Sep 29, 2011

Foundation Medicine grabs for the low-hanging fruit of NGS cancer diagnostics

I was at the CHI APPLYING NEXT-GENERATION SEQUENCING conference in Providence RI, where I heard an extremely interesting presentation from a new Genomics company called Foundation Medicine. This company plans to offer a clinical diagnostic test based on very deep sequencing of all exons from about 300 cancer related genes. They will sequence directly from pathologist's FFPE blocks using Illumina HiSeq to a depth of 500 to 1000X.

Here is a recent poster they presented at ASCO, but the information at the CHI conference was updated and more in depth.
ASCO poster

Here is why I think this is very important. First, this test will include all existing genes that are currently being tested for any type of cancer (BRCA1&2, KRAS, BRAF, HER2, EGFR, etc), but will include all exons and greater diagnostic sensitivity for mutations present in low abundance in heterogenous samples which may suffer from mixed tumor and normal tissue, multiple clones, mixed aneuploidy etc. It will likely also contain the majority of known pharmacogenomic genes. So this one test could put all the other providers of cancer related genetic tests out of business.

It is also very important that the test is highly targeted only at "actionable" genes. Foundation Med. plans to deliver a report for each patient (in 14 days) that lists all mutations observed in the diagnostic genes, as well as some key items drawn from the literature, clinical trials, and a curated knowledge base about treatments relevant to those genes. In the presentation, COO Kevin Krenitsky said that they typically found 2-3 mutated genes per patient. This is an amount of data that the oncologist or pathologist can reasonably be expected to deal with — rather than the hundreds to thousands of mutated genes with questionable to zero clinical implications that will be produced by whole genome sequencing.

Another interesting discovery reported by Foundation Med. was that in a small number of cases (perhaps 5%), they found mutations for genes that were associated with a different type of cancer. This suggests the use of a non-traditional drug, possibly in combination with other more typical therapies, as an individualized treatment for that one patient. There are currently about 30 drugs for which genetic information can aid in treatment decisions, but this is clearly an area of intense development. Foundation Med. can easily modify its test to include any relevant new genes. We are clearly heading to the point where every cancer patient will benefit from an individualized genomics workup.


Shawn Baker said...

It will be really interesting to see how NGS shakes up the diagnostic market over the next several years. Did they mention what the price of this test was going to be?

Stuart Brown said...

they said $4K

James Hadfield said...

I was surprised the test cost is so high, but I guess this is a propietary list they will say is better than anyone else's and comes with analysis.
We have been working on PCR based capture using Fluidigm Access Arrays and this brings costs down to £10-50 per sample for up to 480 loci (dependent on sample multiplexing).
I think the PCR based strategies have more power to disrupt current tests as they can be applied in a screening mode for all cancer patients, since the cost is so low. A $4000 test is going to be hard for the NHS to swallow!
I would also be interested to see how the Foundation Medicine test compares to Illuminas custom capture cancer panel?

Anonymous said...

BRAC1 and BRAC2? How do they get away with Myriad notorious gene patent?

Stuart Brown said...

they appear to be itchin' for the legal fight

Anonymous said...

Nice. Hope they can win. It would open the flood gate, and Myriad would shrink 50% at least, over night.

information technology said...

thanx for sharing

kaka said...

hello sir,
i am working on cancer research so i want a data for next gen sequencing regarding the cancerous genome and reference genome for analysis. can you please tell from which site i download the whole stuff.

Geneticist from the East said...

"There are currently about 30 drugs for which genetic information can aid in treatment decisions" - Where can I find these 30 drugs? Thanks!