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                                               *Confidential Treatment Requested

                                                                   EXHIBIT 10.12

                      COLLABORATIVE DEVELOPMENT AGREEMENT

This Collaborative Development Agreement (the "Agreement") effective as of June
21, 2000 (the "Effective Date") outlines the terms and conditions pursuant to
which Third Wave Technologies, Inc. ("TWT") is willing to develop and transfer
to Novartis Pharmaceuticals Corporation (together with Novartis Pharma AG,
Novartis AG and all of its affiliates including GNF "Novartis") 10,000 unique
genotyping assays based on TWT's proprietary Invader(R) assay platform (each
such assay an "Assay") for detection of certain single nucleotide polymorphisms
(SNPs) mutually designated by the parties to be approximately evenly spaced over
the human genome. Each assay shall be specific for one SNP.

1.      Invader SNP Assays: Each Assay (FRET-detection format) will be comprised
        of the following:

        A. Primary Probe Set including a SNP-specific Primary Invader Probe and
        Primary Probes for each allele of the SNP for which TWT will perform:
        (i) oligonucleotide probe design, (ii) probe synthesis, (iii) probe
        purification (as necessary) and (iv) probe set quality control and
        packaging; and

        B. Standard Invader Reagent Set including: (i) purified Secondary
        Signal/target probe complex oligonucleotide, (ii) Cleavase enzyme, and
        (iii) buffers. All together in each well of a 384-well microtiter plate.

2.      Transfer: TWT will transfer each of the 10,000 Assays to Novartis FOB
        (UCC) TWT's facilities Madison, WI, in accordance with a mutually agreed
        schedule. Each Assay so transferred will be in 384-well format and
        include materials sufficient to perform 384 genotype determinations in
        accordance with TWT's standard protocols therefor. It being understood
        that the total number of determinations to be transferred hereunder will
        be 3,840,000. TWT will use its best efforts to transfer the first 5,000
        Assays to Novartis within 6 months of the Effective Date and the
        remaining 5,000 Assays within 1 year of the Effective Date.

3.      Payment:

        A. Initiation Payment. In consideration of TWTs development of the
        Assays, Novartis will pay to TWT $475,000.00 within 10 days of the
        Effective Date which total amount will be creditable against 1/2 of the
        amounts due on transfer of the Assays below.

        B. Assay Payments. In consideration of TWT transferring the Assays,
        Novartis will pay to TWT [****] per genotyping determination ([****] per
        384 determinations) plus any costs incident to the transfer initially
        paid by TWT but to be borne by Novartis hereunder, within 30 days of
        receipt of the invoice therefor. It being understood that the total
        payments for Assays hereunder will be [****].

4.      Use: All Assays will be used by Novartis solely for its own internal R&D
        applications on a world-wide basis.

5.      Intellectual Property:

        A. General. All right, title and interest in and to all Assays
        transferred hereunder will remain vested in TWT. Novartis will own all
        right, title and interest in and to all Inventions. "Invention" means
        any and all discoveries, inventions, information and other subject
        matter (whether patentable or not) made in the course of Novartis' use
        of the Assays hereunder and all intellectual property rights therein.

        B. Improvements. Novartis hereby grants to TWT a non-exclusive, fully
        paid-up, worldwide right and license, with the right to grant and
        authorize sublicenses, in and to improvements, "Improvement" means any
        Invention which comprise an improvement, modification, or derivative of
        the Assays, including without limitation, improvements and enhancements
        to: (i) assay ease of use methodologies, including sample preparation
        methods or procedures; (iii) detection methods and protocols; (iv) data
        collection or analysis; (v) multiplexing methods; or (vi) automation or
        miniaturization methodologies, techniques and equipment.

        C. Diagnostic Rights. Novartis hereby grants to TWT a first right of
        refusal to obtain an exclusive, worldwide license for all Diagnostic
        Applications to any Patent Rights claiming an Invention that Novartis
        wishes to license to a third party for Diagnostic Applications. For such
        purposes the parties agree as follows: (i) Novartis will promptly
        provide to TWT a copy of each US patent application within the Patent
        Rights that Novartis proposes to license to a third party for Diagnostic
        Applications, referencing this paragraph 5 together with such other
        information as TWT may reasonably request, (ii) TWT will have 45 days
        after receipt of the application and information described in clause (i)
        to notify Novartis of its interest in negotiating such license, (iii) if
        TWT so notifies Novartis, the parties will negotiate in good faith for a
        period of not less than 90 days the terms and conditions of such license
        under the Patent Rights, (iv) thereafter, Novartis may offer such
        license under the Patent Rights to third parties on the same terms and
        conditions as offered to TWT, provided that Novartis offer any more
        favorable terms or conditions to TWT first. "Diagnostic Applications"
        means all applications the purpose of which is to report a patient
        result, including without limitation, detection, diagnosis,


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        prognosis or predisposition of disease states and therapeutic monitoring
        applications, in each case whether or not such applications require
        regulatory approval in any particular jurisdiction; and "Patent Rights"
        means all US patent applications and foreign counterpart patent
        applications claiming an Invention, all divisions, continuations,
        continuations-in-part, substitutions, patents of additions thereof and
        all patents issuing on any of the foregoing, together with all
        registrations, reissues, reexaminations or extensions of any kind with
        respect to any of the foregoing patents.

