Free Memorandum in Opposition to Motion - District Court of Connecticut - Connecticut

Case 3:00-cv- - -
00705 CFD Docu ment 115-11 Filed 10/22/2004 Page 1 of 4
. j` " DEPARTME OF HEALTH HUMAN SERVICES Pwatie Health servlet;
€_ ———-—--— —·———
. A nah T Na tional Institutes ot Health
"” National Human Genome
` _ Research institute
" 31 come: Drive usc 2152
Buldtng 31. Room 4809
Bethesda, MD 2oa92·21s2
(301) 49o0644
r=A x (301) 402-0837
February 28, 2000
.l. Craig Venter, Ph.D.
Mr. Tony White
_ Amold Levine, Ph.D. _
Mr. Paul Gilman
Celera Genomics Corporation
45 West Glide Drive
Rockville, Maryland 20850 .
Dear Dr. Venter, Mr. White, Dr. Levine and Mr. Gilman:
We appreciated the chance to meet with you on December 29, l999. to dist cuss possible grounds for
a collaboration between the public Human Gcnonte Project (HGP) and Cel :ra Genomics, on
deriving the sequence of the human genome. Prior to the December 29 meeting. there had been
numerous discussions about a possible model for collaboration, most notal ·ly those among Eric
Lander. Craig Venter, Hamid Varmus, and Arnie Levine. 'Ilre five largest genome centers (Baylor,
the IGI, Sanger, Washington University, and the Whitehead Institute, referred to as the G5) had
been fully briefed on those discussions, and had asked the four.of us to re; resent the public HGP in
any negotiations. Other merrrbers of the intemational sequencing consortirrm were also briefed in .
general on these developments. We had prepared a proposed statement of "Shared Principles"
(enclosed) which we thought accurately reflected the conclusions of the earlier conversations with
Celera. From the previous contacts, we did not expect these to be particularly controversial, and
were thus disappointed to leam the day before the meeting that sonre of those principles might not
be shared by Celera. Nonetheless, we attempted to negotiate on December 29 in good faith.
A number of important points of agreement between ourselves and Celera. were reached on
December 29. These included the conclusion that an active collaboration to merge the two data sets
could produce a substantially better product, since it would allow bilateral sharing of T
· electrophoretic traces and a joint effort to resolve discrepancies. At a technical level. this kind of
data sharing did not seem to present a substantial hurdle in the irnplememation of a joint effort.
However, several fundamental differences emerged. These are outlined below; `
l) Since its inception, the public HGP has been committed to producing human genomic sequence
for all to use without any barriers or restrictions, in the expectation that this policy would maximize
the benefit to humankind. That policy was explicitly codified in 1996. lf a collaboration were
initiated, however, Celera indicated they would expect exclusive commercial rights of distribution
of the merged product, most likely even beyond the current projected date of completion ofthe
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human genome sequence by the public consortium in 2003 (2005 was mentioned). While we
understand Celera‘s business imperatives, the extent of this claim scented ina ppropiiatc to us. 'The
product of a sequence data merge between the HGP and Celera in the summer of 2000 would
rellect the collection of shotgun data at roughly I0: redundancy, and would not be of equivalent
quality to the finished product expected from the HGP in 2003. Many sequence gaps and regions
of ambiguity would be present in the proposed Celera!}-lGP merged product. By current plans, if no
collaboration were initiated, the public HGP expects to have completed shotgun coverage on
available genomic clones by no later than December 2000. This would argue that the period of
exclusive rights to cornrnercial distribution ofthe merged data set by Celera should be limited to no
° more than 6 - l2 months after the initiation of the collaboration.
1
2) ln view of the public l·lGP's commitment to finishing the human sequence, it would be expected
that ongoing efforts would be needed after the merge to close gaps and clear up ambiguities. 'I`he
design of such finishing strategies would optimally make full use of the merged data set. On
December 29, however, Celera argued that the output of any further improvements in the sequence
that resulted from the use of the merged data set would also fall under their exclusive rights for
commercial distribution. Such a restriction would put the public HGP in an ongoing position of
producing data that was less than fully accessible, which would be inconsistent with the
internationally agreed principle of open access. To avoid this, the public BGP might actually be
forced to continue to collect additional independent and redundant shotgun data in parallel with the
collaborative effort, although this position was apparently also unacceptable to Celera. Given
Celera‘s stated plans to make their own version of the data available to the academic community, -
even in the absence of ajoint effort, it is not clear why or how Celera would expect to prevent the
public HGP from utilizing the complete merged data set in directing finishing efforts.
