized upon delivery which is generally when the title passes to the customer, provided that the Company has completed all performance obligations and the customer has accepted the products. Customers have no contractual rights of return or refunds associated with product sales. Consideration received in multiple element arrangements is allocated to the separate units based upon their relative fair values. The multiple element arrangements involve contracts with customers in which the Company is selling reagent products and leasing equipment to the customer for use during the term of the contract. Based upon the guidance in paragraph 9 of EITF No. 00-21 "Revenue Arrangements with Multiple Deliverables", both the reagents and equipment have value to the customer on a standalone basis, there is objective and reliable evidence of fair value for both the reagents and equipment and there are no rights of return. The Company has sold both the reagents and equipment separately, and therefore is able to determine a fair value for each. The respective fair values are used to allocate the proceeds received to each of the elements for purposes of recognizing revenue. Grant and development revenues consist primarily of research grants from agencies of the federal government and revenue from companies with which the Company has established strategic alliances, the revenue from which is recognized as research is performed. Payments received which are related to future performance are deferred and recorded as revenue when earned. Grant payments designated to purchase specific assets to be used in the performance of a contract are recognized as revenue over the shorter of the useful life of the asset acquired or the contract. License and royalty revenue include amounts earned from third parties for licenses of the Company's intellectual property and are recognized when earned under the terms of the related agreements. License revenues are generally recognized upon receipt unless the Company has continuing performance obligations, in which case the license revenue is recognized ratably over the period of expected performance. RESTRUCTURING AND OTHER CHARGES The restructuring and other charges resulting from the restructuring plan in the third quarter of 2002 have been recorded in accordance with EITF Issue No. 94-3, "Liability Recognition for Certain Employee Termination Benefits and Other Costs to Exit an Activity (including Certain Costs Incurred in a Restructuring)", Staff Accounting Bulletin No. 100, "Restructuring and Impairment Charges," and Statement of Financial Accounting Standards (SFAS) No. 144, "Accounting for the Impairment or Disposal of Long-Lived Assets." The restructuring charge was comprised primarily of costs to consolidate facilities, impairment charges for abandoned leasehold improvements and equipment to be sold or abandoned, prepayment penalties related mainly to capital lease obligations on equipment to be sold or abandoned, and other costs related to the restructuring. The remaining accrued restructuring balance is for rent payments on a non-cancelable lease, net of estimated sublease income. In calculating the cost to consolidate the facilities, we estimated the future lease and operating costs to be paid until the leases are terminated and the amount, if any, of sublease receipts for each location. This required us to estimate the timing and costs of each lease to be terminated, the amount of operating costs, and the timing and rate at which we might be able to sublease the site. To form our estimates for these costs, we performed an assessment of the affected facilities and considered the current market conditions for each site. Our assumptions on the lease payments, operating costs until terminated, and the offsetting sublease receipts may turn out to be incorrect and our actual cost may be materially different from our estimates. 13 LONG-LIVED ASSETS--IMPAIRMENT Equipment, leasehold improvements and amortizable identifiable intangible assets are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount may not be recoverable. For assets held and used, if the sum of the expected undiscounted cash flows is less than the carrying value of the related asset or group of assets, a loss is recognized for the difference between the fair value and carrying value of the asset or group of assets. For assets removed from service and held for sale, we estimate the fair market value of such assets and record an adjustment if fair value less costs to sell is lower than carrying value. Goodwill and intangible assets deemed to have indefinite lives are not amortized, but are subject to annual impairment tests under SFAS No. 142, "Goodwill and Other Intangible Assets." The annual impairment test was completed in the quarter ended September 30, 2006 and resulted in no impairment. STOCK-BASED COMPENSATION EXPENSE Prior to 2006, we accounted for share-based payments to employees using APB Opinion No. 25's intrinsic value method and, as such, generally recognized no compensation cost for employee stock options when granted. On January 1, 2006 we adopted SFAS No. 123(R) as a result of which we recognize expense for all share-based payments to employees, including grants of employee stock options, based on their fair values. We have adopted the modified prospective transition method as permitted by SFAS No. 123(R). In October 2006, our audit committee concluded a voluntary investigation of the Company's historical stock option granting practices and related accounting. This investigation, which was conducted with the assistance of outside legal counsel, covered the