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by mnw21cam 3361 days ago
> 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.
1 comments
gleb 3360 days ago
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.

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mnw21cam 3357 days ago
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 nc74rmec@pliggle.homeip.net if you want. (Yes, that's a throwaway address.) Not sure I can advise you much though.

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