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How do the ftDNA SNP assays and SNP panels “work” at the assay level?

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  • How do the ftDNA SNP assays and SNP panels “work” at the assay level?

    Do people get access to any kind of “raw” data? and How are the assays validated?
    Thanks
    John

  • wkauffman
    replied
    Originally posted by John-02081 View Post
    I have been looking at my BigY BAM file and I’ve noticed several SNPs that are from Y-chr regions that are repeated elsewhere on the Y-chr (segmental duplications). There are a few (~1%) mismatches between the regions which would usually be enough for the BigY reads (160 bp) to be correctly aligned. However, if left me scratching my head about how a SNP assay could be designed for these locations.

    There are several ways to “design” SNP assays and my first question was concerned with “how do I know that the SNP assays were well designed?”. It can be a difficult task. For example, do the designers have DNA available with the SNP variant for every SNP assay they design?
    All testing goes back to the reference sequence. Ideally the testing firm would be able to access both presumed positive and negative samples to serve a validation controls. In these days theoretical estimates can replace physical lab testing during prototyping runs.

    Testing for individual SNPs in palindromic or the x recombination regions is iffy. For Sanger sequencing of say 600 base pair read length one needs to identify positions on either side of the target location which are unique enough for the primers to bind and read the targeted sequence region. Sometimes this can be done but may take several iterations to get the parameters correct. R-L277.1 is an example of a location where it took several designs before a consistent positive and negative read occurred. Note that L277 was initially identified via the 23andMe v2 autosomal chip results. So within the R1b haplogroup region there are the "ZZ-series" snps which have been identified which may originate from 2 or 3 different locations on the Y. While they require manual curation the location present on the tree is consistent with the other parent and child SNPs or haplogroup levels relative to where they positioned on the tree. Generally the ZZ series SNPs cannot be tested for by Sanger but there is a solid subset of them which can successfully be tested for via the SNP packs. SNPs originating from recLOHs will probably need manual curation outside of FTDNA.

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  • John-02081
    replied
    I have been looking at my BigY BAM file and I’ve noticed several SNPs that are from Y-chr regions that are repeated elsewhere on the Y-chr (segmental duplications). There are a few (~1%) mismatches between the regions which would usually be enough for the BigY reads (160 bp) to be correctly aligned. However, if left me scratching my head about how a SNP assay could be designed for these locations.

    There are several ways to “design” SNP assays and my first question was concerned with “how do I know that the SNP assays were well designed?”. It can be a difficult task. For example, do the designers have DNA available with the SNP variant for every SNP assay they design?

    Leave a comment:


  • The_Contemplator
    replied
    No, you don't get any sort of raw data like that. Just a list of SNP names that were tested and you were found positive, negative, or no-call/heterozygous call. If you would like raw data you can look at, you are better off with the Big Y. That one you do get raw data in the form of VCF/BED files and BAM file that you can dig into if you know how.

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  • Jim Barrett
    replied
    I'm not sure if this is what you mean or not. For each SNP tested, either individual SNPs or SNP Pack SNPs you'll be told if you tested or negative for each SNP.

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