        D. Other. Except as expressly provided herein, nothing herein is to be
        construed as granting a license from one party to the other, under any
        patent or other intellectual property rights owned by such party.

6.      Confidentiality: For a period of five (5) years from the date of this
        Agreement, each of Novartis and TWT agrees that the receiving party
        shall not publish or otherwise disclose and shall not use for any
        purpose any information furnished to it by the other party hereto
        pursuant to this Agreement which if disclosed in tangible form is marked
        "Confidential" or with other similar designation to indicate its
        confidential or proprietary nature, or if disclosed orally is confirmed
        as confidential or proprietary by the party disclosing such information
        at the time of such disclosure ("Confidential Information"). Without
        limiting the foregoing, it is understood that the Assays will be deemed
        to be Confidential Information of TWT whether or not marked as such and
        that any patent application furnished by Novartis to TWT pursuant to
        paragraph 5 shall be deemed to be Confidential Information of Novartis,
        whether or not marked as such. Notwithstanding the foregoing, it is
        understood and agreed that Confidential Information shall not include
        information that, in each case as demonstrated by written documentation:
        (a) was already known to the receiving party, other than under an
        obligation of confidentiality, at the time of disclosure; (b) was
        generally available to the public or otherwise part of the public domain
        at the time of its disclosure to the receiving party; (c) became
        generally available to the public or otherwise part of the public domain
        after its disclosure and other than through any act or omission of the
        receiving party in breach of this Agreement; or (d) was subsequently
        lawfully disclosed to the receiving party by a person other than a party
        hereto or developed by the receiving party without reference to any
        information or materials disclosed by the disclosing party.
        Notwithstanding the foregoing provisions of this paragraph 6 above, each
        party hereto may disclose the other's Confidential Information to the
        extent such disclosure is reasonably necessary, in filing or prosecuting
        patent applications, prosecuting or defending litigation, complying with
        applicable governmental regulations, submitting information to tax or
        other governmental authorities, or in exercising its rights hereunder
        (including granting any permitted sublicenses), provided that if a party
        is legally required to make any such disclosure of another party's
        Confidential Information, to the extent it may legally do so, it will
        give reasonable advance written notice to the latter party of such
        disclosure and, save to the extent inappropriate in the case of patent
        applications, will use its reasonable efforts to secure confidential
        treatment of such Confidential Information prior to its disclosure
        (whether through protective orders or otherwise), This paragraph 6 will
        survive expiration or termination of this Agreement.

7.      Term and Termination. This Agreement will be effective as of the
        Effective Date and will remain in effect for 14 months and may be
        extended by mutual written agreement of the parties hereto. Either party
        may terminate this Agreement on 60 days written notice in the event that
        the other party is in material breach of the Agreement and the other
        party fails cure during such 60-day period. In the event that Agreement
        is terminated by Novartis as a result of TWT's breach, TWT will repay
        the amount paid under paragraph 3A less amounts credited for Assays
        transfered. In the event of expiration or termination of this Agreement
        the provisions of paragraphs 4, 5, 6 and 8 will survive. For avoidance
        of doubt, it is understood that Novartis' right to use information
        arising out of its use of the Assays is perpetual.

8.      General: This Agreement will be governed by and construed in accordance
        with, the laws of the State of New York, without reference to conflicts
        of laws principles. This Agreement sets forth the entire agreement
        between the parties with respect to the subject matter herein and
        supersedes all previous or contemporaneous understandings with respect
        thereto. Nonperformance of any party will be excused to the extent that
        performance is rendered impossible by strike, fire, earthquake, flood,
        governmental acts or orders or restrictions, failure of suppliers, or
        any other reason where failure to perform is beyond the reasonable
        control of the nonperforming party. This Agreement may be amended or any
        right or obligation waived only with a written document signed by
        authorized representatives of the parties. Novartis may not assign or
        otherwise transfer its rights and obligations hereunder without the
        prior written approval of TWT. TWT and Novartis agree not to disclose to
        any third party the financial terms of this Agreement without the prior
        written consent of the other party hereto, except to advisors, investors
        and others on a need-to-know basis under circumstances that reasonably
        ensure the confidentiality thereof, or to the extent required by law.
        Notwithstanding the foregoing, within five (5) days after execution
        hereof, the parties will agree upon and issue a press release describing
        the collaboration of the parties.


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IN WITNESS WHEREOF, the parties hereto have caused this Agreement to he duly
executed and effective as of the Effective Date.

THIRD WAVE TECHNOLOGIES, INC.               NOVARTIS PHARMACEUTICALS CORPORATION


By: /s/ LANCE FORS                          By: /s/ R. M. CALIFRE
   --------------------------                  ---------------------------------
Name:  Lance Fors                              Name:  R. M. Califre
      -----------------------                        ---------------------------
Title: President & CEO                         Title: SVP R&D OPS
      -----------------------                        ---------------------------


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