Friday, February 18, 2011

10 years with the human genome

This week marks the 10-year anniversary of the publications of a (nearly) completed human genome sequence. Much has been made already of this passage of time, as well as what we can look forward to in the next ten years.

What I thought I would do in this space is share a little personal story on my connection with this achievement. In late spring of 2001, I happened to search the Internet and PubMed for my name because I wanted to check to see if any presentations at conference or publications from previous laboratories in which I had worked had been released. To my surprise, I found a website in Japan with the title of something like "list of authors" which contained a collection of names of former colleagues from my days in the Genome Sequencing Center at Cold Spring Harbor Laboratory. That seemed strange and so investigating a bit I learned that we were included on the Nature paper describing the human genome - along with some 5000+ other authors (hence the special listing on this website, and no hits in PubMed). Well, needless to say but that was quite a thrill. I quickly updated my CV to include this landmark publication.

Back in 1997 to 1999, as the publicly funded project to sequence the human genome was ramping up and dollars were dangled in front of genome centers around the USA and the globe, we at CSHL were trying to deposit as much finished sequence into GenBank as possible. Monthly and quarterly totals of base pairs deposited were key to securing grant money. An introduction to all this came within my first two weeks as the Computational Fellow (post-doc) with Dick McCombie when I was told I would be leading the analysis segment of his Genome Sequencing course. I learned the ins and outs of a new computer system and new software tools (I came from a cell biology lab) just in time to teach the students. We worked hard during that 2-week course to sequence a 143-kbp BAC clone containing some critical HIV/AIDS-relevant genes: CCR2, CCR5 and CCR6. You can view the sequence entry I deposited to GenBank here, accession U95626.

From this initial BAC, we worked on many more to try to show that we could put high-quality sequence data together and to get as much sequence finished as possible. Of course, our main funding was to contribute to the Arabidopsis thaliana genome and so the human projects (BACs and cosmid/fosmid clones) took second priority. But we did contribute enough sequence to warrant inclusion on the paper and Dick was kind enough to remember everyone who had passed through his lab during those years.

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