PROSPECTUS SUMMARY

The following is a summary which highlights selected information contained in this document. It may not contain all of the information that is important to you. You are urged to carefully read this entire document and the other documents which are annexes to this prospectus/offer to exchange or incorporated herein by reference in order to fully understand the Offer, including the sections entitled “Where You Can Find More Information” on page 106 and “Risk Factors” on page 32.

The Offer (See page 53)

Under the terms of the Offer, each CombiMatrix Series F warrant holder will receive, for each outstanding CombiMatrix Series F warrant to acquire one share of CombiMatrix common stock validly tendered and not withdrawn in the Offer, 0.3056 of a share of Invitae common stock, or the Warrant Exchange Ratio, subject to the procedures described in this document and the related letter of transmittal, and with cash issued in lieu of fractional shares of Invitae common stock (which constitutes the “Offer”). The Warrant Exchange Ratio was calculated as the quotient (rounded to the nearest ten-thousandth) obtained by dividing $2.90 by the average closing price of for shares of Invitae common stock on the NYSE for the immediately preceding period of 30 trading days prior to the date of the Merger Agreement, or $9.491, which is referred to in the Merger Agreement as the Invitae Trailing Average Share Value.

Instead of receiving any fractional shares of Invitae common stock to which CombiMatrix Series F warrant holders otherwise would be entitled, tendering CombiMatrix Series F warrant holders will receive a cash payment in lieu of such fractional share equal to the dollar amount (rounded to the nearest whole cent), without interest, determined by multiplying such fraction by $9.491. See the section entitled “The Offer — Cash Instead of Fractional Shares of Invitae Common Stock” for a description of the treatment of fractional shares.

Invitae’s Reasons for the Merger and the Offer (See page 51)

Invitae’s board of directors concluded that the Merger Agreement, the Merger, the stock issuance in connection therewith and the other transaction documents and the transactions contemplated thereby or undertaken in connection therewith, including the Offer, are advisable and in the best interests of Invitae and its stockholders because, among other factors, the transaction provides Invitae with a unique opportunity to expand its business by acquiring a clinical molecular diagnostic laboratory whose focus is on pre-implantation genetic screening, prenatal diagnosis, miscarriage analysis and pediatric developmental disorders.

Purpose of the Offer; The Merger (See page 63)

Pursuant to the Merger Agreement, the successful completion of the Offer, including the satisfaction of the condition to the Offer that at least 90% of the CombiMatrix Series F warrants outstanding immediately prior to the date of the Merger Agreement shall have been validly tendered and not withdrawn prior to the expiration of the Offer, is a precondition to Invitae’s obligation to consummate the Merger. Promptly after completion of the Offer, Invitae intends to consummate a merger of Merger Sub with and into CombiMatrix, with CombiMatrix surviving the Merger as a wholly owned subsidiary of Invite. After the Merger, the former CombiMatrix Series F warrant holders will no longer have any direct ownership interest in the surviving corporation. See the sections entitled “Background of the Merger and the Offer” and “The Merger Agreement” for a more detailed description of the events leading up to the proposed Merger and Offer and the terms and conditions of the Merger Agreement.

In the Merger, the CombiMatrix Series F warrants held by warrant holders that do not participate in the Offer will be assumed by Invitae in accordance with their terms and converted into warrants to purchase shares of Invitae common stock, with the exercise price and the number of shares of Invitae common stock subject to such

warrants being adjusted appropriately to reflect the merger exchange ratio, or the Merger Exchange Ratio, as described below.

Under the terms of the Offer, each CombiMatrix Series F warrant holder will receive, for each outstanding CombiMatrix Series F warrant to acquire one share of CombiMatrix common stock validly tendered and not withdrawn in the Offer a fraction of a share of Invitae common stock equal to Warrant Exchange Ratio, subject to the procedures described in this document and the related letter of transmittal.

Material U.S. Federal Income Tax Consequences of the Offer (See page 59)

Invitae and CombiMatrix intend the Offer, together with the Merger, to qualify as a reorganization within the meaning of Section 368(a) of the Internal Revenue Code of 1986, as amended, or the Code. In general, and subject to the qualifications and limitations set forth in the section entitled “The Offer – Material U.S. Federal Income Tax Consequences of the Offer,” if the Offer, together with the Merger, qualifies as a “reorganization” within the meaning of Section 368(a) of the Code, the material U.S. federal income tax consequences to U.S. Holders (as defined in the section entitled “The Offer – Material U.S. Federal Income Tax Consequences of the Offer”) of CombiMatrix Series F warrants will be as follows:

Tax matters are very complicated, and the tax consequences of the Offer to a particular CombiMatrix Series F warrant holder will depend on such warrant holder’s circumstances. Accordingly, you are strongly urged to consult your tax advisor for a full understanding of the tax consequences of the Offer to you, including the applicability and effect of federal, state, local and non-U.S. income and other tax laws.

