Foundation Medicine were yestoday granted US Patent 9,340,830 "Optimization of Multigene Analysis of Tumor Samples". This is likely to stir up the can of worms that is tumour testing by NGS and is another patent in a complex landscape. The claims basically cover WGS library prep, exome sequencing, alignment and variant calling. It covers all sorts of mutation calling including SNVs at low freq (5%) and mid-freq (10%) or above, SNPs to assess CNV & LOH, fusions and other structural variants, as well as pharmacogenomic SNPs. It also includes in the test a DNA fingerprint.
Michael Pellini, Foundation's CEO appears to be using some very positive language in describing the award of this patent, he said "we do not intend to block the use of methods covered by the patent in patient testing that may be offered by others". But how much of the patent claim is truly novel and might stand up in court remains to be seen. The basic idea of exome sequencing patients is old hat and Foundation were certainly not the first people to be doing this. The SNP ID of patients is an idea even I'd proposed over four years ago (here & here). But if Foundation's patent makes it harder for others to clamp down on competition that can only be a good thing.