Additional responses to NAASC letter

Joe Ecker jecker at ATGENOME.BIO.UPENN.EDU
Wed Jun 1 16:17:45 EST 1994


Dear Colleagues,

Below are several more responses to the NAASC letter.


Joe Ecker

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Response # 7

In response to your message about whether the US should start a genome 
sequencing programme, my opinion from the UK (since we will not be 
paying!), is overwhelmingly, yes.  I concede all the caveats that 
others have mentioned, e.g. we can't do fancy genetics (yet) like 
the yeast people, the physical map isn't complete etc etc.  However,  
I believe that some sort of genomic sequencing programme is 
necessary now in order to identify and overcome, through practical 
experience, the problems inherent in this type of work and to set 
things up for a wider effort which must happen in the next couple of 
years if the claims of Arabidopsis researchers are to remain 
convincing. Despite the organizational faults of the yeast 
chromosome III project, some fascinating info came from this work.  
And now the organizers presumably know how to organize things better 
next time round.   How about a limited programme on some well mapped 
(in the US) regions of the genome to begin with.  Keep in 
touch/formalize links with European genomic sequencers.  Expand if 
the results are good; presumably impressive data will convince the 
funders and the scientific public.  Expansion should/should not 
happen depending on what happens in cDNA mapping/sequencing.    
Sequencing centres would work best.  Sequence info should be made 
public as soon as possible.  

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Response # 8

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

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.)?	in my opinion, more important than 
est's and rflp's, but less important than completion of the physical map.

3. Who should support systematic genome sequencing if it is a big-$ effort?
  USDA-isn't arabidopsis a plant?
  nsf, nih, doe and walmart too, if they will help

4. What impact on Arabidopsis research will be incurred if sequencing does 
not
begin today (in 2 years; in 5 years,  in 10 years)? the yeast genome will be 
done within 11 months-worms are probably shooting for 2-5 years.  i will be 
thoroughly ashamed if we are more than 2-3 years behind worms-the usda 
should be doing this full blast!!!!!!

5. What type of organizational model for genome sequencing would you 
support: 
sequencing centers vs. individual interested labs?
 definitelty support individual interested labs-spreads the money out and 
helps in other projects too
                        
6. What quality standards would you expect for the sequence: high or low  
accuracy (high accuracy = higher cost)?high accuracy will be cheaper in the 
long run
                        			                                      
7. ANY SPECIFIC OR GENERAL COMMENTS THAT YOU WOULD LIKE TO MAKE!

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Response # 9

>1. Do you think that we are ready to begin some level of directed genome
>sequencing in the US?
No.

>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.)?
A good physical map and a high density genetic map of PCR based markers are
much higher priorities.  As has been stated already in this forum, we need
to know much more about the genes that are involved in biological
processes of interest.  This can most readily be determined through
genetics.  Once genes have been identified, it would be nice to have
sequence already determined.  However, given the probable trade-offs
involved, i.e. fewer dollars for independent research, good genetic and
physical maps will allow more rapid isolation of genes.  Linked clones in
transformation competent vectors would be useful for rescue experiments.  

>3. Who should support systematic genome sequencing if it is a big-$ effort?
Is a consortium of federal agencies feasible?

>4. What impact on Arabidopsis research will be incurred if sequencing does not
>begin today (in 2 years; in 5 years,  in 10 years)?
As mentioned above, the impact may be negative if started today.  In 2-5 years
technology hopefully will have advanced enough to make it a more
cost-effective project.

>5. What type of organizational model for genome sequencing would you support:
>sequencing centers vs. individual interested labs?
Whichever is the most efficient as determined from the experience in other
organisms.



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