Conditions That Must Be Satisfied or Waived for the Offer to Occur (See page 65)

Invitae currently expects to complete the Offer in the fourth quarter of 2017. However, as more fully described in this document, the obligations of Invitae to complete the Offer are conditioned upon a number of items being satisfied or, where legally permissible, waived, including the following:

Subject to the provisions of the Merger Agreement, the conditions to the Offer are for the sole benefit of Invitae and may be asserted by Invitae regardless of the circumstances or may be waived by Invitae, by express and specific action to that effect, in whole or in part at any time and from time to time on or prior to the Expiration Date, except that the conditions relating to receipt of any approvals from any governmental entity may be asserted at any time prior to Invitae’s acceptance of CombiMatrix Series F warrants for exchange pursuant to the Offer.

Expiration of the Offer (See page 54)

The Offer is scheduled to expire at 12:00 midnight, New York City time, on November 13, 2017, which is the Initial Expiration Date, unless further extended by Invitae. Any extension, delay, termination, waiver or amendment of the Offer will be followed as promptly as practicable by public announcement thereof to be made

no later than 9:00 a.m., New York City time, on the next business day after the previously scheduled Expiration Date. “Expiration Date” means the Initial Expiration Date, unless and until Invitae has extended the period during which the Offer is open, in which event the term “Expiration Date” means the latest time and date at which the Offer, as so extended by Invitae, will expire.

Extension, Termination and Amendment (See page 54)

Subject to the provisions of the Merger Agreement and the applicable rules and regulations of the SEC, Invitae may from time to time extend the Offer for one or more periods, including if, at the scheduled Expiration Date, any of the conditions of the Offer shall not have been satisfied or waived until such time as such conditions are satisfied or waived. Invitae shall extend the Offer for any period required by any rule, regulation, interpretation or position of the SEC or the staff of the SEC applicable to the Offer.

Invitae will effect any extension, termination, amendment or delay by giving oral or written notice to the exchange agent and by making a public announcement as promptly as practicable thereafter as described under the section entitled “The Offer — Extension, Termination and Amendment.” In the case of an extension, any such announcement will be issued no later than 9:00 a.m., New York City time, on the next business day following the previously scheduled Expiration Date. Subject to applicable law (including Rules 14d-4(c) and 14d-6(d) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, which require that any material change in the information published, sent or given to CombiMatrix Series F warrant holders in connection with the Offer be promptly disseminated to warrant holders in a manner reasonably designed to inform them of such change) and without limiting the manner in which Invitae may choose to make any public announcement, Invitae assumes no obligation to publish, advertise or otherwise communicate any such public announcement of this type other than by issuing a press release over the news wire. During any extension, CombiMatrix Series F warrants previously tendered and not properly withdrawn will remain subject to the Offer, subject to the right of each CombiMatrix Series F warrant holder to withdraw previously tendered CombiMatrix Series F warrants.

Subject to applicable SEC rules and regulations, Invitae also reserves the right at any time or from time to time on or prior to the Expiration Date to waive any condition identified as subject to waiver in the section entitled “The Offer — Conditions of the Offer” by giving oral or written notice of such waiver to the exchange agent.

No subsequent offering period will be available following the expiration of the Offer.

Withdrawal Rights (See page 56)

Tendered CombiMatrix Series F warrants may be withdrawn at any time prior to the Expiration Date by registered holders of Series F warrants. If Series F warrants are held in “street name” through a broker, dealer, commercial bank, trust company or other nominee, the warrant holder should contact the broker or other nominee for their specific requirements as they may establish a deadline before the expiration of the Offer by which withdrawal instructions must be provided. Additionally, if Invitae has not agreed to accept the CombiMatrix Series F warrants for exchange on or prior to November 13, 2017, CombiMatrix Series F warrant holders may thereafter withdraw their CombiMatrix Series F warrants from tender at any time after such date until Invitae accepts the CombiMatrix Series F warrants for exchange. Once Invitae accepts CombiMatrix Series F warrants for exchange pursuant to the Offer, all tenders not previously withdrawn become irrevocable.

