New vs. Old – a comparison of 23andMe’s health reports and the raw data
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Edit: Ah, it appears that anonymously handing over your DNA may not even be possible: http://www.technologyreview.com/news/509901/study-highlights...
Actually, this sounds eminently plausible. As I understand it, a DNA microarray consists of a bunch of probes that each transmit a signal when they bind to a specific strand of digested DNA. A probe is either bound or not, and since you're applying a mixture obtained from multiple cells, there's many copies of each DNA sequence present in either case. There's no way you could establish whether or not two copies of the same gene were present in an individual cell.
I could be wrong (I'm a bioinformatician, not a biologist), and 23andme could be doing something interesting which reveals this data- in either case, I'd be interested to hear. But this makes fairly bad advertising copy- everyone else with the same cursory understanding of this technology is going to have the same thought, and think that you don't even have said cursory understanding if you don't explain your reasoning better [1].
[1] For that matter, you come off as wildly unscientific simply because you make this sort of conjecture without citing sources. There is a resource out there, somewhere, that would confirm or deny what you're saying, and your ability to make a credible scientific statement rests on you finding it.
There is a nice animation of the technology on Illumina's website. It's a single base extension assay where you have hybridization of a probe, then add a labeled nucleotide where the SNP is that you are studying. For a A/T SNP, if you basepair and add an 'A' you get a green signal, if you add a 'T' you get a red signal. If you end up with a mix of green/red, you have a heterozygous variant.
Illumina has a tech note on the call rate and error rate here: http://www.illumina.com/Documents/products/technotes/technot... At a minor allele frequency of 0.5% their minor allele homozygous error rate was 0.1%.
The nice thing about this technology is that the more data you have, the better your calls get, and 23andMe has real world data on over 1 million customers. (Illumina tech note used data from 2,000 genotyped samples) I think 23andMe has enough data to know which of the SNPs on their genotyping chip are accurate, but they don't exactly open up their data for public inspection.
If you are a 23andMe customer you can see the improvements to the raw data they have made over the years here: ( https://www.23andme.com/you/download/revisions/ ) If you can't see it, it says things like: "July 28th, 2014. Analysis of our data has allowed us to improve the interpretation of over 10,000 SNPs genome-wide on the V4 chip." When they get more data, they are improving their calls.
Finally, the FDA document about 23andMe's approved Bloom Syndrome carrier test says that "all homozygous variant genotype samples receive a 'no-call' result, since the calling software was designed not to detect homozygous variant genotypes." It sounds to me like they designed the software to ignore and throw out homozygous data. http://www.accessdata.fda.gov/cdrh_docs/reviews/DEN140044.pd...
If Enlis grows, they may get a similar letter to 23andme, because they would be offering a medical analysis not approved by the FDA.
It's conceivable that that one could look at each of the 600,000 lines in 23andMe's raw data and find these research reports individually.
We simplify that process and make the connections to research reports for you. Then, wrap it up in a nice package where you can compare your family member's data, get information on genes, generate PDF reports, etc.
Unless the FDA wants to shut down public access to scientific knowledge, then we don't expect to hear from the FDA. Others have been operating in this space for several years.
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Here are some of the differences and advantages of Enlis Genome Personal:
It's a full software application. Rather than just a webpage or single report, Enlis Genome Personal is a full application that you install on your computer and load your genome data.
Ability to load multiple genomes and compare them side-by-side. You can load all your family member genomes together, or load multiple copies of your own genome (i.e. you have data from 23andMe and Ancestry.com), or you can compare your genome to available sample data.
Ability to generate custom disease and trait PDFs, suitable for email or printing. A sample Macular Degeneration PDF is sent with every free genome report.
For a particular disease or trait, this software will tell you how many known disease positions were successfully sequenced in your data, and how many are missing. For example, if you are interested in a hereditary disease like Cystic Fibrosis, it will indicate there are 270 known variants that cause Cystic Fibrosis. Your data covers 101 of those positions, and there is missing data on 169 positions.
More extensive information on each SNP, like variant mammalian conservation, or variant deleterious predictions. Much more information on the function of genes and where in the body those genes are expressed.
User friendly interface that is easy to use. Includes a genome browser so you can see your data in the context of genes and chromosomes.
For 23andMe users - better quality control and more data: We discovered over 500 SNPs with inaccurate data in the 23andMe results, and we automatically filter those out. See blog post here. We are the only service to identify and analyze over 1,000 of 23andMe's proprietary insertions and deletions. Most of these can have a health impact. See blog post here.
For users with whole genome or exome data: We give you the tools to make new discoveries about your data. Advanced variation filter, phenotype explorer, homozygous region analysis, and over 20,000 built-in gene categories. An example - our founder used this software to discover a cause of a rare phenotype in his whole genome data. How long did it take? Less than 30 seconds.