Color Genomics raises $45M to provide genetic tests that detect cancer risk • Hacker News Board

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

#21

Post by jrm5100 » Tue, Sep 27, 2016, 5:48 PM UTC

noname123 wrote: post #13

Here's their white-paper on their testing methodology: https://s3.amazonaws.com/color-static-prod/pdfs/validationWh... "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…

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).

"Copy number variant" refers to larger deletions and duplications that can occur in the genome. There isn't some specific cutoff for size, but some examples in these kinds of genes would be an entire exon or gene. There are countless studies that find correlations between specific variants or CNVs and risk of cancers.

Standard variant detection is pretty straightforward. CNVs are harder because they are longer (several hundred to several thousand base pairs) than the raw data (150 to 250 bp for Illumina)- you don't get single reads that span the entire variant. You have to normalize then look for differences in coverage, or look for split reads (where the read is aligned on the border of one of these CNVs).

This kind of funding baffles me because they don't seem to be proposing anything new at all (maybe slightly better CNV detection?) and there are already lots of labs/companies doing this kind of testing. Maybe they are working on being very efficient to offer a better price.

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

#22

Post by niels_olson » Tue, Sep 27, 2016, 6:09 PM UTC

Folks, everyone in the world who can get their hands on an illumina sequencer is developing these "30 gene", "400 gene", "N gene" 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.

The game is to actually get a lot of patients. Memorial Sloan Kettering, Foundation One, Broad Institute, Venter are the biggest data-gatherers I'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.

And the ethics questions and "we don't know about the environment" questions aren't going to get answered until the data is collected. Wait till the EMRs are tied into the big data pipelines. Oh, nellie.

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

#23

Post by sytse » Tue, Sep 27, 2016, 6:17 PM UTC

brandonb wrote: post #10

mcarlise wrote: post #2

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. We are still unsure of the nature/nuture problem. What if the en…

Elad started his career with a PhD in cancer biology prior to starting the mobile team at Google, so I don't think "academic imperialism" is an accurate descriptor. I think you'll see more people with these hybrid skills over time. They take years to develop, though. If we want advancement in medicine, can we really do it without deep collaboration between biology and computer science? If so, isn't Color Genomics a m…

I agree that Color Genomics is doing the right thing here. Of course any testing has the risk of misunderstandings and overtreatment. But they are aware of this and have counselors available to reduce the risk https://getcolor.com/learn/how-it-works

I think that medicine tends to treats us as patients instead of partners. Making testing much more affordable historically has done more good than bad. I think reducing the price of this testing by one or two orders of magnitude is a wonderful thing.

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

#24

Post by noname123 » Tue, Sep 27, 2016, 6:31 PM UTC

jrm5100 wrote: post #21

noname123 wrote: post #13

Here's their white-paper on their testing methodology: https://s3.amazonaws.com/color-static-prod/pdfs/validationWh... "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…

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). "Copy number variant" refers to larger deletions and duplications that ca…

Thanks for your detailed explanation.

Just out of curiosity and to follow-up, presumably this is a example of the list of detected CNVs in a TCGA Breast Cancer data-set you're referring to: http://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BRCA1#cnv...

According to Sanger (or maybe TCGA?), a gain is when a genomic region (for a diploid) has more than five absolute copies of this region and a loss is when the genomic region has no reads ((http://cancer.sanger.ac.uk/cosmic/help/cnv/overview), where the copy number is perhaps determined by that normalized distribution of read coverage across the reference genome?

(http://bmcbioinformatics.biomedcentral.com/articles/10.1186/...). This is for CNVs that are longer than the 150-200bp Illumina fragments (Fig1c. Read Depth method, e.g., exome#3 looks like it has two absolute copies vs exome #1 and #2)

Then for small CNVs that perhaps span that 150-200bp fragment, we use the split read method to filter for incompletely mapped reads that are only aligned on the edges to the reference. This implies that there was a duplication event that expanded that sequence? (Fig 1b. Split Read method).

Presumably, the pipeline would determine the CNV sites in a specific patient sample, then cross-reference with the TCGA CNV data-set and come up with correlation score of how much those CNVs sites match with consensus CNVs in the cancer data-set? Thanks again for your detailed breakdown.

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

#25

Post by untilHellbanned » Tue, Sep 27, 2016, 6:43 PM UTC

niels_olson wrote: post #22

Folks, everyone in the world who can get their hands on an illumina sequencer is developing these "30 gene", "400 gene", "N gene" 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 mol…

Yep. Academic molecular biolgist here. 100% agree. For as much as this community knows about software it knows shockingly little about the rules of health care.

Hate to break it to everyone breathless over yet another press clipping, but this startup is dead in the water. Another $45M down the tubes.

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

#26

Post by barkbro » Tue, Sep 27, 2016, 7:05 PM UTC

steveplace wrote: post #19

mcarlise wrote: post #2

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. We are still unsure of the nature/nuture problem. What if the en…

Because if people are getting cancer with no genetic markers, then we know it's environment... or at least not genetic.

The human genome and body are extremely complex. Concluding that something is caused by environmental factors just because a few genetic markers can't be found, would be a massive over-simplification.

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

#27

Post by eladgil » Tue, Sep 27, 2016, 7:13 PM UTC

mcarlise wrote: post #2

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. We are still unsure of the nature/nuture problem. What if the en…

Hi, I am one of the founders of Color and have a Ph.D. from MIT working on cancer genetics before later working at Google and other places. Another founder is an MD and clinical pathologist from UCSF, and then two others have backgrounds in software.

Color is focused on testing for characterized genes (e.g. BRCA1, BRCA2, PTEN, etc.) which have an impact to an individuals risk of developing cancer. Environmental and other factors of course play a role, and most cancers are not caused by these genes. However, knowing that you are at high risk of developing cancer is something a patient can work on with their physician to develop a personalized screening and prevention plan. For example, national guidelines from NCCN suggest that women with a BRCA1 mutation get more frequent mammograms. See also cancer.gov risks for having a BRCA1 or BRCA2 mutation: https://www.cancer.gov/about-cancer/causes-prevention/geneti...

Color was developed working closely with some of the leading cancer researchers including Dr. Mary-Claire King, who is credited with discovering BCRA1, and Dr. Laura Esserman and Dr. Laura v'ant Veer at UCSF. Our team includes people with backgrounds in genetics, medicine, and clinical pathology as well as machine learning, big data, and systems engineering.

This unique combination of skills is really crucial to pushing this area forward. For example, the Komen Foundation (one of the world's biggest breast cancer foundation) held a conference I was part of the planning committee for at Rockefeller University last year on big data for breast cancer. http://ww5.komen.org/BD4BC.html

Marrying data science to medicine is a way to drive cancer research forward.

As an aside, one of Color's founders is a BRCA carriers whose mother had breast cancer twice, and whose grandmother died of the disease. So, it is a bit sad to me that the default assumption is we are "academic imperialists" versus people trying to do something good for the world.

Thanks for reading :)

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

#28

Post by rfc » Tue, Sep 27, 2016, 7:28 PM UTC

eladgil wrote: post #27

mcarlise wrote: post #2

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. We are still unsure of the nature/nuture problem. What if the en…

Hi, I am one of the founders of Color and have a Ph.D. from MIT working on cancer genetics before later working at Google and other places. Another founder is an MD and clinical pathologist from UCSF, and then two others have backgrounds in software. Color is focused on testing for characterized genes (e.g. BRCA1, BRCA2, PTEN, etc.) which have an impact to an individuals risk of developing cancer. Environmental and o…

Hi Elad,

First off I want to say that I appreciate the drive to work on problems like this. I personally think it's a much better use of money than funding yet another marketing tool to 'revolutionize push notification blah blah'.

I am wondering if you can answer a question (probably naive but curious nonetheless). Why not sequence the full genome on a 30x coverage? Why find just the mutations on these genes rather than across the board?

The reason I'm asking is that it feels somewhat limiting to focus on only the currently known relationships of mutations rather than collecting the full data set. There's other initiatives, such as SB Genomics, that are doing very interesting work on the Cancer Cloud by utilizing new graphing techniques in data science to understand large scale pattern interactions, but they typically are utilizing the full data set.

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

#29

Post by colbyh » Tue, Sep 27, 2016, 7:35 PM UTC

rfc wrote: post #12

mcarlise wrote: post #2

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. We are still unsure of the nature/nuture problem. What if the en…

Agree. This was my initial reaction as well. While I can appreciate the founders background in Cancer research and drive to do something about the problem, the solution is unfortunately not a "just apply computer science!" one. We don't know what we don't know. Yes, we know that certain genes can contribute towards cancer. However, that doesn't mean you will develop it. You could have a torrent of SNPs underneath BRC…

the solution isn't black and white and Color doesn't act like it should be. they provide licensed genetic counsellors (free of cost) to contextualize your results.

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

#30

Post by futuremeats » Tue, Sep 27, 2016, 7:54 PM UTC

Does anybody know the total number / exact list of SNPs covered in this panel? How about the read depth?

I found this whitepaper on their website, which provides some level of detail...

https://s3.amazonaws.com/color-static-prod/pdfs/validationWh...

However, there were a good many asterisks and caveats about not testing every position along these genes (some of which are quite large).

While I'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.

http://myriadgenetics.eu/products/