Report to the Ciliate Research Community

November 17, 2001

Prepared by Eduardo Orias

On November 5, our concept paper for the Tetrahymena (macronuclear) Genome Sequencing Project was submitted to the Trans-NIH Non Mammalian Models Committee. The concept paper, plus appendix and references, are attached as Microsoft Word documents.

The NMMC committee reviewed our concept paper rather favorably. As a result, we have been invited to submit next month a "Letter of Intent" to the NIH General Medical Sciences Institute to do the whole-genome shotgun (WGS) sequencing phase of the project (see section 2 of the concept paper) and to establish the database resources required to make that information useful to the entire scientific community. The WGS phase represents 40% of the cost of the entire project. If this LOI is approved, that will mean a green light to submit a regular R01 grant application for the WGS sequencing by the February 1, 2002 deadline. The application would then be considered using the normal NIH review process: scientific peer review followed by GMS council review. We are proceeding with the preparation of the LOI and the subsequent grant application. Sequencing could start in about a year from now, if all goes well for us.

To facilitate closure of the genome sequence, we would like to reach at least 8-fold WGS coverage. We are hoping to be able to apply initially for at least 5-fold coverage, because that should give us useful sequence for virtually every gene. However, how much coverage we can apply for will depend on what GMS and various other institutes and agencies can contribute. We approached NHGRI, NIA, NCRR, NICHD, NIAID, NIEHS and NSF with a degree of success still unknown to me, but which should become evident by the time of the LOI submission next month. Finding additional sources of support in the near and more distant future (no matter how modest) seems to be the only rate-limiting factor now and remains critically important. Please let me know if you are aware of additional contacts that could be approached for partial support.

We were also encouraged to submit a "white paper" to a separate, recent Human Genome Institute initiative on genome sequencing projects (see http://www.nhgri.nih.gov/NEWS/org_request_release.html). We intend to do so by the February 10, 2002 deadline. Success in this effort would complement the GMS project by providing sequencing (which represents the bulk of the project) by large-scale centers already funded by NHGRI.

I think that we are well prepared to face the next hurdles thanks to the great contributions from many members of the community to various phases in the preparation of the concept paper. I'll keep you informed of any new milestones we reach.