Document:

<PAGE>

                                                                   Exhibit 10.28

                                   Agreement

                                    between

     Community Technology Fund, Office of Technology Transfer of Community
Technology Fund and Center for Advanced Biotechnology (BU) represented by Matt
Burns, Heather Tullar, Ashley Stevens and Charles Cantor.

                                      and

     Sequenom, San Diego, CA and Sequenom GmbH, Germany represented by Hubert
Koster.

1)   The patents         ***        will be moved from the "Field of Use Limited
License" category to the Exclusive License category, as marked in Exhibit A.

2)   As a precondition of Sequenom submitting payment of all retroactive and
future patent costs according to Section 3, BU will supply to Sequenom copies of
all relevant documents regarding the patent fillings and prosecution of said
cases.

3)   Sequenom agrees that in the case that a license agreement is entered into
between BU and Packard Investments, it will pay retroactive and prospective
patent costs in the amount of *** of the "Field of Use Limited License"
category (estimated through 6/30/97 to be $95,995.00 divided by 2) and 100% of
the "Exclusive License" category (estimated through 6/30/97 to be $80,712.98)
immediately upon receipt of documents described in Section 2.

     Should the License Agreement between BU and Packard not be fully executed
within ten (10) days of this Letter of Agreement, Sequenom agrees to pay the
full cost for retroactive and future patent costs for both the "Field of Use
Limited License" category and the "Exclusive License" category as previously
described. This payment is due immediately upon both delivery of the documents
described in Section 2 and notification of the canceling of the proposed License
Agreement between BU and Packard.

     BU will make a good faith effort to recover a pro rata share of previously
incurred costs for the "Field of Use Limited License" category in future license
agreements and, if successful, will reimburse Sequenom the pro rata share.

4)   The Sponsored Research Agreement will be continued from 9/15/96 through
9/14/98 with payments as listed in the letter from Sequenom dated 9/16/97
attached hereto as Exhibit B.

     *** Portions of this page have been omitted pursuant to a request for
Confidential Treatment and filed separately with the Commission.
<PAGE>

5)   The License Agreement between BU and Sequenom dated 6/1/96 will cover
inventions and patents describing developments in the laboratory of Dr. Charles
Cantor for the duration of the Sponsored Research Agreement in the field of
                                      ***
     ***        This will be clarified by an addendum to the existing license
agreement .
6)   The scientific program of collaboration between Sequenom and BU will be
formulated and continuously updated by the Principal Investigator and Sequenom.

     Agreed in Boston on October 8, 1997

     /s/  illegible
     ------------------------------------
     Sequenom

     /s/  illegible
     ------------------------------------
     Community Technology Fund

     /s/  illegible
     ------------------------------------
     Office of Technology Transfer

     /s/  illegible
     ------------------------------------
     Center for Advanced Biotechnology

     *** Portions of this page have been omitted pursuant to a request for
Confidential Treatment and filed separately with the Commission.
<PAGE>

Invoice
-------

Licensee            Sequenom
Bill Prepared              8/27/97
Law Firm                   Baker & Botts
Agreement Date 7/1/96

Limited Field-of-Use License

<TABLE>
<CAPTION>
          BU Case             Docket                       Services                      Amount
          -------             ------                       --------                      ------
<S>                           <C>                          <C>                           <C>
92-42                         0107                         Inception - 5/15/97           $  14,597.25
92-42                         0124                         Inception - 5/15/97           $  24,354.30
92-42                         0162                         Inception - 5/15/97           $   9,384.62
92-42                         0168                         Inception - 5/15/97           $  28,923.45
92-42B                        0186                         Inception - 5/15/97           $  14,677.37
92-42                         0187                         Inception - 5/15/97           $  17,105.36
92-42                         0215                         Inception - 5/15/97           $   6,347.31
92-42                         0217                         Inception - 5/15/97           $   2,679.20
92-42B                        0228                         Inception - 5/15/97           $   8,283.84
92-42                         0325                         Inception - 5/15/97           $   1,245.45
                              ---------------------------- -----------------------   ------------------
                              Total                                                      $ 127,598.15

Exclusive License

92-42C                        0167                         Inception - 5/15/97           $  22,618.71
92-42C                        0216                         Inception - 5/15/97           $   2,672.64
92-42C                        0276                         Inception - 5/15/97           $  10,010.08
92-42C                        0302                         Inception - 5/15/97           $  13,808.90
---------------------------   ---------------------------- -----------------------   ------------------
                              Total                                                      $  49,110.33

                              Grand Total                                                $ 176,708.48
                              -----------                                            ------------------

                              Payments Received            6/27/97                       $ (19,330.05)
                              ----------------------------
                                                           7/27/97                       $ (19,330.05)
                                                                                     ------------------
                              Balance Due                                                $ 138,048.38
</TABLE>

<PAGE>

September 16, 1997

Charles Cantor
Center for Advanced Biotechnology
Boston University
36 Cummington Street
Boston, MA  02215

Dear Charles,

It was a pleasure having you at our facility in San Diego.