timing, pricing and authorization of all our stock option grants made since our initial public offering in February 2001. Based on this review, the Company determined that it used incorrect measurement dates with respect to the accounting for certain previously granted stock options, primarily during the years 2002 through 2004. The audit committee concluded that deficiencies in the grant process were the result of administrative errors and misunderstanding of applicable accounting rules, and were not attributable to fraud or intentional misconduct. We recorded an additional non-cash stock-based compensation charge totaling $176,000 in the quarter ended September 30, 2006, representing the effect of the adjustment resulting from the non-cash charges discussed above that relate to 2006. Additionally, we expect to record a reclassification between accumulated deficit and additional paid in capital, within the equity section of the consolidated balance sheet to be included in our Form 10-K for the fiscal year ending December 31, 2006, of approximately $731,000. This reclassification represents the effect of the adjustment resulting from the non-cash charges discussed above that related to fiscal 2005 and prior years. Neither the current period charge nor the reclassification affect our cash position. There were no significant income tax effects relating to this adjustment for the Company. INVENTORIES--SLOW MOVING AND OBSOLESCENCE Significant management judgment is required to determine the reserve for obsolete or excess inventory. Inventory on hand may exceed future demand either because of process improvements or technology advancements, the amount on hand is more than can be used to meet future need, or estimates of shelf lives may change. We currently consider all inventory that we expect will have no activity within one year as well as any additional specifically identified inventory to be subject to a provision for excess inventory. We also provide for the total value of inventories that we determine to be obsolete based on criteria such as changing manufacturing processes and technologies. At September 30, 2006, our inventory reserves were $830,000, or 20% of our $4.2 million total gross inventories. NEW ACCOUNTING PRONOUNCEMENTS On December 16, 2004, the Financial Accounting Standards Board (FASB) issued SFAS No. 123 (revised 2004), "Share-Based Payment," which is a revision of SFAS No. 123. SFAS No. 123(R) supersedes APB Opinion No. 25 and amends SFAS No. 95, "Statement of Cash Flows." Generally, the approach in SFAS No. 123(R) is similar to the approach described in SFAS No. 123. However, SFAS No. 123(R) requires all share-based payments to employees, including grants of employee stock options, to be recognized in the income statement based on their fair values. Pro forma disclosure is no longer an alternative. 14 The Company adopted SFAS No. 123(R) on January 1, 2006. SFAS No. 123(R) permits public companies to adopt its requirements using one of two methods: (1) a "modified prospective" method in which compensation cost is recognized beginning with the effective date (a) based on the requirements of SFAS No. 123(R) for all-share based payments granted after the effective date and (b) based on the requirements of SFAS No. 123 for all awards granted to employees prior to the effective date of SFAS No. 123(R) that remain unvested on the effective date; or (2) a "modified retrospective" method which includes the requirements of the modified prospective method described above, but also permits entities to restate based on the amounts previously recognized under SFAS No. 123 for purposes of pro forma disclosures either (a) all prior periods presented or (b) prior interim periods of the year of adoption. The Company adopted the modified prospective approach. In September 2006, the FASB issued FIN No. 48, "Accounting for Uncertainty in Income Taxes," which clarifies the accounting for uncertainty in income taxes recognized in an enterprise's financial statements in accordance with SFAS No. 109, "Accounting for Income Taxes." This interpretation prescribes a recognition threshold and measurement attribute for the financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return. This interpretation also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure, and transition. FIN No. 48 is effective for fiscal years beginning after December 15, 2006. The adoption of Interpretation No. 48 is not expected to have any significant effect on the Company's consolidated financial position or results of operations. In September 2006, the Securities and Exchange Commission ("SEC) issued Staff Accounting Bulletin ("SAB") No. 108, "Considering the Effects of Prior Year Misstatements when Quantifying Misstatements in Current Year Financial Statements." SAB 108 provides guidance on the consideration of effects of the prior year misstatements in quantifying current year misstatements for the purpose of a materiality assessment. The SEC staff believes registrants must quantify errors using both a balance sheet and income statement approach and evaluate whether either approach results in quantifying a misstatement that, when all relevant quantitative and qualitative factors are considered, is material. SAB 108 is effective for the first annual period ending after November 15, 2006 with early application encouraged. The Company adopted SAB 108 in the quarter ended September 30, 2006. The adoption of this guidance has not had a material impact on the Company's consolidated financial statements. In May 2005, the FASB issued SFAS No. 154, "Accounting Changes and Error Corrections - a replacement of Accounting Principles Board Opinion ("APB") No. 20 and SFAS No. 3," which changes the requirements for the accounting for, and reporting of, a change in accounting principle. SFAS No. 154 is effective for accounting changes and correction of errors made in fiscal years beginning after December 15, 2005; however, the statement does not change the transition provisions of any existing accounting pronouncements. The adoption of this guidance has not had a material impact on the Company's consolidated financial statements. 