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FDA Authorizes Ten 23andme Genetic Health Risk Reports

blog.23andme.com

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Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#191

Post by SEJeff »

hawkweed wrote: post #159
moonka wrote: post #110

Earlier quoted context omitted.

If you don't mind me asking, why would you prefer not to know?

Well, it's basically a death sentence for person having this condition. Event though there are some attempts by IONIS HTTRx to find a cure, currently, it's not curable. And it's hard to tell if this disease will ever be curable.

Life is a death sentence, unless someone has unlocked the key to immortality. I'm sure there are people who've lived less years than me who have still lived a fuller life than me. Randy Pausch, of Carnegie Mellon University, comes to mind:

https://www.youtube.com/watch?v=ji5_MqicxSo

Just because you're born knowing you're going to die doesn't mean we should all fret about it (unless you're a Nihlist of course, and then it doesn't matter as everything is futile). Knowing you're more likely to pass sooner would hopefully be a good thing in that you'd hopefully spend more time with your family creating memories than useless stuff like grinding at work and trying to climb corporate ladders only to become a senior middle manager in 20 years.

Personally, I would absolutely want to know to pivot my life towards reality. I'd much rather have an educated guess as to what my future might hold given the options vs sticking my head in the sand and "hopes and prayers" for the best. That being said, I can understand how it might simply be overwhelming for some people who wish to remain blissfully ignorant. Best of luck to them!

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#192

Post by kakarot »

magic_beans wrote: post #45
dikdik wrote: post #34

Earlier quoted context omitted.

There are already companies out there using DNA sequencing for some absolutely bullshit products...Vinome comes to mind, they suggest wine you might like based on your genome. Personally, I'm all for it though. It's a way to have fun with science. As a scientist, it's nice to have stupid "horoscopes" to keep life interesting.

Whoa. That is a pretty fine gimmick there. I'm amazed that anyone wealthy enough to afford that kind of service would be stupid enough to use it.

Poor people are often uneducated by necessity, but blood-rich folk are sometimes uneducated by choice. What a luxury!

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#193

Post by mnw21cam »

searine wrote: post #189
mnw21cam wrote: post #162

Earlier quoted context omitted.

23andme can only detect common variants. In general, common variants do not cause non-mild diseases - certainly nothing worth avoiding a child being born. You should certainly not be making decisions like that based on a report from 23andme.

It can detect whatever variants they put on the SNP chip, be they common or rare. The only caveat is we have to know what variants to put on the chip in the first place. That's the hard part, linking rare variants to disease. After that link is made, the rest is easy. Is it a sure fire shot to detecting all rare genetic disease? Of course not. Is it a good way to become aware that I am a carrier for a rare mendelian…

They still have to have good clustering of samples for each variant they are testing. That is, there needs to be a sufficient number of samples in each of the three states (homozygous normal, heterozygous, and homozygous variant) for the software to look at the analogue signals and draw a box around each of the three clusters. This generally prevents the analysis of rare variants using chip technology.

I would be very curious if you could look up the variant that 23andme have reported you have on http://exac.broadinstitute.org/ and let us know the "Allele Frequency" from there.

The thing is, most people are carriers of several rare mendelian diseases. When we do whole exome sequencing, we get on average a couple of hundred rare potentially pathogenic variants in each patient, of which possibly 20 or 30 are actual causes of rare mendelian disease. However, the patients are only carriers of these disease, and are completely irrelevant to their health. The likelihood of them having children with someone who is a carrier for the same condition is very slim (but something we investigate every day).

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#194

Post by mnw21cam »

gleb wrote: post #177
mnw21cam wrote: post #158

Earlier quoted context omitted.

> 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 routine…

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.

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.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#195

Post by searine »

mnw21cam wrote: post #193
searine wrote: post #189

Earlier quoted context omitted.

It can detect whatever variants they put on the SNP chip, be they common or rare. The only caveat is we have to know what variants to put on the chip in the first place. That's the hard part, linking rare variants to disease. After that link is made, the rest is easy. Is it a sure fire shot to detecting all rare genetic disease? Of course not. Is it a good way to become aware that I am a carrier for a rare mendelian…

They still have to have good clustering of samples for each variant they are testing. That is, there needs to be a sufficient number of samples in each of the three states (homozygous normal, heterozygous, and homozygous variant) for the software to look at the analogue signals and draw a box around each of the three clusters. This generally prevents the analysis of rare variants using chip technology. I would be ver…

>Allele Frequency

For the particular SNP I am heterozygous for in this particular gene, the population level allele frequency is 0.00001649. Missense mutation. Another variant in this gene, a stop loss, is at 0.0017

Yes, of course the likelihood of it being a problem is slim, but definitely not zero. High enough that it is worth knowing.

>but something we investigate every day

You and me both.

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