Recorded: 08 May 2008
So the way it worked was, Jim was sequenced by 454 Technology [454 Life Sciences]. And then Lincoln Stein made his data file publicly available at the Cold Spring Harbor website just a week after the announcement. And I know Lincoln well. So I went, and we got it. And there was a file and we said…I said to my team, “Damn, the data file is here. Let’s take it! Let’s run it!” So I clicked on it like two days after it was announced. We downloaded it on the day. Went over to my team – we have five to eight people on the team - and I said “Come on guys, let’s run it through our system.” So we took it, we analyzed it, and it was very fun. In one week we could run the entire system through because we had everything set up. And came out a big long report of all the genetic variation that we think is clinically relevant out of his genome.
MP: So, hold on. It took one week?
One week. The whole data analysis. Because we had all the analysis pipeline developed over the four years. So the system has been developed and has been tested over many, many years. But it was so automatic because the computer is fast so we could just run it through. Now, what we came out with was like lists of genetic variations from the genome. And we had to go now in and had to basically check every single mutation. Is it right? Did we do the right things? What does the literature say about it? Is the literature even correct? Because what we did is we just transferred from the literature onto the genome. We then had to do a lot of analysis afterwards. But…so for the last couple of months we’ve been working on interpreting that data. And that’s what we basically did. And three weeks ago there was a new publication that came out. And they had a little bit of a different genome file. So we had to, in the last two weeks, we had to redo a little bit of our analysis. And as of yesterday, we have our final version. We wrote a manuscript. And yesterday at the wine and cheese party I went to Jim and said “I have analyzed your genome.” And I said, “I would love to send it to you so that you can take a look.” And he hasn’t even seen the data yet. So… it’s very interesting.
Of course we were very excited; we were looking really hard to find some of them. And I can really tell you we looked at a couple of interesting genes. We looked at BRCA1 and BRCA2, which are the breast cancer genes, which is of course mostly relevant for women. And we found some variation there, but variation is known in BRCA1. So there was nothing really special there for him in this context. But otherwise I can tell you, it was not very interesting. There is one correlation with a drive, like people that are really energetic and driving. Personally we looked at the publication, and we didn’t trust it. So I know what his status is, but I don’t trust the paper. We don’t trust the statistical values, so we didn’t really look into that. In traits we didn’t do. We mostly focused on the medical applications.
Umm…yeah, we …we really just looked what we found. What did he have? We had all the things in the database, so we didn’t look at… particularly look at that disease and try to figure out what he has. We came more [from], where is he different? And where does he have some clinical relevance? And that’s what we picked up. So we didn’t go over much in detail and try to find a particular trait, or find a particular disease.
Oh, he’s very healthy. I can tell you that. And we compared it actually to Craig Venter’s genome. And I can tell you…now again there’s some little bit of problem with the data underneath because we had a little bit more data for Craig than we had for Jim. But I think in general we found less variation in Watson’s genome. So it was…I can say that’s probably a trend that will hold up at the end of the day.
Martin Reese is the Co-founder, Chief Executive Officer, and Chairman of the Board of Omicia.
Dr. Martin Reese is an internationally recognized expert in medical informatics and bioinformatics with a track record of bringing strong, grounded scientific knowledge to the corporate sector. Prior to founding Omicia, Dr. Reese served as Vice President of Discovery Informatics for ValiGen. He organized the state-of-the-art Genome Annotation Assessment Project and was a member of the Berkeley Drosophila Genome Project. This project provided the essential proof-of-concept platform for Celera's famous shotgun sequencing technology, which is now internationally recognized - as driving a new standard of excellence in sequencing. It was while at the Lawrence Berkeley National Laboratories that Dr. Reese developed gene-finding algorithms for the Human Genome Project. He holds a Masters degree in Medical Informatics from the University of Heidelberg and a Ph.D. in Genetics jointly from the University of California, Berkeley and the University of Hohenheim, Germany.