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Wednesday, December 10, 2008

countdown to comps continues..

Today has been a relatively productive day in one sense. I finally finished reading the Biology of Cancer (Weinberg), after about 2 solid weeks of doing a chapter a day. At about 60-75 pages a day, it was pretty intense, but I learned a LOT. (Well, how could I not?)

Since the last chapter was on drug design, an area I'm familiar with, it was pretty easy reading and went by pretty quickly. There are only so many times you can learn about Gleevec.

So I moved on to a few other review questions suggested by my committee... such as "Draw a gene" and "penetrance vs. expressivity," which made for a nice general review.

And then I moved on to a few papers. One of them discussed doing PET sequencing from 2nd generation machines to find chromosomal fusion points in cancer (Bashir et al., 2008). The math was interesting enough, but the end result was that they tested it on BACs. When I get around to doing PET on my samples, this will be a good review to make sure we get the parameters right, but the paper didn't go far enough, really, in my humble opinion. I was hoping for more.

A second paper that I went over was on identifying SNPs in 2nd generation sequencing, using bovine DNA (Tassell et al, 2008). I don't know what to make of their method though. They combined samples from 8 different types of cow (I didn't know there were that many types of cow!), and then sequenced it to a depth of 10x, so that on average, each read covering a specific location should reflect the sequence from a different breed. Maybe I'm missing something, but SNP calling on this should technically be impossible - even assuming you get 0% sequencing errors, how confident can you be in a SNP found only once? Anyhow, I had to abandon this paper... I just didn't understand how they could draw any conclusions at all from this data.

Finally, a colleague of mine (Thanks Simon!) recommended a review by Weinburg himself on "Mechanisms of Malignant Progression." (Weinburg, 2008). For anyone who ends up reading his textbook from cover to cover, I highly suggest following up with his review. Things have changed a bit from the time the textbook was published to now, which makes this review a timely followup. In particular, it flushes out much of the textbook's discussion of Epithelial-Mesenchymal Transitions (EMTs). Not that I want to go into much detail, but it's clearly worth a browse - and it's only 4 pages long. (MUCH shorter than the 790 pages I had to read to understand what he was talking about in the first place.) (-:

So now, this leaves me with 1 day left - just enough time to gather together my 15 minute presentation, to review the chapter summaries from the Biology of Cancer, and still have enough time to freak out a little bit. Perfect timing.

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