3) 'I`he public HGP was also concerned by Celera‘s stated desire to have their proposed commercial
rights over the joint product extend beyond databases to experimental app nications, such as the
. construction of genome chips, large primer sets, or applications to proteomics and analysis of
regulatory sequences. We were not previously aware of the intention for · hose commercial rights to
extend beyond databases. While establishing a monopoly on commercial uses of the human
genome sequence may be in Celera‘s business interests, it is not in the best interests of science or
the general public.
4) While both panics agreed that wide distribution via both a DVD and the intemet was desirable to
facilitate access to the sequence, there appeared to be substantial differences in how this might be
implemented. The public HG? feels that the sequence. along with jointly derived annotation, must
be available from one or more noncommercial sites, whereas Celera wisles any intemet access to
be exclusively through a Celera portal.
5) We were concemed about Celera's possible intention to publish the rt suits of their merge of the
V public data and their own data, in the event that no agreement is reached. Although the public
r effort has explicitly made preliminary sequence available for all to use for both academic and
commercial research purposes, the public consortium reasonably reserws the right to be the first to
publish its own data in a peer-reviewed journal. Publication of other grr »ups‘ primary data without
consent is considered to be a breach of scientific ethics. ln addition, it is counter to accepted
scientific practice for authors to present results without having examined the primary data.
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These are substantive issues. We left the December 29 meeting grateful that the exchange had been
so open and wide·ranging, but uncertain whether Celera's stated positions we re hardened or still
open to negotiation. At the conclusion of the meeting, all parties agreed that a follow-up meeting
would probably be needed.
One of us (FSC) attempted to reach Dr. Venter to set up a follow·up meeting. but was directed
instead to Mr. White. ln a phone call on January 22, Mr. White reiterated the points outlined
above, and indicated that a follow·up meeting would only make sense if the public consortium
agreed to grant Celera commercial protection for the sequence in their database well beyond the
time it would have taken the public HGP to generate an equivalent product. Mr. White stated that
he expected commercial protection for at least 3 to 4 years, and preferably longer. He also held fast
to the demand that finishing efforts by the public consortium, carried out aft :r the merge, would
need to be under the same restrictions. _ When it was pointed out that this was particularly puzzling,
since if there were no collaboration the HGP could presumably use Celera's proposed DVD to aid
finishing and then place those additional new reads in public databases, Mr. White indicated that
they were rethinking their DVD plans, and that the sequence data might onl y be available on their
web site, perhaps with some restriction on this sort of linishing activity by others.
When asked about the extent to which Celera would see their restrictions applying to uses of the
genome sequence other than commercial databases, Mr. White reiterated th at Celera would expect
chip companies to pay a license for this use. As to other genome-wide use: of the human sequence,
he said that Celera has not yet defined which types of experiments would require a license, but left
the door open to that being broader than just chips.
When asked whether there was some flexibility in the positions outlined by Celera on Dec. 29, Mr.
White did not encourage that view.
Despite this discouraging interaction, one of us (FSC) has been attempting for more than two weeks
to reach Dr. Venter to see whether there are any remaining grounds for pursuing the collaborative
model. After several unanswered phone calls and e-mails outlining the renson for the attempted
contact, Dr. Venters assistant indicated that he is too busy with other matters right now to discuss
this until some time after March 6L
_ A clear conclusion seems to arise from Celcra's actions on and subsequent to December 29: that
there is no real interest on the part of Celera in continuing to pursue this p articular collaborative
model. This is disappointing, since much work has gone into exploring st tch an option, and we had
been hopeful in light of the success of the collaborative effort on the Drowophila sequence that
something similar could be worked out for the human project.
Continued ambiguity is not conducive to early completion of the hurmn genome sequence.
Therefore, unless Celera indicates in the next week (by March 6, 2000) that the conclusions of this
letter are substantively incorrect, we will conclude that the initial proposal whereby the data from
the public HGP and Celera are collaboratively merged is no longer work able. ‘
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We sund ready and willing to engagc in lurthcr conversations at any rimc.
Wiili bcsi regards.
l Sinccrcly yours.
Francis S. Collins, M .D., Ph.D. Hnmld Vnrmus, MD.
Manin Bohrow. CBE DSC FRCPA Rnben H. Wexewnn, MD., Ph.D.
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