Dash Genomics is able to process all the versions of raw data files from 23andMe and Ancestry.com.
To accommodate the difference among the raw data files of different versions or different platforms and to meet our quality standards, our algorithm uses loci that are generally shared by both of the 23andMe and Ancestry platforms and that were present in our library of raw data test files. We also require that the allele frequencies of those loci are consistent with the allele frequencies in 1000 Genomes Projects and between 23andMe and Ancestry platforms. We have thus identified
600,000 high confident loci as the input for the Alzheimer's risk model. Because we only use those high confident loci for our analysis, instead of using every single locus in the raw data file, we don't believe minor changes between different versions should affect the result significantly.
For individuals who have both 23andMe and Ancestry data, we recommend using the 23andMe file. The primary reason is that the Ancestry.com raw data file often fails to include or may misreport the genotypes of rs7412 and rs429358, 2 key loci for the APOE status (see details of this known issue at
https://www.snpedia.com/index.php/APOE “Word of caution” section). Thus, we have to first impute (infer) the genotypes of these loci based on other loci in the genome and identify the correct APOE status, then perform the analysis. We have compared the results for several users with both 23andMe and Ancestry raw data, and have observed only marginal differences.
circular wrote:xingxu wrote:While the researchers have not yet published an updated journal article regarding their use of ~ 600,000 high-quality SNPs based on 23andMe and Ancestry, this updated algorithm was developed by the same UCSF and UCSD researchers using the same peer-reviewed methodology that has been published in ...
Thanks very much for joining the conversation xingxu! It sounds like there's some hope that publication of the additional data is planned. I hope so.
Can you also comment on the question about how uploading different versions of results from Ancestry or 23andMe might affect the outcome?
For those who don't know, every so often these companies test with a newly updated version. I'm not an expert on this, but I think this might mean they are using a different genotyping chip and/or testing a different but largely overlapping set of SNPs. I don't think re-downloading one's data obtains results from the latest version; ie, the version applies to the front end of what SNPs were tested and on what genotyping chip, not to the results when you request a new download. To get the latest version one would need to be tested afresh on it. Is that an accurate statement?
The problem I'm having with the test is that without a report of the specific loci that most increase my risk, say the top three or top five, there's not much to do with the result?
Part of me is tempted to run it now in the event the FDA puts the quash on it?
Disclaimer: I am one of the co-founders of Dash Genomics.