Color Genomics raises $45M to provide genetic tests that detect cancer risk

Folks, everyone in the world who can get their hands on an illumina sequencer is developing these &quot;30 gene&quot;, &quot;400 gene&quot;, &quot;N gene&quot; tests, liquid biopsies, blah, blah, blah. Even the fact that they got a VC to shell out $45M is something happen pretty regularly now. Source: senior pathology resident in San Diego, driving past illumina and the Craig Venter Institute every day. Developing these tests is literally all molecular pathologists do. All day long.<p>The game is to actually get a lot of patients. Memorial Sloan Kettering, Foundation One, Broad Institute, Venter are the biggest data-gatherers I&#x27;m aware of right now, with the DoD starting to get in the game. But who really wins will be the platforms that do the bioinformatics analysis: Google Genomics, illumina (basespace), etc.<p>And the ethics questions and &quot;we don&#x27;t know about the environment&quot; questions aren&#x27;t going to get answered until the data is collected. Wait till the EMRs are tied into the big data pipelines. Oh, nellie.

This is border line academic imperialism. The founders seem to think that software engineering and data science applied to biological data will provide insight that traditional biology has not found. Unneccessary screening from a single dimension (genome) is only going to misguide patients into oppurtunistic drug companies and non-FDA approved remedies.<p>We are still unsure of the nature&#x2F;nuture problem. What if the environment is more attributable to cancer development?

Here&#x27;s their white-paper on their testing methodology: <a href="https:&#x2F;&#x2F;s3.amazonaws.com&#x2F;color-static-prod&#x2F;pdfs&#x2F;validationWhitePaper.pdf" rel="nofollow">https:&#x2F;&#x2F;s3.amazonaws.com&#x2F;color-static-prod&#x2F;pdfs&#x2F;validationWh...</a><p>&quot;Color has developed a next-generation sequencing based test for hereditary cancer. This test analyzes 30 genes associated with increased risk to develop breast, ovarian, colorectal, melanoma, pancreatic, prostate, stomach, and uterine cancers... The assay has a high degree of analytical validity for the detection of single nucleotide variants, small insertions and deletions (indels), and larger deletions and duplications (copy number variants, or CNVs).&quot;<p>So not micro-arrays like 23andMe that test for SNPs ($99?), but not full genome sequencing either (~$1,000?); but specific sequencing for the sites of these genomic regions of those 30 genes.<p>Wet Lab sequencing method: &quot;Specifically, it includes target enrichment by Agilent’s SureSelect method (v1.7) and sequencing by Illumina’s NextSeq 500 (paired-end 150bp, High Output kit)&quot;; Unanswered question, are they doing the sequencing in-house or using a facility somewhere else?<p>Computational method: &quot;The bioinformatics pipeline was built using well-established algorithms such as BWA-MEM, SAMtools, Picard and GATK. CNVs are detected using dedicated internally developed algorithms for read depth analysis and split-read alignment detection.&quot;<p>So basically perform the standard genome assembly, alignment with human reference genome of your partial assembly, and then identify what variant of these 30 genes the patient sample has; plus a special sauce for counting the number of specific bp repeats, due to in-del events, this is not something I am not too familiar, but presumably the number of a specific k-mer repeats you have in these genes of interest might correlate to a specific type of cancer? (would love to hear someone who is an expert in this field their opinion).<p>&quot;These [30] genes are APC, ATM, BAP1, BARD1, BMPR1A, BRCA1,BRCA2, BRIP1, CDH1, CDK4, CDKN2A (p14ARF and p16INK4a), CHEK2, EPCAM, GREM1, MITF, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, POLD1, POLE, PTEN, RAD51C, RAD51D, SMAD4, STK11, and TP53&quot;. (You can follow up by searching them here, e.g., <a href="http:&#x2F;&#x2F;www.genecards.org&#x2F;cgi-bin&#x2F;carddisp.pl?gene=BRCA2&amp;keywords=BRCA2" rel="nofollow">http:&#x2F;&#x2F;www.genecards.org&#x2F;cgi-bin&#x2F;carddisp.pl?gene=BRCA2&amp;keyw...</a>).<p>Also interesting to note, since it&#x27;s clinical, each of their test has to be verified by a certified &quot;genetics counselor&quot; and also meet lots of clinical standards.

I am not sure there is really a large enough corpus of data out there that covers multiple facets of this system to really give us a strong predictive value. Just variant calls is probably not enough. There might be, if we can somehow consolidate and integrate disparate datasets from various publications and labs. But I don&#x27;t think we are at that stage yet.<p>I am all for them trying though. I just don&#x27;t think we are at a point where we can make a good diagnosis&#x2F;conclusion yet.

Does anybody know the total number &#x2F; exact list of SNPs covered in this panel? How about the read depth?<p>I found this whitepaper on their website, which provides some level of detail...<p><a href="https:&#x2F;&#x2F;s3.amazonaws.com&#x2F;color-static-prod&#x2F;pdfs&#x2F;validationWhitePaper.pdf" rel="nofollow">https:&#x2F;&#x2F;s3.amazonaws.com&#x2F;color-static-prod&#x2F;pdfs&#x2F;validationWh...</a><p>However, there were a good many asterisks and caveats about not testing every position along these genes (some of which are quite large).<p>While I&#x27;m not aware of any other companies that are doing this type of direct to consumer testing, companies like Myriad have offered targeted panels on some of these gene targets for some time.<p><a href="http:&#x2F;&#x2F;myriadgenetics.eu&#x2F;products&#x2F;" rel="nofollow">http:&#x2F;&#x2F;myriadgenetics.eu&#x2F;products&#x2F;</a>

There are already companies that do this... Today they are called innovators, tomorrow they&#x27;ll be called money-grubbing, unethical, anti-FDA maniacs for do the same thing.