Procedure for Tendering (See page 56)

To validly tender CombiMatrix Series F warrants pursuant to the Offer, registered holders of CombiMatrix Series F warrants must:

CombiMatrix Series F warrant holders who hold such warrants in “street name” through a broker, dealer, commercial bank, trust company or other nominee, and who desire to tender their CombiMatrix Series F warrants pursuant to the Offer, should instruct their broker or other nominee to tender their Series F warrants in the Offer prior to the Expiration Date and within the time period provided by the broker or other nominee. The broker, dealer, commercial bank, trust company or other nominee may establish a deadline before the expiration of the Offer by which you must provide it with instructions to tender. Please contact your broker or other nominee for their specific requirements.

Exchange of CombiMatrix Series F warrants; Delivery of Shares of Invitae Common Stock and Cash Instead of Fractional Shares (See page 55)

Upon the terms and subject to the conditions of the Offer (including, if the Offer is extended or amended, the terms and conditions of any extension or amendment), promptly following the Expiration Date, Invitae will accept for exchange, and will exchange, all CombiMatrix Series F warrants validly tendered and not withdrawn prior to the Expiration Date. Invitae will deliver the consideration for your validly tendered and not properly withdrawn CombiMatrix Series F warrants by depositing the stock and any cash consideration therefor with the exchange agent, which will act as your agent for the purpose of receiving the Offer consideration from Invitae and transmitting such consideration to you if you are a registered Series F warrant holder.

Comparative Market Price Data and NASDAQ Capital Market Listing (See pages 27 and 64)

Shares of Invitae common stock are listed on the NYSE under the symbol “NVTA.” The CombiMatrix Series F warrants are currently listed on the NASDAQ Capital Market under the symbol “CBMXW.” However, in connection with the completion of the Offer and the Merger, CombiMatrix and Invitae intend to make the appropriate filings to delist any remaining unexchanged CombiMatrix Series F warrants from trading on the NASDAQ Capital Market, presuming any such unexchanged warrants will qualify for delisting. The CombiMatrix Series F warrants that are not validly tendered in the Offer, if any, and that remain outstanding and unexercised at the time of the Merger will be assumed by Invitae in accordance with their terms and converted into a warrant to purchase shares of Invitae common stock, with the exercise price and the number of shares of Invitae common stock subject to such warrants being adjusted appropriately to reflect the Merger Exchange Ratio. It is currently anticipated that, at the closing of the Merger, the Merger Exchange Ratio would be between approximately 0.91 and 0.84 shares of Invitae common stock. The Merger Exchange Ratio is determined pursuant to a formula in the Merger Agreement and described in this prospectus/offer to exchange, and the estimate of the Merger Exchange Ratio is subject to adjustment. For example, the estimated Merger Exchange Ratio of 0.91 was calculated assuming that 100% of the CombiMatrix Series F warrants are exchanged in the Offer. Based on the average closing price of $9.491 per share of Invitae common stock on the NYSE for the 30 trading days prior to July 31, 2017, the date on which the Merger Agreement was executed, and estimated CombiMatrix net cash of negative

$0.8 million (the calculation of which includes a reduction for CombiMatrix transaction bonuses payable), the estimated Merger Exchange Ratio represented $8.60 in value for each share of CombiMatrix common stock. If, instead of being exchanged, 100% of the CombiMatrix Series F warrants were exercised prior to the Merger, the Merger Exchange Ratio would be reduced to 0.84, representing $8.00 in value for each share of CombiMatrix common stock, based on estimated CombiMatrix net cash of negative $2.3 million (which excludes warrant exercise proceeds). Alternatively, if none of the CombiMatrix Series F warrants are exchanged in the Offer or exercised prior to the Merger and all such warrants are assumed by Invitae, although Invitae’s obligation to proceed with the Merger is subject to a participation level in the Offer of at least 90% as described in this prospectus/offer to exchange, the Merger Exchange Ratio would be reduced to 0.87, representing $8.25 in value for each share of CombiMatrix common stock, based on estimated CombiMatrix net cash of negative $0.7 million. These dollar values may fluctuate higher or lower prior to the closing of the Merger depending on fluctuations in the price of Invitae common stock on the NYSE. See the sections entitled “The Merger Agreement — Merger Consideration and Exchange Ratio” and “The Merger Agreement — Determination of CombiMatrix’s Net Cash; Merger Consideration Sensitivity Analysis” for additional factors that may affect the Merger Exchange Ratio. Invitae does not intend to list such warrants for trading on any national stock exchange.

