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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

#121

Post by cariaso »

zimzam wrote: post #104
mrfusion wrote: post #83

Earlier quoted context omitted.

I see genetic counselors as gatekeepers to the information about our own bodies. Just give me my results and let me figure it out for myself. If some people want the service of a counselor let them get it but don't bar people from their own bodies. We research other issues ourselves and the world hasn't ended. Imagine if you weren't allowed to read the Bible but had visit a "bible counselor" if you wanted to find out…

Not sure if you're trying to be ironic but that's exactly how it worked for many hundreds of years: remember that historically speaking, outside the Church most people couldn't read. One source estimates that in 1300 CE only 6% of England's population was literate! "Bible counselors", aka priests, were indeed the only way for most people to get information from the bible.

It didn't matter that they were literate, since printing a bible in english was still illegal. It was only in 1526 that https://en.wikipedia.org/wiki/William_Tyndale created the first bible in English, allowing the common folk to go around the 'Bible counselors'. As a result the church had him convicted of heresy and executed by strangulation, after which his body was burnt at the stake.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#123

Post by jinxedID »

deusofnull wrote: post #122

Can't wait till the require these for health insurance... Seriously, is there regulation protecting people from "pre-existing conditions" discovered by their genetic analysis?

Yes, there is in the United States. Oddly enough there are no such laws in Canada.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#124

Post by nommm-nommm »

Florin_Andrei wrote: post #46
cjbprime wrote: post #41

Earlier quoted context omitted.

soneca has a good point here (perhaps accidentally), which is that you'll notice that 23andme doesn't return Huntington's or CF results, and it sounds like the reason is because they would be so useful and predictive of disease. Which does put 23andme's health results in this realm soneca described of "things that might be interesting, but can't be very actionable because they don't want to scare you by returning act…

No. What's really happening is that they did provide a lot of probability estimates for some pretty serious stuff - back in the day before the FDA told them to stop doing it. I know because I carry a higher risk allele for a non-trivial disease (along with lower risk alleles for some other non-trivial diseases), and the test placed me in those corresponding statistical risk buckets which are different from the genera…

>I carry a higher risk allele for a non-trivial disease (along with lower risk alleles for some other non-trivial diseases), and the test placed me in those corresponding statistical risk buckets which are different from the general population.

How do you know this is accurate?

https://mobile.nytimes.com/2013/12/31/science/i-had-my-dna-p...

>23andMe said my most elevated risks — about double the average for women of European ethnicity — were for psoriasis and rheumatoid arthritis, with my lifetime odds of getting the diseases at 20.2 percent and 8.2 percent. But according to Genetic Testing Laboratories, my lowest risks were for — you guessed it — psoriasis (2 percent) and rheumatoid arthritis (2.6 percent).

>In the case of Type 2 diabetes, inconsistencies on a semantic level masked similarities in the numbers. G.T.L. said my risk was “medium” at 10.3 percent, but 23andMe said my risk was “decreased” at 15.7 percent. In fact, both companies had calculated my odds to be roughly three-quarters of the average, but they used slightly different averages — and very different words — to interpret the numbers. In isolation, the first would have left me worried; the second, relieved.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#125

Post by nojvek »

sushid wrote: post #14
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…

Have you already done a 23andMe analysis? If so, you can check out https://promethease.com/ . It's exactly what you're looking for as they have constant updates that make it worth your while to rescan every year or so.

Are you saying 23&Me gives you a file with the full list of chromosome's ACGT data? I've always wanted that.

Also is prometheus and open source analyzer?

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#126

Post by gravelc »

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 for posting it.

Sequence files are just text (if they're in FASTQ format), and all the common tools are open-source. No doubt someone somewhere has put together a Docker image with software for the entire workflow (FASTQ file processing --> read alignment --> variant calling), so processing isn't a big issue. As there's no de novo genome assembly or anything like that, the whole thing can be done on a run-of-the-mill PC, and would take a few days, depending on the depth of sequencing.

My guess is cost would be approaching US$1000 now.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#127

Post by nojvek »

Animats wrote: post #11
jjeaff wrote: post #5

Earlier quoted context omitted.

If you have already submitted a sample, you will get a report. Since 23andme maps your whole genome, they simply compare the existing data as new finding are approved. OR if you are like some and signed up early before the FDA crackdown, you already got all this information and now they are just reappearing little by little.

Since 23andme maps your whole genome... They don't go that far. A full genome sequencing costs around $2900 as of 2015. (Which is amazing, since the first one cost billions.) Maybe $1000 with the new Illumina HiSeq X Ten sequencing system. Data from a full genome sequencing is about 80GB. (Opportunity here for specialized compression - 98% of the genome for humans is the same.) 23andme is testing for about 100,000 kn…

Where can I get my full genome sequenced?

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#128

Post by berberous »

nojvek wrote: post #125
sushid wrote: post #14

Earlier quoted context omitted.

Have you already done a 23andMe analysis? If so, you can check out https://promethease.com/ . It's exactly what you're looking for as they have constant updates that make it worth your while to rescan every year or so.

Are you saying 23&Me gives you a file with the full list of chromosome's ACGT data? I've always wanted that. Also is prometheus and open source analyzer?

23&Me will let you download a text file with the ACGT data, but only for the SNPs that it has. 23&Me does not sequence your full genome, so the SNPs available are a small subset of your DNA.

Prometheus is not open-source (I think), but all it does is read various files with DNA data (like the 23&me export), and match it up with the information in SNPedia (a Wikipedia-like open repository of what we know about certain SNPs), and then exports it to a pretty HTML/JS web report for you that you can download and save.

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#129

Post by Animats »

nojvek wrote: post #127
Animats wrote: post #11

Earlier quoted context omitted.

Since 23andme maps your whole genome... They don't go that far. A full genome sequencing costs around $2900 as of 2015. (Which is amazing, since the first one cost billions.) Maybe $1000 with the new Illumina HiSeq X Ten sequencing system. Data from a full genome sequencing is about 80GB. (Opportunity here for specialized compression - 98% of the genome for humans is the same.) 23andme is testing for about 100,000 kn…

Where can I get my full genome sequenced?

Lots of places. Genomics Personalized Health in Santa Monica offers the service to individuals for $2500.[1] Includes cloud storage for the data. They have a list of medical consultants who can help interpret the data; they just give you the bits.

List of service providers.[2]

[1] https://genomicspersonalizedhealth.com/ [2] https://www.scienceexchange.com/services/whole-genome-seq

Re: FDA Authorizes Ten 23andme Genetic Health Risk Reports

#130

Post by Latty »

nommm-nommm wrote: post #112
problems wrote: post #102

Earlier quoted context omitted.

I'd much rather that kind of thing be available as clicking a button personally. Getting information that could help you make big decisions is very useful.

What sort of big decisions does knowing you have Huntington's disease help you make? It's a debilitating disease with no treatment or any way to prevent it.

I mean, all of them beyond the day-to-day?

I plan my life expecting to live to an average age, as I assume most of us do. I save for retirement, I make investments that will pay off at times useful to me.

If I knew I had a serious condition that changes my quality of life and life expectancy, that means I need to change my life plans. Sure, it may not be 100%, but working off the most likely outcome seems sensible.

Not to mention, no treatments right now - if I know I've got something, I can follow developments and if treatment does become available, I can do something. Obviously, you could monitor this if you knew you were higher-risk anyway, without testing, but not everyone knows that.

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