[gleb]

Yes, that's exactly what they are saying. That's how they make money. And if that concerns realize that your doctor sells your EMR data, your pharmacy sells your prescription data, the labs sell your blood work data too.

https://genos.co/ will do a 75x whole exome sequencing (very good quality even for a clinical test) for $500 with a good customer experience and they don't sell your data. You can then feed the data to https://www.promethease.com/ for interpretation.

[mnw21cam]

> 75x whole exome sequencing (very good quality even for a clinical test)

You say that, but at the lab where I work, that level of quality would be a big fat fail - re-sequence the sample and get more data. They further describe their sequencing quality as "≥ 90% loci with 20x or more coverage AND ≥ 99% loci with 1x or more coverage". That's poor quality - very poor quality. We aim for 97% coverage at 20X and routinely get 98.5% They only get away with saying "Genos yields 50 times more data than comparable services" because they are comparing against 23andme, which uses a completely different test methodology.

[gleb]

Is your lab research or clinical? Genos coverage seems to be similar to GeneDx. I am told GeneDx is excellent on the clinical side. https://www.genedx.com/genedx-blog/exome-sequencing-at-gened...

Separately, can I get in touch with you somehow? I am dealing with clinical genetics as a patient right now, and would love to get some advice.

[mnw21cam]

Having a quick skim over that web page, yes it does look like they know what they are doing. However, they are still using SureSelect Whole Exome v4, when v6 has been available for quite some time now, and is so much better than v4. Their mean read depth is decent at 136X - that's about what we do. They quote a 31% pick up rate, where we have about 50%.

They talk about confirming variants using Sanger sequencing, but there is quite a bit of talk nowadays of stopping doing that, because NGS is becoming more reliable than Sanger. The problem with NGS is false positives, and the problem with Sanger is false negatives due to allelic dropout (the strand of DNA with the variant doesn't make it to the sequencer, so all you see is normal DNA). There is some concern that doing Sanger confirmation is rejecting more true positives than it is correcting false positives.

Our lab is both clinical and research. We don't do many research whole exomes any more - mostly doing whole genome instead.

You could mail me at [e-mail] if you want. (Yes, that's a throwaway address.) Not sure I can advise you much though.

[tonyhb]

No, doctors, pharmacies and labs do not sell data; it's illegal under HIPAA regulations and you do not want to be caught liable under those laws.

[nradov]

HIPAA regulations explicitly allow for using de-identified data in research. https://www.hhs.gov/hipaa/for-professionals/privacy/special-...

[gleb]

https://www.bloomberg.com/news/articles/2014-12-10/they-know...

[tschwimmer]

Dang, this promethease thing is awesome. It's crazy that they're offering all this data for free.

It reminded me a bit of an RPG character sheet: +60% resistance to prostate cancer, 2x weakness to alcoholism.

[kregasaurusrex]

Is there a list of genetic services and what data they provide somewhere, maybe a comparison of sorts? My father recently passed away of arryhtmia and I'm looking for a way to determine if said condition is hereditary or not.

[marchenko]

If you have concerns about a specific trait in your family history, I would suggest speaking to a genetic counselor. Many genetic conditions are influenced by a suite of relatively rare mutations not commonly included in commercial kits. A geneticist can tell you if this condition localizes to a specific chromosomal region or set of regions and sequence those target regions in depth for a better estimate of your risk profile. Perhaps more importantly, they can tell you if it is worthwhile to do so. Some conditions are too complex to reduce to effective testing, or result from poorly-characterized private mutations, but may have associated non-genetic biomarkers that your physician can monitor if you bring the problem to his attention. If your father's condition was well characterized and you have access to his history, you can do preliminary research on SNPedia (SNPedia lists whether a SNP of interest is included in the 23andMe kit), or do a PubMed search on "genetic risk factors" /"targeted next-generation sequencing" $condition to get a sense of the state of the art.

[gleb]

Look on Promethease wiki and Reddit.