reply to NAASC letter

Joe Ecker jecker at ATGENOME.BIO.UPENN.EDU
Mon Jun 6 14:59:17 EST 1994


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RESPONSE # 16


1. Do you think that we are ready to begin some level of directed genome 
sequencing in the US?  
IT IS NOT A HIGH PRIORITY NOW.

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.)?
MOST IMPORTANT:
1)ADDING MORE PCR-BASED MARKERS TO THE MAP
2)COMPLETION OF THE PHYSICAL MAP
3)PLACING CDNAS ON THE MAP
4)GENOME SEQUENCING
I BELIEVE THAT THIS ORDER OF PRIORITIES WOULD BE MOST HELPFUL SO THAT THE
GENOME PROJECT CAN BE OF USE TO RESEARCHERS WHO WANT TO START WITH A MUTATION
AND CLONE THE DNA CORRESPONDING TO THAT GENE.  AT PRESENT, THIS PROCESS IS
DONE BY CHROMOSOME WALKING OR TAGGING AND BOTH ARE SLOW AND NOT SO EFFICIENT.
 IN C. ELEGANS, THE CLONING OF GENES BECAME MUCH EASIER WHEN COMPLEMENTATION
BY COSMIDS FROM THE FREEZER BECAME ROUTINE.  STARTING FROM A MAPPED YAC IS
STILL A LOT OF WORK WITHOUT THE FINER STRUCTURE MAP AND SMALLER CLONES.

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

UNCLEAR TO ME, BUT OTHER ARABIDOPSIS RESEARCH FUNDING SHOULD NOT BE DECREASED
TO FUND THIS EFFORT.

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

BETTER TO WAIT 2-5 YEARS AS THE TECHNOLOGY IMPROVES AND THE EFFORT CAN BE
UNDERTAKEN AT LOWER COST AND HIGHER EFFICIENCY.

5. What type of organizational model for genome sequencing would you support:

sequencing centers vs. individual interested labs?
            
SEQUENCING CENTERS (LIKE DONE WITH C. ELEGANS)

6. What quality standards would you expect for the sequence: high or low  
accuracy (high accuracy = higher cost)?
                        			             
HIGH ACCURACY WILL BE MORE EFFICIENT IN THE LONG RUN.  OTHERWISE DATA MAY NOT
BE INTERPRETED CORRECTLY AND LABS MAY HAVE TO RESEQUENCE RELEVANT REGIONS.
                         
7. ANY SPECIFIC OR GENERAL COMMENTS THAT YOU WOULD LIKE TO MAKE!

WITHOUT POWERFUL REVERSE GENETIC TECHNIQUES, THE GENOMIC SEQUENCE INFORMATION
OBTAINED WILL NOT BE THAT USEFUL.  EFFORT SHOULD BE PUT INTO REVERSE GENETIC
TECHNIQUES IN PARALLEL.   MORE REALISTICALLY, CONCENTRATE EFFORTS ON A
DETAILED  PHYSICAL MAP WITH MANY PCR-BASED MARKERS.  I DO NOT SEE ARABIDOPSIS
'FALLING BEHIND' OTHER MODEL SYSTEMS SIGNIFICANTLY BY WAITING TO SEQUENCE THE
GENOMIC DNA.

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