On July 31, 2017, the date of the public announcement of Invitae’s proposal to acquire CombiMatrix, the closing sales price of Invitae common stock on the NYSE was $9.28 and the closing sales price of CombiMatrix Series F warrants on the NASDAQ Capital Market was $1.25. On September 27, 2017 the last practicable trading day before the date of this document, the closing sales price of Invitae common stock on the NYSE was $9.11 and the closing sales price of CombiMatrix Series F warrants on the NASDAQ Capital Market was $2.38. CombiMatrix Series F warrant holders should obtain current market quotations for Invitae common stock and CombiMatrix Series F warrants before deciding whether to tender CombiMatrix Series F warrants in the Offer.

See the sections entitled “Comparative Market Prices and Dividends” and “The Offer – Effect of the Offer on the Market for CombiMatrix Series F warrants; NASDAQ Capital Market Listing; Registration Under the Exchange Act; Margin Regulations.”

Regulatory Approvals (See page 89)

Invitae is not aware of any governmental license or regulatory permit that appears to be material to CombiMatrix’s business that might be adversely affected by Invitae’s acquisition of CombiMatrix Series F warrants pursuant to the Offer or, except as described below, of any approval or other action by any government or governmental administrative or regulatory authority or agency, domestic or foreign, that would be required for Invitae’s acquisition or ownership of CombiMatrix Series F warrants pursuant to the Offer. Pursuant to the Merger Agreement, Invitae and CombiMatrix have agreed to cooperate and use commercially reasonable efforts to obtain all regulatory approvals required to complete the transactions contemplated by the Merger Agreement, including the Offer. Invitae must comply with applicable federal and state securities laws and the rules and regulations of the NYSE in connection with the issuance of shares of Invitae common stock upon completion of the Offer and the filing of this prospectus/offer to exchange and other documents with the SEC.

The Merger Agreement also provides that CombiMatrix and Invitae will file any notification and report forms required to be filed under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended, and respond as promptly as practicable to any inquiries or requests received from the Federal Trade Commission or the Department of Justice for information or documentation or any inquiries or requests received from any other governmental body in connection with antitrust or competition matters.

Interests of Certain CombiMatrix Directors and Officers (See page 67)

In considering whether to tender your CombiMatrix Series F warrants, you should recognize that some of the members of management and of the CombiMatrix board of directors may have interests in the Merger and the Offer that differ from, or are in addition to, their interests as CombiMatrix stockholders. These interests include:

These interests are further described in the section entitled “The Offer — Interests of Certain CombiMatrix Directors and Officers.”

Comparison of Rights of Invitae and CombiMatrix Stockholders (See page 97)

Upon the completion of the Merger and the Offer, CombiMatrix Series F warrant holders who tender in the Offer will become holders of Invitae common stock. The rights associated with Invitae common stock are different from the rights associated with CombiMatrix common stock. The differences are described in more detail in the section entitled “Comparison of Rights of Invitae and CombiMatrix Stockholders.”

The Companies

Invitae Corporation (See page 38)

Invitae’s mission is to bring comprehensive genetic information into mainstream medical practice to improve the quality of healthcare for billions of people. Invitae’s goal is to aggregate most of the world’s hereditary genetic tests into a single service with higher quality, faster turnaround time and lower pricing than many single gene tests today. Invitae was founded on four core principles: patients should own and control their own genetic information; healthcare professionals are fundamental in ordering and interpreting genetic information; driving down the price of genetic information will increase its clinical and personal utility; and genetic information is more valuable when shared. Invitae utilizes an integrated portfolio of laboratory processes, software tools and informatics capabilities to process DNA-containing samples, analyze information about patient-specific genetic variation and generate test reports for clinicians and their patients. Invitae currently has more than 20,000 genes in production and provides a variety of diagnostic tests that can be used in multiple indications. Invitae’s tests include multiple genes associated with hereditary cancer, neurological disorders, cardiovascular disorders, pediatric disorders, metabolic disorders and other hereditary conditions, as well as recently acquired capabilities in preimplantation and carrier screening for inherited disorders. Invitae now provides comprehensive genetic information for every stage of life, from preconception through adult diagnostics.

Invitae common stock is currently listed on the New York Stock Exchange under the symbol “NVTA.”

