Tuesday 27 August 2013

Back from my holidays

Two weeks away from the lab, from papers, from email and from Core Genomics - I’ve just got back from Finland’s wilderness: wood-fired sauna, lakes to swim in, fish to catch and no-one for miles; and all with fantastic 4G connection! Holidays are great and I think cutting yourself off from work is important if you’re truly going to relax and unwind. On my return to work there was the usual mass of email to work through. I thought I’d summarise the things that happened in the world of Genomics that I thought were interesting while I was away.

MiSeq gets a boost with PE300 and 25M reads per run; does anyone still use 454?
Qiagen is getting ready to launch the GeneReader; are Illumina getting ready to launch the lawsuits?

The Sanger led publication of an international Cancer genome studythat reveals the diversity of mutational signatures in Cancer. The study published in Nature used 6500 cancer exomes and 500 genomes, with all samples being analysed with an algorithm developed to study mutational signatures in breast cancer.

NICE approved multiple tests for NSCLC but stopped short of approving an NGS-based assay. The tests approved show how much we still rely on Sanger sequencing, something I feel we need to go cold-turkey on in the next few years (and maybe MiSeq PE500 will help)! The approved tests cost about £150 each according to GenomeWeb. Hopefully NGS-based tests will soon be rolled out for multiple cancers and multiple genes and they won’t be much more expensive. I’m off to a meeting today to discuss stratified medicine and the impact of NGS.

NICE also approved an mRNA test for Breast Cancer, Sysmex’s RD-100i OSNA (one-step nucleic acid amplification) cytokeratin-19 test. Results are available in 30-45 minutes and allows surgeons to make decisions in the operating room, healthy lymph node tissue does not express CK19 so the test allows doctors to decide how aggressive to be. A national registry of results is also being set up.

The NIH is setting up a core-facility for the Undiagnosed Diseases Program, that will use about 4% of the $145M budget. If they’re looking for a good core lab director, perhaps someone can give me a call?

Foundation Medicine took $11M in revenue in the first six-months of 2013 and plans to go public.

The battle against Myriad continues with Gene-by-gene joining Ambry Genetics in a lawsuit. I hope this is successful and BrCa data and analysis is freed for everyone to benefit from.

Familial fingerprinting is helping to solve crimes; the current tests still rely on STR profiling and it will be interesting to see how the reliability improves (or not) as this kind of testing moves over to NGS.

Some news from Identitas who are developing methods to determine physical appearance from genome data; they’ve formed a commercial partnership with Akesogen, a genomic services company.

Italy's national committee for cultural heritage is aiming to identify the grave of the model for Da Vinci’s Mona Lisa and compare DNA from the bones to known relatives. As it gets easier and easier to generate genome data from ancient DNA perhaps grave-robbing will come back in vogue?

Lastly NASA and Ion Torrent might put a sequencer into space, I’m not sure who’ll do the emulsion PCR though!

PS: Thanks to GenomeWeb for their coverage of everything Genomics.

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