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Stats Biotech Medicine Science

New vs. Old: a Comparison of 23andMe's Health Reports and the Raw Data (enlis.com) 96

"With much fanfare," writes an anonymous reader, "last month 23andMe returned to reporting health information to their genetic service customers. How does their new service stack up?" According to the Enlis Genomics Blog, it's a good move but not perfect. The linked post explains that "the raw data from 23andMe contains significantly more health information than they are reporting in their health reports," and says "23andme has a long way to go to get back to reporting the same number of variants they were before the FDA ban. However – both the previous and new 23andMe reports pale in comparison to an analysis of the raw data. 23andMe’s new reports tell you about less that 1% of the health-related variants that are in their raw data." It's an interesting statistical blow-by-blow; the company making the comparison has a vested interest in you letting them run the numbers, but is not the only option.
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New vs. Old: a Comparison of 23andMe's Health Reports and the Raw Data

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  • by PopeRatzo ( 965947 ) on Friday November 06, 2015 @09:44PM (#50881269) Journal

    According to the data, one can predict the stupidity of a Slashdot comment by whether the poster is an Anonymous Coward. Studies have proven this time and time again.

    Data, like hips, don't lie.

  • by kromozone ( 817261 ) on Friday November 06, 2015 @10:52PM (#50881459)

    Instead of opening your data up to yet another corporation by trusting someone else to analyze your raw data, why not create an open source application that you can download to analyze your raw genetic data? I'm sure the molecular biologists out there would be more than willing to help contribute.

    • They would still have the data.
      • by KGIII ( 973947 )

        It would be awesome to have a small finger sticker and analytics device, like used for diabetes blood sugar testing kits, that, maybe, hooked into a USB port and did the work there and was able to spit the data out. Then you could do all sorts of things, up to and including things like removing any easily identified PII and sharing the results with the research communities of your own volition.

        They took a bunch of blood when I joined the military. While this was, indeed, many years ago (mid 1980s when I wen

        • Now you can get glucometers with BluTooth data sharing :-)
        • by Agripa ( 139780 )

          It would be awesome to have a small finger sticker and analytics device, like used for diabetes blood sugar testing kits, that, maybe, hooked into a USB port and did the work there and was able to spit the data out.

          You do not think such a device would be used by the authorities like in GATTACA?

          • by KGIII ( 973947 )

            Well then I'd be on the lookout for agents with little stabby pens. Just because it can be abused doesn't make me not want it.

    • by ponos ( 122721 )

      The data is quite simple. At the most basic level it's just a photo of bright spots on a chip, as read by the machine. Knowing that spot A corresponds to variant A and spot B to variant B, an algorithm then decides ("calls"), depending on the relative brightness whether the person has variants AA, AB or BB (or impossible to tell). This is the only real processing and there IS open source software for that (packages for R, most famously CRLMM).

      So, the whole point is getting the variant calls, ie what sort of

    • by Anonymous Coward

      ...why not create an open source application that you can download to analyze your raw genetic data?

      Many, if not most of the major analysis tools are already freely available (usually even fully open source).

      Let's say your raw data is a full genome sequence reads from an Illumina sequencer (which costs about $1,000 from a few drops of saliva at the going rate). Well, first thing you're going to do is map your raw reads to a reference genome. The most common reference genome in use is freely available from the NCBI ftp site that is provided by the US NIH. And there are plenty of free read mappers available

      • by RDW ( 41497 )

        23andMe use SNP arrays (custom Illumina BeadChips) rather than NGS at the moment. The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:

        http://www.snpedia.com/index.p... [snpedia.com]

        You can convert this into something standard like VCF, which most tools that deal with variants will read.

        • The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:

          No, but it is cheap, which is not to be underestimated. If we want affordable healthcare, we have to care about cost and not just the new shiny. The other thing is, focusing on select variants allows them to do a targeted analysis. In a world plagued by systems biology, people like to think a "global picture" is always better, but having some idea what you are looking for before you start collecting data makes your statistical analysis, you know...meaningful.

          • by RDW ( 41497 )

            That was really just a comment for biology geeks about the kind of data they provide. With a true raw file, you can get more out of SNP array data (e.g. genomic copy number). The 23andMe pricing is pretty keen, though, perhaps only about double what what you'd pay an academic service provider to run a SNP array of similar size (you'd get full raw data, but would have to do the DNA extraction and data interpretation yourself). An exome costs about 10x the price of the cheapest SNP array, and a whole genome m

      • And getting back on topic, 23andMe was focused on just that problem: putting together a website that could help ordinary people understand their genomes. And the FDA shut them down

        The FDA requires analytical verification ( does the test or service accurately and reproducibly provide the data that you are saying within acceptable margins of error? ) and clinical validation ( can the results of the test or service be reliably associated with specific health outcomes, after accounting for statistical significance and effect sizes? ) for medical devices and services sold in the USA. 23andMe has to go through this process as does every medical services company. This is not a conspiracy. T

  • Slashvertising (Score:5, Informative)

    by goodmanj ( 234846 ) on Saturday November 07, 2015 @12:40AM (#50881739)

    Clearly nobody read the link, because it's one big fat ad for a third-party genome-analysis tool and nobody's complained yet. Come on, people, keep up!

    • So are we allowed to mention any company names in a slashdot news article? Or is it all Slashvertisement? As one who is a user of 23andme, this is actually fairly significant news for me. It also has enormous privacy implications and is seems quite news-for-nerds worthy.
      • I thought about trying their service but for $199 I'll pass.

        • I thought about trying their service but for $199 I'll pass.

          I thought about trying their service but for the ultimate invasion of privacy [scientificamerican.com] and an open door to future violations of human rights, I'll pass. I really want to know what they have to tell me but I certainly am not willing to find out under these terms. Now, when I can do it anonymously...

  • Ok, this is very simple, and something all the developers here need to know.

    If you're reporting medical information in the US, you need all of the processes you use to generate that health information to go through the FDA before you ADVERTISE you can do it (yes, your website is an advertisement). Fitness is fine any time, go crazy with that. Medical information, only after FDA approval. If you think you may be doing something health related, go find a regulatory consultant and find out what you need to

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