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

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

#31

Post by jrm5100 »

noname123 wrote: post #24
jrm5100 wrote: post #21

Earlier quoted context omitted.

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…

The Sanger/TCGA (The Cancer Genome Atlas) stuff seems to be specific to microarray data which is different (older, more expensive) than the newer high-throughput data.

The figure you linked is a good explanation. The split read method is helpful for finding the edges of the CNV, while the number of reads (relative to other regions that were tested) can give an idea of the number of copies. The problem is that these methods all have their own unique biases/noise that makes it non-trivial to figure out the absolute copy number change.

Ideally they would find a similar CNV that has some clinical association.

The DGV has a lot of reference CNVs. Here are some in BRCA1: http://dgv.tcag.ca/gb2/gbrowse/dgv2_hg19/?name=id:3087443;db...

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

#32

Post by adenadel »

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…

As someone in the field, this is a refreshingly accurate viewpoint. What do you think are some of the needs in the genomics space that aren't being tackled?

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

#33

Post by eladgil »

rfc wrote: post #28
eladgil wrote: post #27

Earlier quoted context omitted.

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 t…

It is really a matter of cost and utility. My answer is specific to "germline genetics" - i.e. inherited risk of disease, rather then sequencing a tumor sample or microbiome.

[Cost] In order to provide clinical results in a CAP/CLIA environment we need to ensure sufficient coverage to call all SNV/indels and all CNVs. This means we need much higher average coverage then 30X.

Since your exome is just 1-2% of your genome, and your exome encodes 20,000 to 25,000 genes, this means that 30 genes is Now, there are some caveats to this, e.g.: -You would use a slower, higher output more expensive machine like an X10 to do a whole genome at scale. -You can save some costs by doing whole genome versus a targeted panel as the pulldown step of the panel adds additional unique costs of its own. -This does not include fixed costs of sample collection, or secondary confirmation, or other costs that increase the price per test. This does not include labor costs, bioinformatics, or other items where sometimes dealing with a whole genome is cheaper per bp of DNA then doing a smaller panel of genes. -I think the "$1000 genome" isn't really here yet.

In a few years, the cost of sequencing the whole genome will be a few hundred dollars, at which point I think it makes sense to do the whole thing.

[Usefulness] It is important to note, however, that most of the genome is not very actionable right now. At Color our focus is on providing you with information you and your doctor can use, which means most of your genome is not characterized well enough to be clinically useful. At this point, depending on who is doing the estimate, only 30-60% of the 20,000+ genes you have are ascribed to a function, and even then it is often unclear how impactful a mutation in those genes are....

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

#34

Post by noname123 »

jrm5100 wrote: post #31
noname123 wrote: post #24

Earlier quoted context omitted.

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…

The Sanger/TCGA (The Cancer Genome Atlas) stuff seems to be specific to microarray data which is different (older, more expensive) than the newer high-throughput data. The figure you linked is a good explanation. The split read method is helpful for finding the edges of the CNV, while the number of reads (relative to other regions that were tested) can give an idea of the number of copies. The problem is that these m…

Thanks jrm5100 for the link. I see the variants under the "DGV Structural Variants" track. Really appreciate your explaining what CNVs are and also following up on my questions/confusions!

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

#35

Post by niels_olson »

adenadel wrote: post #32
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…

As someone in the field, this is a refreshingly accurate viewpoint. What do you think are some of the needs in the genomics space that aren't being tackled?

The consent forms for surgery and research need to be for whole genome or even multi-omics sequencing. There a bazillion IRB protocols, and they all have their own consent form, wasting the samples on just 10 or 20 genes.

Which would require getting IRBs on board. Which requires working with IRB systems vendors, like iRIS. (google for "iRIS IRB system")

Also, beating iRIS would be nice.

Also, marrying CROs to investigators and vice versa would be super helpful.

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

#36

Post by rfc »

eladgil wrote: post #33
rfc wrote: post #28

Earlier quoted context omitted.

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 t…

It is really a matter of cost and utility. My answer is specific to "germline genetics" - i.e. inherited risk of disease, rather then sequencing a tumor sample or microbiome. [Cost] In order to provide clinical results in a CAP/CLIA environment we need to ensure sufficient coverage to call all SNV/indels and all CNVs. This means we need much higher average coverage then 30X. Since your exome is just 1-2% of your geno…

Awesome, thanks so much for the response. It's clearer now the behind the scenes on what you're doing so appreciate you sharing. You're effectively providing a much needed and critical clinical tool for making more informed decisions on a patient diagnosis - something desperately needed.

I can sympathize with many of the regulatory and cost hurdles, especially for dealing with humans. We're in the purchasing process for a MiSeqDX and starting out specifically only on bacterial and viral sequences with an eventual path towards humans once we accomplish CLIA compliance. Long and costly effort...

Agree on the "$1000 genome" comment. Our average prep kit is ~$700 and, like you mentioned, once you factor in time, labor, computing costs, etc. the cost is well into the thousands.

I've had 4 relatives pass from various cancers which is what got me interested in the field to begin with. Truly hoping we can make some breakthroughs and it is encouraging to see startups such as yours pushing to make that happen. Best of luck!

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

#37

Post by jghn »

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…

The Precision Medicine Initiative will be wiring EMR into the pipelines. It'll be worked on by Vanderbilt, Google Genomics and the Broad Institute

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

#38

Post by srunni »

niels_olson wrote: post #35
adenadel wrote: post #32

Earlier quoted context omitted.

As someone in the field, this is a refreshingly accurate viewpoint. What do you think are some of the needs in the genomics space that aren't being tackled?

The consent forms for surgery and research need to be for whole genome or even multi-omics sequencing. There a bazillion IRB protocols, and they all have their own consent form, wasting the samples on just 10 or 20 genes. Which would require getting IRBs on board. Which requires working with IRB systems vendors, like iRIS. (google for "iRIS IRB system") Also, beating iRIS would be nice. Also, marrying CROs to investi…

> marrying CROs to investigators and vice versa would be super helpful.

Can you explain this idea in more detail? Many CROs are already establishing preferred-provider relationships with investigators.

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

#39

Post by dmix »

untilHellbanned wrote: post #25
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.

Are you saying the lack of access to data will be the issue? Or following health laws?

If they get some limited access to data, develop the machine learning software better than anyone, whats stopping one of the big pharma companies from shelling out $1B to acquire the company? Getting access to a tech team + IP could be very valuable. Pharma companies aren't known for their software teams either and this seems to be the core of their business offering here. Not the tests that everyone's already doing... I mean I just reread the article and they aren't claiming this is their core business proposition at all (as the OP seems to imply).

Even Illumina makes $2B in revenue currently. There's lots of money in the pharma industry and they always converge on a few big firms. They don't need to be original to provide real technical value here.

Unlike the pharma industry where you shield your IP with lawyers for 10 yrs, being first means nothing in the software world. It's about who can do it best.

The founders comments here also clarifies that they aren't going after new interesting areas because they are focusing on commercializing something that works right now and advancing that data science aspect of it, instead of making a future play on some original R&D.

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

#40

Post by untilHellbanned »

dmix wrote: post #39
untilHellbanned wrote: post #25

Earlier quoted context omitted.

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.

Are you saying the lack of access to data will be the issue? Or following health laws? If they get some limited access to data, develop the machine learning software better than anyone, whats stopping one of the big pharma companies from shelling out $1B to acquire the company? Getting access to a tech team + IP could be very valuable. Pharma companies aren't known for their software teams either and this seems to be…

Fair enough. Though to prove that their tech is better is definitely a data access issue. I obviously wish them luck but some ex-Twitter employees doesn't sound like a very leveraged team to be better at health data acquisition or data science. Unlike Twitter or Facebook, being good at science requires acquired knowledge. So even starting a bio PhD as one of the guy's did, the strength of their competitors and the carcasses of people before wouldn't give me any confidence to throw any amount of money let alone $45M at this thing.
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