15 RESULTS OF OPERATIONS Three and Nine Months Ended September 30, 2006 and 2005 NET LOSS. Net loss for the three months ended September 30, 2006 improved to $5.2 million from $7.4 million for the corresponding period of 2005. Net loss for the nine months ended September 30, 2006 improved to $14.3 million from $17.3 million for the corresponding period of 2005. REVENUES. Revenues for the three months ended September 30, 2006 of $6.6 million represented an increase of $1.4 million, compared to revenues of $5.2 million for the corresponding period of 2005. Revenues for the nine months ended September 30, 2006 of $21.2 million represented an increase of $3.1 million, compared to revenues of $18.1 million for the corresponding period of 2005. Following is a discussion of changes in revenues: Clinical molecular diagnostic product revenue increased to $5.4 million in the quarter ended September 30, 2006 from $4.0 million in the quarter ended September 30, 2005. Clinical molecular diagnostic product revenue increased to $15.1 million in the nine months ended September 30, 2006 from $11.4 million in the nine months ended September 30, 2005. Research product revenues increased to $1.2 million in the three months ended September 30, 2006 from $1.0 million in the three months ended September 30, 2005. Research product revenues decreased to $5.8 million in the nine months ended September 30, 2006 from $6.1 million in the nine months ended September 30, 2005. The decrease in research product sales during 2006 resulted from a decrease in genomic research product sales to a Japanese research institute for use by several end users. The decrease in research revenue from the Japanese research institute was partially offset by an increase in revenue from our Agbio business. Significant Customers. We generated $2.8 million, or 13% of our revenues, from sales to a major Japanese research institute for use by several end-users during the nine months ended September 30, 2006, compared to $3.6 million, or 20% of our revenues during the nine months ended September 30, 2005. In addition, we generated $2.2 million or 10% of our revenues, from sales to a large clinical lab during the nine months ended September 30, 2006. COST OF GOODS SOLD. Cost of goods sold consists of materials used in the manufacture of product, depreciation on manufacturing capital equipment, salaries and related expenses for management and personnel associated with our manufacturing and quality control departments and amortization of licenses and settlement fees. For the three months ended September 30, 2006, cost of goods sold increased to $2.2 million, compared to $1.6 million for the corresponding period of 2005. For the nine months ended September 30, 2006, cost of goods sold increased to $6.3 million, compared to $5.4 million for the corresponding period of 2005. The increase in the three and nine month periods was primarily due to the increase in sales volume, amortization of new licenses and the write-off of defective inventory due to a supplier relocation in the third quarter. RESEARCH AND DEVELOPMENT EXPENSES. Research and development expenses consist primarily of salaries and related personnel costs, material costs for assays and product development, fees paid to consultants, depreciation and facilities costs and other expenses related to the design, development, testing, (including clinical trials to validate the performance of our products) and enhancement of our products, and acquisition of technologies used in our products. Research and development costs are expensed as they are incurred. Research and development expenses for the three months ended September 30, 2006 were $3.5 million, compared to $2.1 million for the three months ended September 30, 2005. Research and development expenses for the nine months ended September 30, 2006 were $8.8 million, compared to $6.6 million for the nine months ended September 30, 2005. The increase in research and development expenses was primarily due to an increase in personnel, product development expense (including costs incurred by us in pursuit of FDA premarket approval for our HPV offering), and an increase in stock based compensation expense of $0.2 million and $1.0 million in the three and nine month periods, respectively, compared to the same periods in 2005. We will continue to invest in research and development, and expenditures in this area will increase as we expand our product development efforts. In addition, as the Company moves towards consideration of FDA cleared or approved products, there will be increased expenses attributed to these activities. SELLING AND MARKETING EXPENSES. Selling and marketing expenses consist primarily of salaries and related personnel costs for our sales and marketing management and field sales force, commissions, office support and related costs, and travel and entertainment. Selling and marketing expenses for the three months ended September 30, 2006 were $2.7 million, a decrease of $1.0 million, compared to $3.7 million for the corresponding period of 2005. Selling and marketing