Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

FDA Authorizes Ten 23andme Genetic Health Risk Reports

blog.23andme.com

Post reply on HN
Print view View original

151–160 of 195 posts

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#151

Post by rubatuga »

oceanghost wrote: post #142
butisaidsudo wrote: post #4

> For several years, 23andMe has worked on demonstrating that its reports are easy to understand and analytically valid... I guess these are different reports, but I know a genetic counsellor who describes 23andMe's carrier screening tests as "the bane of their existence". Those reports seem not-so-easy to understand based on the patients she sees. One problem is that they warn that your offspring are at high risk fo…

I have very weird metabolic problems... the US medical model --- if you can't diagnose it in two or three visits-- it doesn't exist. I actually have the 23andme kit right here-- I plan to get the genome data to submit to some other services to see if there's ANYTHING I can learn about what's going on with my body. My doctors have basically been watching me die.

Best of luck. If you really didn't have a diagnosis after 3 visits, you probably should see another doctor. I'm just curious, what you mean by metabolic problems?

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#152

Post by marchenko »

astrange wrote: post #137
decebalus1 wrote: post #73

Earlier quoted context omitted.

Yeah, for now but in general, that's useless. They have the leverage to change the policy whenever they want as long as they notify the customers at the login screen and via email. And hey, they can change the policy to not even notify anyone. And of course, they can be bought out and the customer data is part of the company value so there's that. Unless they provide an anonymous way of consuming their product I woul…

Not only your genes worthless, since everyone has genes, but you leave them everywhere, like when you get a haircut. Might be important if you were planning on a life of crime, or if you owe someone child support. But for the moment there's no good way to use them to make money off you.

There's a big difference between leaving your DNA on a cup and storing it in an easily-queried database. To collect your DNA from a cup , an interested party has to have an a priori interest in you specifically. To get it from a database (or databank, if 23 and Me is retaining physical samples, as their terms indicate they might), the interested party just has to have an a posteriori interest in "people's DNA", and hoover yours (and by probabilistic inference, your relatives') up along with everyone else's.

In the US, the protections against insurance companies using your genetic data against you are about as deeply entrenched as the protections against letting ISPs sell your internet history, and subject to much more intensive lobbying. Other countries have no protections at all - Canada's current bill is strongly opposed by the Trudeau government. Remember, even though most of these genetic risk scores are incredibly weak predictors, it is only necessary for insurers to believe they improve their actuarial models slightly to have a huge effect on differential insurance costs.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#153

Post by rubatuga »

gravelc wrote: post #126
phkahler wrote: post #6

Is there any way to just have your entire genome sequenced and get all the data in a software-friendly format? At that point there could/should be some open source software for analyzing it and finding common or well understood things like this. That way the software could be updated and people could re-run their analysis to look for newly discovered stuff. I think this would be an awesome amount of fun. I for one wo…

I'm a bioinformatician, but haven't really pondered doing this on my own DNA too much. Wouldn't be terribly complicated to sequence and analyse your entire genome though. Provided you could purify your DNA, sequencing wouldn't be an issue - just send it off to someone like BGI (Beijing Genomics Institute) and download the seq files when they're done. Purified DNA is stable and inert, so no special conditions required…

Totally agree with everything you said, although I believe the price is closer to 500 than a 1000. I worked at a lab last year which did methylation analysis on rat genomes, and the price for sequencing was not nearly a 1000. Although the analysis was slightly different since they pulled out all the non methylated DNA, we still ended up with >50GB of 50 bp reads that had a decent coverage of the genome. I'm certain that whole genome sequencing would be easier than what I described.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#155

Post by marchenko »

kregasaurusrex wrote: post #105
gleb wrote: post #96

Earlier quoted context omitted.

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…

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.

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.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#156

Post by marchenko »

grandalf wrote: post #146

I'm surprised to see all the fear-mongering in this thread. We leave genetic material behind everywhere we go. 23andme analyzes only a small subset of one's DNA. The most important thing to realize about genetics is that very few health conditions (and even traits) are highly correlated with a specific genotype. Some are, but the reason something like 23andme hasn't revolutionized health is because the correlations f…

Your comment could also be taken as an argument for being a late-adopter of commercial genetic testing services:

