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