CombiMatrix Corporation (See page 38)

CombiMatrix is a family health-focused clinical molecular diagnostic laboratory specializing in pre-implantation genetic screening, prenatal diagnosis, miscarriage analysis, and pediatric developmental disorders. CombiMatrix strives to provide best-in-class clinical laboratory support to healthcare professionals, allowing them to maximize the clinical utility of their patients’ test results and to optimize patient care. CombiMatrix’s testing focuses on advanced technologies, including single nucleotide polymorphism, or SNP, chromosomal microarray analysis, next-generation sequencing, fluorescent in situ hybridization, or FISH, and high resolution chromosome analysis (also referred to as karyotyping). CombiMatrix’s approach to testing is to offer sophisticated technology along with high quality clinical support to its ordering physicians and their patients. CombiMatrix also owns a one-third minority interest in Leuchemix, Inc., a private drug development company focused on developing a series of compounds to address a number of oncology-related diseases.

CombiMatrix was originally incorporated in October 1995 as a California corporation. In September 2000, CombiMatrix was reincorporated as a Delaware corporation. In August 2007, CombiMatrix became publicly traded on NASDAQ under the symbol “CBMX,” where it is currently listed and traded. The CombiMatrix Series F warrants are listed on NASDAQ under the symbol “CBMXW.” Following completion of the Merger, the CombiMatrix common stock and the CombiMatrix Series F warrants will cease trading on NASDAQ and CombiMatrix will file the appropriate forms with the Securities and Exchange Commission to suspend its reporting obligations under the Securities Exchange Act of 1934, as amended, or the Exchange Act.

Coronado Merger Sub, Inc. (See page 39)

Coronado Merger Sub, Inc., or Merger Sub, is a wholly owned subsidiary of Invitae and was formed solely for the purpose of carrying out the Merger. In the Merger, Merger Sub will merge with and into CombiMatrix and Merger Sub will cease to exist. Merger Sub has engaged in no business activities to date and it has no material assets or liabilities of any kind, other than those incident to its formation and those incurred in connection with the Merger.

Questions about the Offer

CombiMatrix Series F warrant holders should contact Advantage Proxy, Inc., Invitae’s information agent for the Offer, at the following telephone number and email address with any questions about the Offer, or to request additional copies of this document or other documents:

ADVANTAGE PROXY, INC.

PO Box 13581

Des Moines, WA 98198

Telephone: (877) 870-8565 (toll free); (206) 870-8565 (collect)

Email: ksmith@advantageproxy.com

SELECTED HISTORICAL FINANCIAL DATA OF INVITAE

Set forth below are highlights from Invitae’s consolidated financial data as of and for the periods indicated. The historical consolidated financial data presented below for each of the five fiscal years through the period ended December 31, 2016 are derived from the selected financial data included in Invitae’s Annual Report on Form 10-K for the year ended December 31, 2016. The historical consolidated financial data for the six months ended June 30, 2017 are derived from the unaudited condensed consolidated financial statements included in Invitae’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2017.

Invitae’s unaudited condensed consolidated financial statements have been prepared in accordance with U.S. GAAP on the same basis as its audited annual consolidated financial statements and, in the opinion of management, reflect all adjustments, consisting only of normal, recurring adjustments, necessary for the fair presentation of those unaudited interim condensed consolidated financial statements. Invitae’s historical results are not necessarily indicative of the results that may be expected in any future period, and the results for the six months ended June 30, 2017 are not necessarily indicative of results to be expected for the full year ending December 31, 2017 or any other period.

The selected historical consolidated financial data below should be read in conjunction with the section entitled “Risk Factors” and Invitae’s audited annual and unaudited condensed consolidated financial statements and related notes that have been incorporated into this document by reference. See the section entitled “Where You Can Find More Information.”

SELECTED HISTORICAL FINANCIAL DATA OF COMBIMATRIX

Set forth below are highlights from CombiMatrix’s consolidated financial data as of and for the periods indicated. The historical consolidated financial data presented below for each of the five fiscal years through the period ended December 31, 2016 are derived from the consolidated financial statements included in CombiMatrix’s Annual Reports on Form 10-K for the five years ended December 31, 2016 included as Annex B to this prospectus/offer to exchange. The historical consolidated financial data for the six months ended June 30, 2017 are derived from the unaudited interim financial statements included in CombiMatrix’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2017 included as Annex C to this prospectus/offer to exchange.

