Wednesday, 1 June 2011


I’ve picked up that cold that’s going around.

Now a question to those from medical backgrounds, is it possible to over does on vitamin C?

Stud-udios and Single Cell Sequencing.

I think I might be in trouble.

Tuesday night is date night.

Normally this is no problem we go out or cook something nice and more often than not, wind up the evening by watching Doctor Who.

However, this Wednesday morning at about ten, I was on for journal club.

Now in a sign of great-minded-ness I decided on doing a snazzy paper about recurrent genomic rearrangements in prostate cancer. But after a weekend of reviewing, it turned out that it had been presented the week before I started.

So last night after Doctor Who, I snuck into the stud-udio* and began typing up on my replacement paper.

The stud-udio is a magic place – not quite study – not quite studio.

So, while I’m in the dog house for the neglecting date night, I have my opinions about a recent letter in nature to keep me warm at night and because you’re here I’d be happy to share them with you.

Tumour evolution inferred by single-cell sequencing.

In my limited understanding of it, this paper showed that single nuclei sequencing can be used to observe some of the complexity present in the genomes of cancer cells. When the team compared the genomes of individual cancer cells to one another as well as healthy diploid cells using phylogentic clustering they saw that the cancer cells clustered into distinct subpopulations.

This is cool because from this data we can see how the tumour has developed. What they don’t say is that it’s still pretty cool that there’s decent concordance with whole tumour sequencing / microarray data.

What’s not so cool is how they did it. The 76bp single fragment reads, covering 6% of the genome isn’t stellar. Neither is dividing the genome into 50,000 bins and mapping using bowtie.

But perhaps that just it’s way of trying to counter for all the crap introduced by whole genome amplification.