expenses for the nine months ended September 30, 2006 were $8.6 million, a decrease of $1.6 million, compared to $10.2 million for the corresponding period of 2005. The decrease in selling and marketing expenses was due to a decrease in personnel related and equipment expense, offset by an 16 increase in stock based compensation expense of $0.2 million and $0.5 million in the three and nine month periods, respectively, compared to the same periods in 2005. GENERAL AND ADMINISTRATIVE EXPENSES. General and administrative expenses consist primarily of salaries and related expenses for executive, finance and other administrative personnel, legal and professional fees, office support and depreciation. General and administrative expenses increased to $3.5 million in the three months ended September 30, 2006, from $2.9 million for the corresponding period in 2005. General and administrative expenses increased to $11.5 million in the nine months ended September 30, 2006, from $8.5 million for the corresponding period in 2005. The increase in general and administrative expense was due to an increase in legal fees related to our patents and the equity investment in our Japan subsidiary, a sales tax charge and an increase in stock based compensation expense of $0.2 million and $1.5 million in the three and nine month periods, respectively compared to the same periods in 2005. LITIGATION EXPENSE. Litigation expense consists of legal fees and other costs associated with patent infringement and other lawsuits. Litigation expense decreased to $0.3 million in the three months ended September 30, 2006 from $2.7 million in the corresponding period in 2005. Litigation expense decreased to $1.4 million in the nine months ended September 30, 2006 from $5.2 million in the corresponding period in 2005. The decreases were the result of the decreased litigation activity due to the resolution of the lawsuits with Innogenetics, Chiron Corporation, Bayer Corporation, and Digene Corporation. We anticipate litigation expense to remain below the 2005 levels for the remainder of the year. IMPAIRMENT. In the nine months ended September 30, 2005 an impairment charge of $0.2 million was recorded for the loss on equipment that was sold. RESTRUCTURING. In the three and nine months ended September 30, 2006 a credit of $0.2 million was recorded to adjust the restructuring accrual due to an amendment to the building lease. INTEREST INCOME. Interest income for the three months ended September 30, 2006 and 2005 was $0.4 million and $0.5 million, respectively. Interest income for the nine months ended September 30, 2006 and 2005 was $1.1 million and $1.2 million, respectively. INTEREST EXPENSE. Interest expense for the three months ended September 30, 2006 and 2005 was approximately $0.1 million. Interest expense for the nine months ended September 30, 2006 and 2005 was $0.2 million and $0.3 million, respectively. OTHER INCOME (EXPENSE). Other expense for the three months ended September 30, 2006 was approximately $0.1 million compared to $31,000 for the same period in 2005. Other expense for the nine months ended September 30, 2006 was approximately $0.1 million compared to $0.3 million for the same period in 2005. The change in other expense was primarily due to the adjustments related to foreign currency transactions in the periods. MINORITY INTEREST. Minority interest for the three and nine months ended September 30, 2006 was $65,000 and $106,000, respectively. Minority interest represents Third Wave Japan's minority investors' share of the equity and earnings of the subsidiary. LIQUIDITY AND CAPITAL RESOURCES Since our inception, we have financed our operations primarily through private placements of equity securities, research grants from federal and state government agencies, payments from strategic collaborators, equipment loans, capital leases, product sales, a convertible note and an initial public offering. As of September 30, 2006, we had cash and cash equivalents and short-term investments of $33 million. Net cash used in operations for the nine months ended September 30, 2006 was $10.7 million, compared to $12.7 million in the corresponding period in 2005. The change was primarily due to lower operating losses. Net cash provided by investing activities for the nine months ended September 30, 2006 was $8.8 million, compared to net cash used of $0.9 million in the corresponding period in 2005. Investing activities included capital expenditures of $0.6 million in the nine months ended September 30, 2006 versus $0.3 million for the same period in 2005. Investing activities in the nine months ended September 30, 2006 included the payment on license fee arrangements of $0.7 million and a change in the restricted cash balance of $0.8 million. Investing activities in the nine months ended September 30, 2005 also included proceeds from the sale of equipment of $0.2 million. In addition, net cash provided by investing activities included $9.3 million from the maturity of short term investments in the nine months ended September 30, 2006, compared to cash usage of $0.8 million to purchase short-term investments in 2005. 