CombiMatrix’s unaudited interim financial statements have been prepared in accordance with U.S. GAAP on the same basis as its audited annual consolidated financial statements and, in the opinion of management, reflect all adjustments, consisting only of normal, recurring adjustments, necessary for the fair presentation of those unaudited interim consolidated financial statements. CombiMatrix’s historical results are not necessarily indicative of the results that may be expected in any future period, and the results for the six months ended June 30, 2017 are not necessarily indicative of results to be expected for the full year ending December 31, 2017 or any other period.

The selected historical consolidated financial data below should be read in conjunction with the section entitled “Risk Factors” and CombiMatrix’s audited annual and unaudited interim consolidated financial statements and related notes that are included within Annex B and Annex C attached to this document. See the section entitled “Where You Can Find More Information.”

UNAUDITED PRO FORMA CONDENSED COMBINED FINANCIAL INFORMATION

The following unaudited pro forma condensed combined balance sheet as of June 30, 2017 and the unaudited pro forma condensed combined statements of operations for the year ended December 31, 2016 and the six months ended June 30, 2017 are based on the separate historical consolidated financial statements of Invitae and CombiMatrix after giving effect to the Merger.

The unaudited pro forma condensed combined balance sheet as of June 30, 2017 combines the balance sheet of Invitae as of June 30, 2017 with the balance sheet of CombiMatrix as of June 30, 2017. The unaudited pro forma condensed combined statement of operations for the year ended December 31, 2016 combines Invitae’s results of operations for the year ended December 31, 2016 with CombiMatrix’s results of operations for the year ended December 31, 2016. The unaudited pro forma condensed combined statement of operations for the six months ended June 30, 2017 combines Invitae’s results of operations for the six months ended June 30, 2017 with CombiMatrix’s results of operations for the six months ended June 30, 2017.

The unaudited pro forma condensed combined balance sheet as of June 30, 2017 assumes the Merger and related events had been consummated on June 30, 2017. The unaudited pro forma condensed combined statements of operations for the year ended December 31, 2016 and the six months ended June 30, 2017 give pro forma effect to the Merger and related events as if they had been consummated on January 1, 2016, the beginning of Invitae’s 2016 fiscal year. The historical financial information has been adjusted to give effect to pro forma adjustments that are (i) directly attributable to the Merger, (ii) factually supportable, and (iii) with respect to the unaudited pro forma condensed combined statements of operations, expected to have a continuing impact on the combined entity’s consolidated results. The unaudited pro forma condensed combined statements of operations do not include the impact of any operating synergies that may result from the Merger.

The Merger will be accounted for as an acquisition by Invitae, and Invitae was determined to be the accounting acquirer. See the section entitled “The Offer — Accounting Treatment” for more information. In summary, Invitae has concluded that Invitae is the accounting acquirer based on its evaluation of the facts and circumstances of the acquisition. The purpose of the Merger is for Invitae to acquire the business of CombiMatrix so that Invitae can expand its products and services offerings. Invitae is the larger of the two entities and will be the operating company within the combining companies. Invitae’s board members will continue to hold all of the seats on the Invitae board of directors and CombiMatrix stockholders do not have any board appointment rights. Invitae’s senior management will be continuing as the senior management of the combined company.

The completion of the Merger is subject to various closing conditions, including, among others, (i) approval by the CombiMatrix stockholders of the proposal to approve and adopt the Merger Agreement, or the Merger Proposal, (ii) completion of the Offer (which may be completed at the same time as the Merger is completed), which requires the participation by holders of at least 90% of the CombiMatrix Series F warrants outstanding immediately prior to the date of the Merger Agreement, (iii) the accuracy of the representations and warranties of CombiMatrix and Invitae, (iv) the performance by CombiMatrix and Invitae in all material respects of their respective obligations under the Merger Agreement, (v) the effectiveness of the registration statements for the issuance of shares of Invitae common stock in the Merger and Offer, (vi) the repurchase by CombiMatrix of all of its outstanding Series A, Series B, Series C, Series E and PIPE warrants, and (vii) receipt of NYSE listing approval for the shares of Invitae common stock to be issued in the Merger and Offer.

The unaudited pro forma condensed combined financial statements assume that (i) the Merger Proposal is approved by 100% of the CombiMatrix stockholders, (ii) none of the CombiMatrix Series A, Series B, Series C, Series D, Series E, Series F or PIPE warrants are exercised; and (iii) all other Merger-related transactions (e.g., the outstanding CombiMatrix Series F preferred stock is converted into Invitae common stock; the outstanding

CombiMatrix Series A, Series B, Series C, Series E and PIPE warrants are repurchased; and the Offer for CombiMatrix Series F warrants is accepted by 100% of such warrant holders) are consummated.

