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Thread: Genographic Project uses a low amount of SNPs

  1. #1
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    Genographic Project uses a low amount of SNPs

    Below is an analysis of National Geographic Genographic Project 2.0 Helix's raw data. I ran it through DNA Kit Studios and was surprised at how low the actual amount of SNPs were that were tested. Especially because the company Helix purports to have cutting edge insight into ancestry analysis, because they sequence your DNA. Nevertheless, despite the fact that the parent company Helix sequences the customer, Geno 2.0 still only utilizes a small portion of it to determine their results. This is very misleading in my opinion. I was initially given the impression that Geno 2.0 was looking at sequenced information. But instead it was genotyping it, and at a sub-par rate. Considering the fact that the 23andme, and Ancestry DNA look at around 650,000-700,000 SNPs, while Geno 2.0 looks at a fraction of that. Helix does allow you to purchase your fully-sequenced data for $499. But right now I don't know of any service that it could be used for.

    ANALYZING RAW FILE Genetic.csv

    > Format: Geno2
    > Total SNPS: 199904
    > Flipped SNPS: 0 (0%)
    > Heterozygous SNPS: 59713 (29.87%)
    > Homozygous SNPS: 107617 (53.83%)
    > NoCalls SNPS: 32574 (16.29%)
    > Total SNPS by Chromosome:
    >> Chr 1: 11752
    >> Chr 2: 12345
    >> Chr 3: 9728
    >> Chr 4: 8297
    >> Chr 5: 8360
    >> Chr 6: 9518
    >> Chr 7: 7885
    >> Chr 8: 8767
    >> Chr 9: 7344
    >> Chr 10: 8212
    >> Chr 11: 7866
    >> Chr 12: 7447
    >> Chr 13: 5292
    >> Chr 14: 5055
    >> Chr 15: 4769
    >> Chr 16: 4939
    >> Chr 17: 4264
    >> Chr 18: 4660
    >> Chr 19: 3034
    >> Chr 20: 4139
    >> Chr 21: 2307
    >> Chr 22: 2217
    >> Chr X: 0
    >> Chr Y: 3623
    >> Chr MT: 15510
    >> Chr 26: 0
    ‚Äč

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    After converting with DNA kit Studio, I added the Xs from another RawData file, I passed through again with DNA kit studio. On Gedmatch got very similar results as 23 or Ancestry.

    I also experimented by adding only blank Xs SNPs, I runned through Gedmatch, and my results were still very similar as 23 and Ancestry. Maybe because Xs, or no Xs, my Parents are from the same Town.

    EDITED

    It would be nice to know how the original Sequenced RawData compares to 23 and Ancestry on Gedmatch and others.

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    Quote Originally Posted by Jovialis View Post
    Below is an analysis of National Geographic Genographic Project 2.0 Helix's raw data. I ran it through DNA Kit Studios and was surprised at how low the actual amount of SNPs were that were tested. Especially because the company Helix purports to have cutting edge insight into ancestry analysis, because they sequence your DNA. Nevertheless, despite the fact that the parent company Helix sequences the customer, Geno 2.0 still only utilizes a small portion of it to determine their results. This is very misleading in my opinion. I was initially given the impression that Geno 2.0 was looking at sequenced information. But instead it was genotyping it, and at a sub-par rate. Considering the fact that the 23andme, and Ancestry DNA look at around 650,000-700,000 SNPs, while Geno 2.0 looks at a fraction of that. Helix does allow you to purchase your fully-sequenced data for $499. But right now I don't know of any service that it could be used for.
    Taking into account Helix business model, as a Vendor put limits on its Clients, in this case the client is NatGeo.

    The Free RawData given to NatGeo customers is limited in order to avoid a Breach of Contract.

    It should not be assumed that NatGeo uses only the free RawData to run its predictions.

    imo

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