This letter comprises in principle our intention to move forward on a
renegotiated Research Agreement in return for a "field of use" on related
technology developed in your lab. It includes our budget proposal for the
retroactive period including September 1996 through September 1997 and outlines
the budget for September 1997 through September 1998.

The following budget proposals include consideration of the August 29, 1997 memo
from Matt Barber regarding the lab budgets for 9/96 -  9/97 and 9/97 - 9/98.

1996 - 1997 Budget
------------------

Our attached budget proposal for 1996 - 1997 of $112,454 though less than your
budget of $130,903 is a significant increase from our original proposal of
$81,657.  The salary of the lab manager and reduced supplies are the material
items reduced from your proposal.

1997 - 1998 Budget
------------------

Budget restraints require us to reduce your 1997 - 1998 budget proposal.  The
major items deleted include reducing Dr. Cantor's time reduced to 20% and
deleting the Lab Manager and grad student.  The supplies and other expenses were
also reduced by 45%.  The adjusted budget total of $219,013 still represents a
major investment over the coming year.

We hope you view this proposal as a significant commitment to continue our
valuable relationship with Boston University.

Best Regards,

/s/ Steve Zaniboni

Steve Zaniboni
Vice President, Finance & Administration

CC:  H. Koster
     M. Barber

<PAGE>

                                   Sequenom,
                         Boston University Lab Budget
                       September 1996 to September 1997

<TABLE>
<CAPTION>
Salary                                       F.T.E.
<S>                            <C>           <C>            <C>
     C. Cantor - academic      $155,687           10%       $ 15,667
     C. Cantor - summer        $ 53,000           10%       $  5,300
     J. Cantor - annual        $ 32,887           76%       $  5,100
     A. Hatch - annual         $ 25,000           20%       $  5,101
     C. Smith - academic       $ 84,558          4.5%       $  3,805
     C. Smith - summer         $ 28,600          4.5%       $  1,287
     Secretary                 $ 24,312          4.8%       $  1,167

     Total Salary                                           $ 37,327

Fringe
     23.6% rate                                             $  6,809

     Total Salary & Fringe                                  $ 46,138

Direct Costs
Supplies
     Chemicals                               $ 3,738
     Biochemicals                            $ 4,486
     Radioscopes                             $ 2,243
     Photographic                            $   748
     Disposables                             $ 6,230
                                                            $ 17,444

Other Expenses
     Communications                          $   908
     Equip. Maintenance                      $ 1,997
     Publications                            $   320
     Journals & books                        $   160
     Miscellaneous                           $   171
                                                            $  3,557

Total Direct Costs                                          $ 67,137

Indirect Costs                     67.5%                      45,317

Total Direct and Indirect Costs                             $112,454
</TABLE>

<PAGE>

                                   Sequenom,
                         Boston University Lab Budget
                       September 1996 to September 1997

Salary                                            F.T.E
      C. Cantor - academic         $162,533              20%    $  32,507
      C. Cantor - summer           $ 55,120              20%    $  11,024
      J. Graber - annual           $  5,236              75%    $   5,236
      C. Smith - academic          $ 87,707             4.5%    $   3,947
      C. Smith - summer            $ 29,744             4.5%    $   1,338
      Post Doc                     $ 28,747             100%    $  28,747
      Secretary                    $ 24,312             5.5%    $   1,337

      Total Salary                                              $  84,136

Fringe

      23.8% rate                                                $  19,858

      Total Salary & Fringe                                     $ 103,992

Direct Coals
Suppliers
      Chemicals                                    $  5,294
      Biochemicals                                 $  6,353
      Racfiosdopas                                 $  3,176
      Photographic                                 $  1,059
      Disposables                                  $  5,294
                                                                $  21,175

Other Expenses
      Communications                               $  1,426
      Equip. Maintenance                           $  3,137
      Publications                                 $    503
      Journals & books                             $    252
      Miscellaneous                                $    288

                                                                $   5,587

Total Direct Costs                                              $ 130,754

Indirect Costs                        67.5%                        88,259

Total Direct and Indirect Costs                                 $ 219,013<PAGE>

                                                                   EXHIBIT 10.29

                            Collaboration Agreement

                                by and between

Bruker-Franzen Anajytik GmbH
Fahrenheitstr. 4
28359 Bremen                            hereinafter referred to as `Bruker'

and

Sequenom Instruments GmbH
Mendelssohnstr. 15 D
22761 Hamburg                           hereinafter referred to as `Sequenom'

                                        November 24, 1997

                                   Preamble

(1)  Bruker-Franzen Analytik develops and manufactures mass spectrometers and
     supplies such instruments on a worldwide scale.