The unaudited pro forma condensed combined financial statements are presented for informational purposes only. The unaudited pro forma condensed combined financial statements are not necessarily indicative of what Invitae’s financial position or results of operations actually would have been had Invitae completed the Merger with CombiMatrix as of the dates indicated. In addition, the unaudited pro forma condensed combined financial statements do not purport to project the future financial position or operating results of the combined company. You should read this information together with the following:

The unaudited pro forma condensed combined financial information has been compiled in a manner consistent with the accounting policies adopted by Invitae. Invitae believes these accounting policies are similar in most material respects to those of CombiMatrix. Upon completion of the Merger, or as more information becomes available, Invitae will perform a more detailed review of the CombiMatrix accounting policies. As a result of that review, differences could be identified between the accounting policies of the two companies that, when conformed, could have a material impact on the combined financial statements.

INVITAE CORPORATION

UNAUDITED PRO FORMA CONDENSED COMBINED BALANCE SHEET

JUNE 30, 2017

(in thousands)

INVITAE CORPORATION

UNAUDITED PRO FORMA CONDENSED COMBINED STATEMENT OF OPERATIONS

FOR THE YEAR ENDED DECEMBER 31, 2016

(in thousands except per share data)

INVITAE CORPORATION

UNAUDITED PRO FORMA CONDENSED COMBINED STATEMENT OF OPERATIONS

FOR THE SIX MONTHS ENDED JUNE 30, 2017

(in thousands except per share data)

NOTES TO UNAUDITED PRO FORMA CONDENSED

COMBINED FINANCIAL STATEMENTS

1. Description of Transaction and Basis of Presentation

Description of Transaction

On July 31, 2017, Invitae Corporation, (“Invitae”) entered into an Agreement and Plan of Merger and Reorganization (“Merger Agreement”) with CombiMatrix Corporation, (“CombiMatrix”), pursuant to which, among other things, subject to the satisfaction or waiver of the conditions set forth in the Merger Agreement, Coronado Merger Sub, Inc., a wholly owned subsidiary of Invitae, will merge with and into CombiMatrix, with CombiMatrix surviving as a wholly owned subsidiary of Invitae (the “Merger”). The CombiMatrix Merger is intended to qualify for federal income tax purposes as a tax-free reorganization under the provisions of Section 368(a) of the Internal Revenue Code of 1986, as amended (the “Internal Revenue Code”). Invitae is considered to be the acquiring company for accounting purposes in this transaction.

The completion of the Merger is subject to various closing conditions, including, among others, (i) approval by the CombiMatrix stockholders of the Merger Proposal, (ii) completion of the Offer (which may be completed at the same time as the Merger is completed), which requires the participation by holders of at least 90% of the CombiMatrix Series F warrants outstanding immediately prior to the date of the Merger Agreement, (iii) the accuracy of the representations and warranties of CombiMatrix and Invitae, (iv) the performance by CombiMatrix and Invitae in all material respects of their respective obligations under the Merger Agreement, (v) the effectiveness of the registration statements for the issuance of shares of Invitae common stock in the Merger and Offer, (vi) the repurchase by CombiMatrix of all of its Series A, Series B, Series C, Series E and PIPE warrants, and (vii) receipt of NYSE listing approval for the shares of Invitae common stock to be issued in the Merger and Offer.

The unaudited pro forma condensed combined financial statements assume that (i) the Merger Proposal is approved by 100% of the CombiMatrix stockholders, (ii) none of the CombiMatrix Series A, Series B, Series C, Series D, Series E, Series F or PIPE warrants are exercised, and (iii) all other Merger-related transactions (e.g., the CombiMatrix Series F preferred stock is converted into Invitae common stock; the CombiMatrix Series A, Series B, Series C, Series E and PIPE warrants are repurchased; and the Offer for CombiMatrix Series F warrants is accepted by 100% of such warrant holders) are consummated.

Basis of Presentation

The accompanying unaudited pro forma condensed combined financial statements were prepared in accordance with the regulations of the Securities and Exchange Commission (SEC) and are intended to show how the Merger might have affected the historical financial statements if the Merger had been completed on January 1, 2016 for the purposes of the condensed combined statements of operations, and as of June 30, 2017 for purposes of the condensed combined balance sheet. Both Invitae and CombiMatrix’s historical audited and unaudited financial statements were prepared in accordance with U.S. GAAP and are presented in thousands of U.S. dollars. The historical CombiMatrix financial statements included within the unaudited pro forma condensed combined balance sheet and statements of operations include certain reclassifications that were made to conform CombiMatrix’s financial statement presentation to that of Invitae.

