Feb 20, 2012

$18,000 Cancer Genome

Illumina has announced an updated and improved cancer genome sequencing service for $18,000. This will provide genome sequencing of the tumor at 80x and of normal tissue from the same patient at 40x. This is similar to the coverage offered by Complete Genomics for a similar service (at $12K). Illumina also offers a novel sample prep method (by partnership with the Broad Inst.) for very small samples and FFPE.

Perhaps the most interesting thing about the Illumina service is the bioinformatics support, which will include a new variant detection algorithm that looks at both the tumor and normal together, in order to reduce the false positives. The standard approach, available from other software, does variant detection separately for each sample, then tries to subtract the variants found in the normal from those found in the tumor. This method works very poorly, since many variants cannot be called accurately in tumor samples which contain various amounts of normal tissue mixed in as well as tumor genomic heterogeneity. Many other existing variants are simply not called in the normal sample (ie. false negatives) due to poor coverage, poor quality, nearby insertion/deletions or any other feature that fails stringent variant detection software.  We have been working on this same approach to the problem, but Illumina brings a much bigger team with a access to a LOT more data. Illumina will also provide custom annotation of discovered variants provided by a team of human bioinformaticians (rather than just running the data through a static annotation software pipeline).

I think this is a more realistic milestone for clinical sequencing than the mythical $1000 genome. Cancer patients are one of the few (common) clinical scenarios where whole genome sequencing could really pay off with actionable discoveries - allowing genetic information to be used to chose targeted drugs and other interventions. A simple genome sequence (at whatever coverage) of a healthy person does not provide much medically actionable data today. Furthermore, the informatics that can currently be applied to a single, cheaply acquired, genome sequence range from relatively inexpensive but simplistic one-size-fits-all software pipelines to the equally mythical $100,000 interpretation (presumably provided by a dedicated project team of expert informaticians and medical geneticists).

3 comments:

Geneticist from the East said...

Any open-source effort going on to do the type of mixed (tumor and normal) variant calling that is implemented by Illumina as you mentioned?

sree wify said...
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Weight Loss Punch said...

The Cancer Genome Project, based at the Wellcome Trust Sanger Institute, aims to identify sequence variants mutations critical in the development of human cancers. Thanks.