Application of Second Generation Sequencing to Cancer Genomics

A review by me titled "Application of Second Generation Sequencing to Cancer Genomics" is now available on the Advance Access section of Briefings in Bioinformatics. You'll need a subscription to read it.

I got a little obsessive about making the paper comprehensive. While the paper does focus on using second generation sequencing for mutation, rearrangement and copy number aberration detection (explicitly ruling out of scope RNA-Seq and epigenomics), it does attempt to touch on every paper in the field up to March 1st. To my chagrin I discovered just after submitting the final revision that I had omitted one paper. I was able to slide it into the final proof, but not without making a small error. There's one other paper I might have mentioned that actually used whole genome amplification upstream of second generation sequencing on a human sample, though it's not a very good paper, the sequencing coverage is horrid and wasn't about cancer. In any case, it won't shock me completely -- but a lot -- if someone can find a paper in that timeframe that I missed. So don't gloat too much if you find one -- but please post here if you find any!

Of course, any constructive criticism is welcome. There are bits I would be tempted to rewrite if I went through the exercise again and the part on predicting the functional implications of mutations could easily be blown out into a review of its own. I don't have time to commit to that, but if anyone wants to draft one I'd help shepherd it at Briefings. I'm actually on the Editorial Board there and this review erases my long-term guilt over being on the masthead for a number of years without actually contributing anything.

As I state in the intro, in a field such as this a printed review is doomed to made incomplete very quickly. I'm actually a bit surprised that there has been only one major cancer genomics paper between my cutoff and the preprint emerging -- the breast cancer quartet paper from Wash U. I fully expect many more papers to appear before the physical issue shows up (probably in the fall) and certainly a year from now much should have happened. But, it is useful to mark off the state of a field at a certain time. In some fields it is common to publish annual or semi-annual reviews which update on all the major events since the last review; perhaps I should start logging papers with that sort of concept in mind.

One last note: now I can read "the competition". Seriously, another review on the subject by Elaine Mardis and Rick Wilson came out around the time I had my first crude set of paragraphs (it would be stretch to grant it the title of draft). At that time, I had two small targeted projects in process and they had already published two leukemia genome sequences. It was tempting to read it, but I feared I would be overly influenced by it or worse would be paranoid about plagiarizing bits, so I decided not to read it until my review published.