The unaudited pro forma condensed combined statements of operations also include certain acquisition accounting adjustments, including items expected to have a continuing impact on the results of the combined company, such as increased amortization expense on acquired intangible assets. The unaudited pro forma condensed combined statements of operations do not include the impacts of any operating synergies that may result from the Merger or any related restructuring costs that may be contemplated.

Based on the terms of the Merger, Invitae is deemed to be the acquiring company for accounting purposes and the transaction represents a business combination pursuant to Financial Accounting Standards Board Accounting Standards Codification Topic 805, Business Combinations.

The proposed transaction is accounted for using the acquisition method of accounting. Under the acquisition method of accounting, identifiable assets and liabilities of CombiMatrix, including identifiable intangible assets, are recorded based on their estimated fair values as of the date of the closing of the proposed transaction. Goodwill is calculated as the difference between the estimated acquisition consideration and fair values of identifiable net assets acquired. Invitae has not completed a full, detailed valuation analysis necessary to determine the fair values of CombiMatrix’s identifiable assets to be acquired and liabilities to be assumed. As of the date of this prospectus/offer to exchange, the valuation studies necessary to estimate the fair values of the assets acquired and liabilities assumed have been performed based on publicly available benchmarking information as well as a variety of other assumptions, including market participant assumptions, as there are limitations on the type of information that can be exchanged between Invitae and CombiMatrix at this time. Until the Merger is complete, all the relevant information will not be known. Differences between preliminary estimates and the final acquisition accounting will occur. For purposes of these unaudited pro forma combined condensed financial statements, the acquisition consideration is estimated assuming the 30-day trailing average closing price of $9.49 for Invitae’s common stock on July 31, 2017, the date the Merger Agreement was executed, assuming that the transaction closed on July 31, 2017. Total consideration transferred as of this date is estimated to be $31.5 million. Total acquisition consideration is estimated to be $31.0 million, which excludes post-combination expense of $488,000. The pro forma adjustments described below were developed based on Invitae’s management’s assumptions and estimates, including assumptions relating to the consideration paid and the fair value of the identifiable assets acquired and liabilities assumed from CombiMatrix. The amounts of the acquisition consideration, assets acquired and liabilities assumed that will be used in acquisition accounting will be based on their respective fair values as determined at the time of closing, and may differ significantly from these preliminary estimates.

2. Preliminary Purchase Price

The estimated preliminary consideration for the acquisition is as follows (in thousands):

The fair value of the total acquisition transferred is calculated using the closing price of Invitae’s common stock on July 31, 2017. Invitae will issue approximately 2,845,100 shares of common stock in exchange for CombiMatrix’s (i) common stock, (ii) outstanding and unexercised in-the-money stock options and outstanding restricted stock. Invitae will also issue approximately 631,633 shares of common stock in exchange for CombiMatrix’s Series F warrants.

The estimated fair values of outstanding in-the-money stock options and restricted stock units is approximately $33,000 and $1.1 million, respectively, of which $25,000 and $463,000, respectively, will be recognized as expenses immediately upon the closing of the transaction.

The fair value of the assets acquired and liabilities assumed, assuming the Merger has closed on June 30, 2017, are summarized below (in thousands):

The application of the acquisition method of accounting is dependent upon the completion of a full, detailed valuation analysis that has yet to be completed. The estimated values of the assets acquired and liabilities assumed will remain preliminary until after closing of the transaction, at which time Invitae management will determine the fair values of assets acquired and liabilities assumed. The final determination of the purchase price allocation is anticipated to be completed as soon as practicable after completion of the transaction and will be based on the fair values of the assets acquired and liabilities assumed as of the transaction closing date. The final amounts allocated to assets acquired and liabilities assumed could differ significantly from the amounts presented in the unaudited pro forma condensed combined financial statements for the reasons described in Note 1.

3. Pro Forma Adjustments

Pro forma adjustments are necessary to reflect the acquisition consideration exchanged and to adjust amounts related to the tangible and intangible assets and liabilities of CombiMatrix to a preliminary estimate of their fair values, and to reflect the impact on the statements of operations of the proposed transaction as if the companies had been combined during the periods presented therein. The pro forma adjustments included in the unaudited pro forma condensed combined financial statements are as follows: