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Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

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Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#31

Post by jarmstropreamp »

niekmaas wrote: post #24
jarmstropreamp wrote: post #18

Earlier quoted context omitted.

Hi daemonk, Jon Armstrong from Cofactor Genomics here. You hit on some excellent points. So you can detect circ. RNA that come from specific tissues and partition those reads out as expression for those tissues? In reality, we are detecting circRNA that arises or predominates during a specific disease state and then partition those reads out as a signal for the disease state. On a related note, the circRNA molecule r…

Finally a topic on hackernews that I am getting my PhD in..! Anyway, do you have any data indicating what percentage of circRNA is "free" in the plasma versus inside of other entities like platelets or extracellular vesicles (exosomes)?

The work with these molecules is early enough, that to my knowledge, there are no studies of this type that are published. And, in fact one could pose the same question for linear mRNA and ncRNA in exosomes (or ESVs). Most of the studies are on miRNA in ESVs, however we have done considerably work internally on characterizing long- mRNA and ncRNA in exosomes. These vesicles are fascinating!

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#32

Post by jarmstropreamp »

i000 wrote: post #27
davemessina wrote: post #26

Earlier quoted context omitted.

That some circRNAs are lower in cancer than in normal tissue is a reliably detectable difference and is precisely what makes them an excellent biomarker. There's additional evidence shown here: "Using circular RNA as a novel type of biomarker in the screening of gastric cancer". http://dx.doi.org/10.1016/j.cca.2015.02.018

I am aware of this study. Funny, how they show expression in deltaCT to make it appear higher in cancer ;). But regardless, the marker has a specificity of 0.62 - really that excellent? Such a high false-positive rate does not belong anywhere near a patient sample.

Our goal is to add additional markers to current candidates using our enrichment tech. It helps to remember that up until the ILMN/Solexa machine came online around 2005-6, we could not reliably detect (statistically) MAFs in heterogenous tumor samples below about 20% on the 454 platform (depending on how much cash you threw at the sample). Point is, our enrichment platform allows a deep dive into signals that have yet to be identified as reliable and low variance biomarkers.

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#33

Post by danieltillett »

davemessina wrote: post #17
danieltillett wrote: post #16

Earlier quoted context omitted.

Dave what is the patent landscape like for circular RNA? I hope it is better than RNAi or antisense?

Hi Daniel, We've filed patents on our work. Is there any biotech patent landscape as bad as RNAi? :)

Not that I know of :)

Good luck with your venture.

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#34

Post by mmaunder »

Related: Check out Jorge Soto's talk on NPR's Ted Radio Hour:

http://www.npr.org/programs/ted-radio-hour/

Soto is the CTO of Miroculus and they're using MicroRNA analysis to develop a cost effective way to provide early diagnosis for a variety of cancers.

So far they've made progress with pancreatic, breast and IIRC two others. This is huge because usually cancer is discovered when you become symptomatic which is usually stage three or worse and it's much harder to treat then.

If they can make this cost effective enough to be included in a regular doctor 'check up', then we may catch a large proportion of cancers early which makes treating them way easier.

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#35

Post by jeffdavis »

davemessina wrote: post #29
carbocation wrote: post #28

The article has a DNA versus RNA spin that, scientifically, is more of a distractor than anything when it comes to cancer. I understand that for marketing, it's useful. In blood cell cancers, Steve McCarroll's group has shown that oncogenic somatic DNA changes are readily discovered through routine sequencing, and these are prognostic of poor outcome.[1] If you do this on a pre-disease schedule based on the risk esti…

Thanks for your comments, and yes, you've got it exactly. In cancer, both DNA and RNA can be effective diagnostics, and there's been a lot of great work on the DNA side in cancer. In essentially all other diseases, though, there are changes in RNA but not in DNA.

"In essentially all other diseases, though, there are changes in RNA but not in DNA."

Is that true for autoimmune diseases like Type I Diabetes?

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#36

Post by navi54 »

davemessina wrote: post #2

Hi everyone! Dave Messina from Cofactor Genomics here. I'd be happy to answer any questions you might have. We're excited to launch!

Would you ever hire someone from Europe? And what skills do you seek after in a employee?

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#38

Post by davemessina »

jeffdavis wrote: post #35
davemessina wrote: post #29

Earlier quoted context omitted.

Thanks for your comments, and yes, you've got it exactly. In cancer, both DNA and RNA can be effective diagnostics, and there's been a lot of great work on the DNA side in cancer. In essentially all other diseases, though, there are changes in RNA but not in DNA.

"In essentially all other diseases, though, there are changes in RNA but not in DNA." Is that true for autoimmune diseases like Type I Diabetes?

Yes.

Re: Cofactor Genomics (YC S15) Pursues RNA Testing, Offers Better Diagnoses Than DNA

#39

Post by davemessina »

robbiep wrote: post #37

So they're getting 20k from YC to get valley contacts, at the cost of a percentage of the company, when they already have pharmaceutical and NIH funding? Or is there a different deal in place for biotechs?

Over half of the YC companies (us included) don't really need the money. The $120k investment is only a small part of what YC does.

See http://www.ycombinator.com/atyc/

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