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reply to NAASC letter

Joe Ecker jecker at ATGENOME.BIO.UPENN.EDU
Mon Jun 6 16:30:03 EST 1994



1. Do you think that we are ready to begin some level of directed genome 
sequencing in the US? 

Yes, but only if funded by new money.

2. How important is genome sequencing in terms of funding priorities (vs. 
placing cDNAs on the map, completion of the physical map, adding more 
PCR-based markers to the map, etc.)?

Adding more markers (especially PCR-based) and completing the physical map
are much more important than sequencing.  The sequencing will eat up a lot
of resources and will not be useful without the markers.  We cannot wait
for the availability of the sequence (which would immediately facilitate
marker identification) before mapping our genes!

3. Who should support systematic genome sequencing if it is a big-$ effort?

If the USDA could get new money that would be great.  An interagency
program with USDA, NSF and DOE may be more practical.  Because they already
have a mechanism set up for the current tiragency grants this should be a
possibility at least.  Responder #10 (who is apparently used to NIH funding
levels) does not realize that the $20M effort he/she suggests USDA fund
cost about as much as the entire current USDA budget for competitive grants
in plant biology!

4. What impact on Arabidopsis research will be incurred if sequencing does not
begin today (in 2 years; in 5 years,  in 10 years)?

Little impact on research today, cannot predict effects of longer delays.

5. What type of organizational model for genome sequencing would you support: 
sequencing centers vs. individual interested labs?

If it is done in earnest then it would probably best be done at centers for
cost efficiency.
6. What quality standards would you expect for the sequence: high or low  
accuracy (high accuracy = higher cost)?

A greater number of errors can be accepted in genomic than in cDNA
sequences.  Finding ORFs in genomic sequence is difficult due to introns

Push the mapping tools and contig assembly first!  If we can't find where
our genes our then we will not be able to interpret the sequence as
effectively.  The contigs are necessary for completion of the sequence and
proper assembly as well.

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