[Coral-List] Porite genome 2

craigdowns craigdowns at envirtue.com
Tue Sep 9 18:15:41 EDT 2003

Dear Coral List Serv,

For some reason, the attachment never came through on the list serv, so
I have pasted the letter below.


I am coordinating an effort to sequence (likely 6x coverage) the genome
of Porites lobata.   NHGRI has a deadline of October 10 for "white
papers" for sequencing projects and I have enlisted TIGR (Steven
Salzberg) and the President of EnVirtue Biotechnologies, Inc. (Craig
Downs) as partners.  This effort also has the endorsement of Craig
Venter, founder of TIGR and President of The Center for the Advancement
of Genomics (TCAG).  If approved, the sequencing project would be
undertaken by one of the NHGRI-funded sequencing centers.  We believe it
is likely that TIGR and its new Joint Technology Center will shortly
join that group of centers, with their new project to be headed by Dr.

A very significant part of the application is the letters of support
from the community that anticipates using the genomic information that
will be generated.  In fact, I have learned from others who have written
successful papers that these letters are essential and play a major role
in determining the priority of the organisms for sequencing.  To this
end I am soliciting as many member of the coral reef community as
possible to provide letters.  Without a significant number of these
letters (25+) this project has little chance of being selected and

Letters should be no more than one page, must be signed, and should be
on your institution's letterhead.  Your letter must be specific and
should include the following:

		1.    How will sequencing the Porties lobata genome will
help your own work?  Again, be as specific.  What are you studying and
what fundamental questions or experiments of significance will you now
be able to do with this information?  For example, you can just say,
we'll expand our efforts in blah blah.  Instead, state that your are
interested in positional cloning of several genes of the XX disease
family and we now have to clone every gene in the region of linkage that
we've defined one at a time by screening libraries with degenerate
primers, which works only some of the time and often gives us false
positives, especially for the XX gene family which is complex.  But if
the sequence were available we'd just download the sequence, make PCR
primers, and screen for mutations in our disease population.  You should
make it clear that you have the resources to use the sequence
deformation and that you in fact will use it.  In short, NHGRI wants to
know that significant work will now be completed as a result of this

2.	 How will sequencing of the Porites lobata genome help you in
the funding of your work (regardless of the agency supporting you) and
in particular will this bring others to the field?  NHGRI wants to know
that this will impact a significant number of individuals and may even
expand the number of workers in the field.  It would be a severe
criticism to NHGRI if they funded the sequence of an organism for 9+
million dollars and 3 years later only a handful of groups were using
the information. 

3.	If you agency or organization can provide any funding toward
this effort in any capacity (even "in-kind" efforts) it should be
mentioned.  For example, it would be great if an agency were willing to
underwrite the cost of a meeting, once the data becomes available, to
train individuals on how to use the data etc.  I have been told that any
kind of support from other organizations will carry a lot of weight.

4.	 A minor point, check your ego at the door.  While I have asked
you to tell me how the sequencing of Porties lobata will help you.. I do
not need a lengthy discourse on your own research.  What they are
looking for is how completion of this project going to be of global
significance.  So, as much as possible please, provide some example of
the cosmic significance of this undertaking.  Feel free to comment about
work that may not be related to your own corner of the world/reef!  I
have been told by someone who helped write the guidelines the committee
is not interested so much in the quality/quantity of the science that
you have done in the past as they are in what will come out of this
effort.  They want to see vision.  In fact, they don't even ask for

5.	I need your letter by October 1st.  Please send me a hard copy
or at least a FAX by that time to:  Dr. Gary K. Ostrander, Department of
Biology, 237 Mergenthaler Hall, 3400 North Charles Street, Johns Hopkins
University, Baltimore, MD  21218.   My FAX number is 410/516-4100 and
you can call (410/516-8215) or email (gofish at jhu.edu) with questions.

6.	Please give very serious consideration to this request.  This
may be our one opportunity to accomplish this objective in the near
future.  Many groups are gearing up for large scale sequencing projects
and the competition to access this resources will only get stiffer.
Also, there are a finite number of centers and "lanes" available for
sequencing at this time.

7.	Finally, if you would be kind enough to drop me an email now as
to what the major impact of this project will be for you..I can be sure
to include it in the text of the white paper now.

	Thank you in advance,

	Gary K. Ostrander
	Department of Biology
	Johns Hopkins University

Craig A. Downs
EnVirtue Biotechnologies, Inc.
35 W. Piccadilly Street
Winchester, Virginia 22601   U.S.A.

Phone: 540-723-0597
Fax: 540-723-0598

Saving Tomorrow Today

More information about the Coral-List mailing list