17 Net cash provided by financing activities was $5.4 million in the nine months ended September 30, 2006 compared to $0.4 million in 2005. Cash provided by financing activities in the nine months ending September 30, 2006 consisted of proceeds from the sale of common stock under the Company's employee stock purchase plan and stock option plans of $0.7 million compared to $0.7 million in the corresponding period of 2005. In the nine months ended September 30, 2006, $0.3 million was used to repay debt, compared to $0.1 million in the same period in 2005. Additionally, in the nine months ended September 30, 2006 and 2005, $107,000 and $71,000 was used for capital lease obligations, respectively. Financing activities in the nine months ended September 30, 2005 also included proceeds from long-term debt of $0.8 million and the repurchase of common stock for treasury of $0.9 million. Financing activities in the nine months ended September 30, 2006 also included proceeds from a minority equity investment in our Japan subsidiary of $5.1 million. The proceeds from the equity investment are required to be used in the operations of our Japan subsidiary. The Company has three notes payable to a bank in the original amounts of $200,000, $270,000, and $800,000. These notes have respective final maturity dates of July 1, 2007, October 1, 2009, and July 1, 2008, bear annual interest at 4.25%, 4.93%, and 5.2%, respectively, and require monthly principal and interest payments. The borrowings under the notes payable are secured by short-term investments consisting of certificates of deposit in the aggregate amount of $775,000. The Company has an available and unused $1,000,000 letter of credit with the same bank that expires on September 1, 2007. We believe that current cash reserves together with our ability to generate cash through operations, financing activities and other sources will be sufficient to support short-term and long-term liquidity requirements for current operations (including annual capital expenditures). However, we cannot assure you that our business or operations will not change in a manner that would consume available resources more rapidly than anticipated. We also cannot assure you that we will not require substantial additional funding before we can achieve profitable operations. Our capital requirements depend on numerous factors, including the following: - our progress with our research and development programs; - the needs we may have to pursue FDA clearances or approvals of our products; - our level of success in selling our products and technologies; - our ability to establish and maintain successful collaborative relationships; - the costs we incur in securing intellectual property rights, whether through patents, licenses or otherwise; - the costs we incur in enforcing and defending our patent claims and other intellectual property rights; - the need to respond to competitive pressures; - the possible acquisition of complementary products, businesses or technologies; and - the timing of capital expenditures CONTRACTUAL OBLIGATIONS During the quarter ended September 30, 2006 we amended our facility lease. As a result of the amendment, our operating lease obligations have changed as follows (in thousands): FOURTH 2011 AND TOTAL QUARTER 2006 2007-2008 2009-2010 THEREAFTER ---------- ------------ ---------- ---------- ---------- Pre-amendment operating lease obligation $ 10,481 $ 470 $ 3,986 $ 4,311 $ 1,714 (Decrease)/increase in obligation $ 542 $ (152) $ (291) $ (1,396) $ 2,381 Post-amendment operating lease obligation $ 11,023 $ 318 $ 3,695 $ 2,915 $ 4,095 18 FORWARD-LOOKING STATEMENTS This Form 10-Q contains forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and Section 27A of the Securities Act of 1933, as amended. When used in this Form 10-Q the words "believe," "anticipates," "intends," "plans," "estimates," and similar expressions are forward-looking statements. Such forward-looking statements contained in this Form 10-Q are based on current expectations. Forward-looking statements may address the following subjects: results of operations; customer growth and retention; development of technologies; losses or earnings; operating expenses, including, without limitation, marketing expense, litigation expense, and technology and development expense; and revenue growth. We caution investors that there can be no assurance that actual results, outcomes or business conditions will not differ materially from those projected or suggested in such forward-looking statements as a result of various factors, including, among others, our limited operating history, unpredictability of future revenues and operating results, competitive pressures and also the potential risks and uncertainties discussed under the heading "Overview" in the Management's Discussion and Analysis of Financial Condition and Results of Operations section of this Form 10-Q and in the "Risk Factors" and Management's Discussion and Analysis of Financial Condition and Results of Operations sections of our annual report on Form 10-K for the fiscal year ended December 31, 2005 filed with the Securities and Exchange Commission, which factors are specifically incorporated herein by this reference. You should also carefully consider the factors set forth in other reports or documents that we file from time to time with the Securities and Exchange Commission. Except as required by law, we undertake no obligation to update any forward-looking statements. We expressly disclaim any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in our expectations with regard thereto or any change in events, conditions, or circumstances on which any such statements are based. ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK Our exposure to market risk is currently confined to changes in foreign exchange and interest rates. Our exposure to market risk was discussed in the Quantitative and Qualitative Disclosures About Market Risk section of our annual report on Form 10-K for the fiscal year ended December 31, 2005 filed with the Securities and Exchange Commission. There have been no material changes to such exposures during the third quarter of 2006. ITEM 4. CONTROLS AND PROCEDURES As required by Rule 13a-15(b) under the Securities Exchange Act of 1934, the Company's management, including our Chief Executive Officer and Chief Financial Officer, conducted an evaluation as of the end of the period covered by this report, of the effectiveness of the Company's disclosure controls and procedures as defined in Rule 13a-15(e) under the Securities Exchange Act of 1934. Based on that evaluation, our Chief Executive Officer and Chief Financial Officer concluded that the Company's disclosure controls and procedures were effective as of the end of the period covered by this report. There have been no significant changes during the period covered by this report in the Company's internal control over financial reporting that have materially affected, or are reasonably likely to materially affect, internal controls over financial reporting. As a result of our review of Stock Option Grants and Procedures (see Footnote 3 to the financial statements), subsequent to the period covered by this report we modified our procedures for granting stock options to ensure correct measurement dates are used in the future. PART II - OTHER INFORMATION ITEM 1. LEGAL PROCEEDINGS. From time to time, we may be involved in litigation relating to claims arising out of our operations in the usual course of business. In September 2004, we filed a suit against Stratagene Corporation in the United States District Court for the Western District of Wisconsin. The complaint alleged patent infringement of two of our patents concerning our proprietary Invader(R) technology by Stratagene's sale of its QPCR and QRTPCR Full Velocity products. The case was tried before a jury in August 2005, and the jury found that Stratagene willfully infringed our patents and that our patents were valid. The jury awarded us $5.29 million in damages. The Court subsequently entered a permanent injunction barring Stratagene from making, selling or offering to sell its Full Velocity QPCR and QRT-PCR products and any other products that practice our patented Invader(R) methods. In December 2005, the Court tripled the damages award to $15.9 million and ruled that Stratagene must pay attorney fees of $4.2 million. In January 2006, the Court awarded additional interest on the damages award in the amount of $485,716, increasing the total damages amount to $16.4 million. Also in January 2006, Stratagene posted a $21 million civil bond to stay payment of the judgment while it conducts its appeal. Stratagene has appealed the verdict, the award of enhanced damages, and the award of attorneys' fees and costs to the Court of Appeals for the Federal Circuit in Washington, D.C. Appellate briefing was completed on July 10, 2006. Oral arguments before the 19 Appellate court are set for December 7, 2006. In May 2005, Stratagene Corporation filed suit against us in the United States District Court for the District of Delaware. The complaint alleges patent infringement of claims of two Stratagene patents relating to our Invader Plus(R) chemistry. The complaint was served on us in September 2005. Recently, at the request of both parties, the Court rescheduled the trial date to April 7, 2008. In October 2005, we filed a declaratory judgment suit in the United States District Court for the Western District of Wisconsin against Digene Corporation seeking a ruling that our HPV ASRs do not infringe any valid claims of Digene's human papillomavirus related patents. In January 2006, we reached an agreement with Digene to dismiss the suit without prejudice. We also agreed that neither party would file a suit against the other relating to the Digene HPV patents for one year. The Company intends to vigorously pursue its infringement claims against third parties and to vigorously defend itself against infringement claims brought against it by third parties. There can be no assurance, however, that the Company will prevail in these proceedings and should the outcome of any of these actions be unfavorable, the Company's business, financial condition, results of operations and cash flows could be materially adversely affected. ITEM 1A. RISK FACTORS There have been no material changes in our risk factors from those disclosed in our Form 10-K for the fiscal year ended December 31, 2005 filed with the Securities and Exchange Commission. ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS. - None. ITEM 3. DEFAULTS UPON SENIOR SECURITIES - None. ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS -- None. ITEM 5. OTHER INFORMATION. - None. ITEM 6. EXHIBITS The exhibits required to be filed as a part of this Report are listed in the Exhibit Index. 20 SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. THIRD WAVE TECHNOLOGIES, INC. Date: November 8, 2006 /s/ Kevin T. Conroy ----------------------------------------- Kevin T. Conroy, Chief Executive Officer Date: November 8, 2006 /s/ Maneesh K. Arora ----------------------------------------- Maneesh K. Arora, Chief Financial Officer 21 EXHIBIT INDEX EXHIBIT NO. DESCRIPTION INCORPORATED BY REFERENCE TO - ----------- ----------- ---------------------------- 10.1 Amendment Two to Lease dated September 1, 2006, by and between University Research Park, Inc. and Third Wave Technologies, Inc. 31.1 CEO's Certification Pursuant to Section 302 of the Sarbanes Oxley Act of 2002 31.2 CFO's Certification pursuant to Section 302 of the Sarbanes Oxley Act of 2002. 32 CEO and CFO Certification pursuant to 18 U.S.C. Section 1350, of Chapter 63 of Title 18 of the United States Code 22