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Community Briefing on Mouse Genome Sequencing Network

On February 1, 1999, the staff of the National Human Genome Research Institute (NHGRI) held a briefing for prospective applicants who were interested in responding to RFA HG-99-001, Mouse Genome Sequencing Network. This report summarizes the issues discussed at that briefing.

 

NHGRI Briefing on RFA HG-99-001
Network for Large-Scale Sequencing of the Mouse Genome

On February 1, 1999, the National Human Genome Research Institute (NHGRI) held a briefing on the initiation by NIH of a program to sequence the mouse genome (this briefing had been announced in RFA HG-99-001). Dr. Francis Collins, Director of NHGRI opened the briefing with some background information, Dr. Jane Peterson reviewed the RFA and Dr. Bettie Graham discussed a plan that NHGRI is developing to prioritize biologically interesting regions of the mouse genome for sequencing. The floor was then opened for questions and discussion. The following issues were discussed:

  • The production of finished sequence was not adequately discussed in the RFA. NHGRI will publish an update shortly to clarify two issues:
    • Sequencers will be responsible to eventually finish any clone they start.
    • The long-term objective of this program is to generate a highly accurate, complete, finished sequence of mouse DNA. The purpose of the cooperative agreements that will be funded will be to support the establishment of sequencing facilities capable of making a significant contribution to this objective. During the third year of the project, there will be a stringent competitive review that will evaluate whether the group has established a process that will be sufficiently robust to be scaled for completing the sequence of the entire mouse genome; toward the end of year 2, there will be a review that will assess the group's progress. Therefore, the applicant must propose a plan that will demonstrate the center's capability to finish data in an efficient and cost effective way. In the first year of support, a center should finish at least two BAC clones (the minimum number required for quality assessment).
  • In addition to producing a finished sequence of the mouse by 2005, a nearer term goal of the program is to produce enough sequence data by 2003 to generate complete coverage of the genome in sequence of "working draft" quality. Working draft sequence is a concept that has been discussed widely in the genomics community in the past several months; however, NHGRI recognizes that the definition of working draft has never been crisp and is still confusing to some investigators. The NHGRI Five-Year Plan defines working draft as "a product…that covers most of the region of interest but may still contain gaps and ambiguities." Thus, working draft is, at a minimum, that level of shotgun coverage of the genome at which contigs begin to coalesce. The amount of shotgun data needed to achieve this benchmark will differ depending upon the particular sequencing strategy chosen. Furthermore, different strategies may choose to pause between working draft coverage and finished sequence at different levels of shotgun coverage. Therefore, NHGRI does not specify numerically a shotgun depth that should be proposed for a center's working draft. Rather the application should address both goals of the RFA (coverage in working draft by 2003 and finishing the genome by 2005), taking into account the issues involved in later finishing a clone that was initially sequenced to low redundancy.
  • The C57BL6/J BAC library mentioned in the RFA (which is derived from a female) is available from Dr. Pieter de Jong at Roswell Park Cancer Institute (http://bacpac.med.buffalo.edu/). It is currently an 11-fold genomic equivalent library and an additional library is being constructed from a male of the same strain that will add an additional ten-fold worth of clones, bringing the overall depth of available clone coverage to about 20 genomic equivalents. If additional libraries are needed (for example a male library), NHGRI will fund the characterization of that library through a competitive supplemental mechanism. Requests for funds to generate and/or characterize additional libraries beyond the one currently available should not be included in applications submitted in response to RFA HG-99-001.
  • The RFA defines an existing sequencing center to be one that has deposited 2 Mb or more of sequence in a public database. This amount of sequence need not be in a single contig. If the group's sequence product is not genomic sequence, the investigator is urged to speak with NHGRI staff to discuss whether to apply as an existing center or as a new center. NHGRI did reaffirm its strong intention to use the funds available for supporting new sequencing groups as well as expanding existing efforts.
  • The January 8, 1999 meeting at Princeton was not organized by NHGRI, but by members of the mouse community. The report of the meeting should, therefore, not be considered to be an NHGRI policy document or a guideline for this RFA. Rather it is a summary of the most recent discussion of genomic sequencing issues by the mouse community. For example, there are several specific recommendations contained in the report that, while perhaps reasonable, do not define the scope for this RFA.
  • NHGRI recognizes that during the initial year of funding, the fingerprint and BAC end sequence data will not be available to assist in choosing clones for sequencing. During this period, sequencers pursuing the sequence first, map second strategy will have to choose clones at random, not knowing whether they overlap with other clones being sequenced.
  • The previous NHGRI policy of allowing human DNA large-scale sequencing labs to devote up to 10% of their effort to sequencing mouse DNA was articulated prior to this initiative. Now that there is a specific program for mouse genomic sequencing, all NHGRI support for sequencing the mouse genome will be provided through it, and its peer review process.
  • Dr. Greg Schuler of the National Center for Biotechnology Information, described plans for constructing the central server that will be used for mouse genomic sequencing. Specific recommendations as to data items that will be needed on the server may be found in the report from the Princeton meeting. Dr. Schuler said that he expects the central server to be available by the end of the summer.

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