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Monday, December 7, 2009

Talk: Peter Campbell - A lung Cancer genome: Complex signatures of tobacco exposure

I had the pleasure of accompanying my supervisor and a few other people from the BC Genome Sciences Centre down to St. Louis last week for a "joint lab meeting" and symposium on Cancer Genomics. The symposium had a fantastic line up of the "who's who" of 2nd generation sequencing (next-gen) cancer genomics, and was open to the public, so I thought I'd take the time to blog some of my notes. (I have a couple servers chugging away on stuff, so I've got a few minutes...) As always, this is drawn from my notes, so if there are mistakes, they are undoubtedly my fault either in interpretation, or in reading my own messy handwriting.

First talk: Peter Campbell.
Title: A lung Cancer Genome: complex signatures of tobacco exposure.

  • Tobaco usage (cigarettes/day) is dropping in USA, and lung cancer deaths is starting to fall. About a 20 year lag.
  • However, usage in China, Indonesia, etc, is rising dramatically, and thus, tobacco cancer research is sill important.
  • Tobacco causes DNA adducts to be formed, including benzo[alpha]pyrane, which distortes residues on either side, and also causes backbone distortions. This leads to DNA copying errors
  • Used NCI-H209 cell line, and generated 30-40 fold coverage using ABI SOLiD machine.
  • observed 22,910 somatic mutations, 334 CNVs, 65 indels, 58 genomic
  • rearrangements.

(My notes are a little sketchy at this point) They were able to show a sensitivity of 76%, however, they sacrificed some sensitivity for specificity, and were able to show 97% true positives in coding regions, 94% true positives in non-coding regions.

The break down of the 23,000 snps appears to be: 70.41% intergenic, 28.21% intronic, 0.79% non-coding, 0.58% coding. There is a Kn/Ks ratio of 2.6:1. These are fairly standard.

They then characterized it by nucleotide change, and showed a significant number of A->G and T-> C changes, which is expected for smoking patients. They also compared the spectrum of changes seen in the literature for Tp53, using IARC database.

Another interesting point is that G mutations enrich at CpG islands, and there is some evidence that mutations are preferentially targeting methylated CpGs. However, there are fewer adenine mutations at GpA locations.

Looking at this data suggested that there are repair mechanisms: eg, transcription coupled repair. This can cause a difference in mutation on transcribed vs non-transcribed DNA. In fact, this is known for G->T mutations, however, a change in A->G mutations is also seen, and is lower as expression increases. Also interesting, G-> Mutations decrease as transcription increases on both strands, however the mechanism of that observation is not yet known. This also seems to hold for other changes as well.

On the subject of genomic rearrangements, a large complex array of rearrangements was observed, however it was not mainly classical inversions as was expected. Instead, insertions in the midst of translocations were observed. What they did see matched FISH digital karyotyping, so that seems to be working.

Finally, some discussion was included on a CHD7 fusion in Small cell lung carcinomas, however, my notes end at this point without further discussion.

Overall, I really enjoyed this talk - as you'd expect, it was well done and covered a wide range of techniques that are available with 2nd gen sequencing. I wasn't aware of the range of nucleotide changes, or the specificity of tobacco-related carcinogens for specific nucleotides - nor even the repair mechanisms, so I got quite a bit out of it. My notes are relatively sparse, but just the few points I've recorded were of great interest to me.

I'll post the remaining talks as I have time over the next few days.

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