1. The AUC (predictive power)for most traits is currently very weak

2. The genetic privacy protection landscape is currently quite volatile

Taken together this puts the consumer in the situation of having data that is of middling utility for them personally, but is of great potential utility for the testing company and insurers. A small increase over the average population susceptibility for trait X is often non-actionable for you personally, but over several traits might be sufficient to shift you into a different insurance risk class. If you have privacy concerns and are interested in your risk profile for certain traits, look into whether a kit is available for those traits alone. You may wish to combine different kits from different providers to interrogate multiple regions (a more expensive strategy for the privacy-sensitive). There are a few companies that will put together a bespoke panel. At present, it may be prudent to take a hacker approach to genetic testing. https://isogg.org/wiki/List_of_DNA_testing_companies

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#157

Post by hawkweed »

peteretep wrote: post #101
butisaidsudo wrote: post #4

> For several years, 23andMe has worked on demonstrating that its reports are easy to understand and analytically valid... I guess these are different reports, but I know a genetic counsellor who describes 23andMe's carrier screening tests as "the bane of their existence". Those reports seem not-so-easy to understand based on the patients she sees. One problem is that they warn that your offspring are at high risk fo…

Yah. I've got a 50% chance of having Huntington's. When my parent was first diagnosed with it, me + all siblings were immediately going to get screened. Half of us actually booked to get the test done. But we later cancelled our screenings, and we're all now rather we didn't know. As I understand, genetic counselling in the case of HD is people telling you over and over again not to get tested. One of the constraints…

I completely understand you, because I'm in the same boat. It's hard to tell what is the right approach. I think that people should be tested. I'm still afraid to do that because I'm 31 years old and already started to experience some symptoms.

Yes, it's not easy decision but if you are not tested you can ruin life of your partner. It's better to prevent passing this terrible disease to your children.

Anyhow, 23andMe cannot tell you whether you have HD or not because they don't have sequences for that.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#158

Post by mnw21cam »

gleb wrote: post #96
Balgair wrote: post #24

Are they still saying that by submitting a sample to them, that they then own your genome and can sell it to whoever they want? I'd love to get mine sequenced and check it out a bit, but not if they are going to sell it off to a million shady companies whenever they go bankrupt (maybe 50+ years, but still)

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…

> 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.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#159

Post by hawkweed »

moonka wrote: post #110
peteretep wrote: post #101

Earlier quoted context omitted.

Yah. I've got a 50% chance of having Huntington's. When my parent was first diagnosed with it, me + all siblings were immediately going to get screened. Half of us actually booked to get the test done. But we later cancelled our screenings, and we're all now rather we didn't know. As I understand, genetic counselling in the case of HD is people telling you over and over again not to get tested. One of the constraints…

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.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#160

Post by mnw21cam »

gravelc wrote: post #143
soneca wrote: post #19

My opinion is that this test is useless at the least and dangerous at the most. It provides information that in almost the totality of the cases no one can correctly interpretate and transform in actionable health advice. Not scientists, not doctors, much less consumers. But it is sold as a cutting edge scientific resource that will improve your life. It wont. Not even increasing the chance that you might avoid somet…

I agree with this to a point. Obviously, genetic information can be quite informative for non-complex traits or diseases caused by variants in only 1 or a few genes. The reality is the genome isn't the complete instruction set for what makes you you. The interaction with the environment dataset is missing, along with any heritable epigenetic information. Add to that, our understanding of function is still extremely l…

> Obviously, genetic information can be quite informative for non-complex traits or diseases caused by variants in only 1 or a few genes.

And (unfortunately) those are the exact variants that services like 23andme do not detect.

23andme uses an array chip. These only detect common variants, in locations that have been pre-planned while designing the chip. A batch of patient samples are all tested together, and the probe for each variant produces a signal. Software then tries to cluster samples into three groups, which are homozygous normal, heterozygous, and homozygous abnormal. If the variant isn't common, then there would not be a decent number of samples in each group, and the clustering would fail. These tests are literally incapable of detecting any variant that is rare.

To detect rare variants, you need to do proper sequencing, for example with Sanger (single gene), or high throughput sequencing (AKA NGS, Next Generation Sequencing). This can be targeted panels of selected genes, whole exome sequencing, or whole genome sequencing.

A disease caused by a variant in a single gene (a monogenic disease) is usually caused by a rare variant. The more severe the disease, the more rare the variant is. A gene may have loads of common variants that do not cause disease. A gene may have a really rare variant that does not cause disease. Or it may have a rare variant that does cause disease - but this needs to be determined by someone with training and experience in the field.

As a lab, we regularly get inquiries by people saying "I have a variant detected by 23andme in - could this be causing my ?" The answer is "No - this test is incapable of detecting disease-causing variants - it only detects the benign ones."

Post reply on HN