     Bruker-Franzen Analytik has exclusive intellectual property rights and
     know-how, covering
     .   MALDI-TOF mass spectrometer technology
     .   Pulsed Ion Extraction
     .   Multi-Target Acquisition
     .   Postprocessing XMASS(TM) software.

     Bruker-Franzen Analytik maintains an organisation appropriate for the
     manufacture, marketing and customer service with regard to such mass
     spectrometers.

(2)  Sequenom has exclusive intellectual property rights and know-how, covering
     Sequenom's DNA MassArray(TM) technology basis and comprising
     .   Sample preparation and sample conditioning of nucleic acids, optimized
         for MS separation and detection
     .   DNA analysis application formats specifically designed for MS analysis
         (BiomassSIZE(TM), BiomassSCAN(TM), BiomassPROBE(TM) BiomassSEQUENCE
         (TM), BiomassINDEX(TM))
     .   Parallel processing features, applying DNA chips (SpectroChip(TM)) and
         multiplexing
     .   Separation and detection of nucleic acids by MS, incl. analytical and
         diagnostic applications.

(3)  The parties intend to establish a broad relationship focusing on Nucleic
     Acid Analysis by Mass Spectrometey subject to the experience within this
     Collaboration.

<PAGE>

Collaboration

(1)  Bruker-Franzen and Sequenom intend to collaborate in the manufacture and
     marketing of and in the provision of customer service for ZD-Array MALDI-
     TOF Mass Spectrometers designed to process Sequenom's SpectroChips(TM) (the
     "Mass Spectrometer") under a joint Bruker-Franzen -- Sequenom logo.

     The Mass Spectrometer will be made available as stand-alone instrument and
     will be integrated by Sequenom in collaboration with highly qualified
     instrument manufacturers in the area of microliter and nanoliter liquid
     handling, mass spectrometry and system integration in modular analytical
     lines (the "Modular System"), comprising automatic liquid handling modules,
     DNA amplification and sequencing modules, sample-to-chip transfer modules
     and controlling and data management units. The Modular System will be
     designed to run applications of Sequenom's DNA MassArray(TM) technology

(2)  Bruker-Franzen will design and manufacture the Mass Spectrometer, meeting
     the specifications required for use in the DNA MassArray(TM) process and
     dedicated and appropriate to process Sequenom's Spectrochips(TM) ,
     including the XY-stage component and signal acquisition software. The
     parties will mutually agree on specifications for the Mass Spectrometer and
     the SpectroChip. Bruker will make available to Sequenom the complete
     details of the interface, including software protocols and time behavior,
     enabling Sequenom to develop the specific application DNA MassArray(TM)
     software.

(3)  The Mass Spectrometer will be available by June 30, 1998.

(4)  Bruker-Franzen and Sequenom will promote the Mass Spectrometer under a
     joint label. The procedure will be defined on a case-by-case basis.

(5)  Bruker-Franzen will market and provide service for the Mass Spectrometer on
     a world-wide scale and under the name of Bruker-Franzen and Sequenom.

(6)  Sequenom will provide nucleic acid analysis services to customers and to
     corporate partners using DNA MassArray(TM)
     Sequenom will provide DNA MassArray(TM) application development, including
     necessary software, to Mass Spectrometry users.
     Sequenom will develop, manufacture and market SepctroChips(TM) for whatever
     applications.

                                       2
<PAGE>

Business Terms

(1)  Bruker-Franzen will supply the Mass Spectrometer to the market at a
     competitive market price (the "Market Price").

(2)  Sequenom maintains the option to purchase from Bruker-Franzen the Mass
     Spectrometer *** (the "Supply Price"). The Supply Price will be calculated
     by ***, referring to the basic instrument, in the respective country of
     instrument delivery.

(3)  Bruker-Franzen Analytik will provide one Mass Spectrometer to Sequenom,
     Hamburg as Beta test site by June 30, 1998 ***. Initially, a
     prototype instrument equipped for handling of a single SpectroChip (TM)
     will be supplied by March 30, 1998. The Modular System in Hamburg will be
     used as demonstration and test site by both parties.

     A second Mass Spectrometer will be supplied to Sequenom, San Diego, the
     price being the Supply Price, by June 30, 1998.

(4)  The Mass Spectrometer will be *** for the exclusive processing of
     Sequenom's SpectroChip(TM).

Timelines

(1)  The Collaboration Agreement will come into force with the date of
     signature.

(2)  The Collaboration agreement may be terminated by either party at 12 months
     notice; such first notice of termination may, however, not be given earlier
     than 30 Dec. 1999.

Date:     December 4, 1997                     Date:    December 4, 1997
     -------------------------                      ------------------------
Bruker-Franzen                                 Sequenom

/s/ Dr. Frazen                                 /s/ Dr. H. Koster
                                               (Dr. H. Koster)

/s/ ppa H.J. [illegible]

*** - Portions of this page have been omitted pursuant to Confidential Treatment
request and filed separately, with the Commission.

                                       3

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