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Thread: Fraud and frequent preprocessing in Genetic data

  1. #31
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    Quote Originally Posted by Vadim Verenich View Post
    This smells like a conspiracy theory's stink to me.
    I was also thinking in same lines. May be some unseen money pot is investing in few urban hotspots where few disgruntled upper caste people trying to erase all other people from their genome history.
    Y: H-M69 -> H-M82 -> SK1225 -> H-Z5888 -> H-Z5890 -> H-CTS8144 [CTS8144/PF1741/M5498] -> Z34531 (H1a1a4b3b1a8~)
    mtDNA: U2a1a
    extras 309.1C 315.1C 522.1A 522.2 CG8572A G8860A T11368C T16093a T16154C C16519T C195T

    G25 Ancients Dist 0.99 Shahr_I_Sokhta_BA3:S8728.E1.L1 65.2 Saidu_Sharif_IA_o:S7722.E1.L1 17.8 Udegram_IA:I1985 7.8 Jordanian:S_Jordanian-1 4.4 Barikot_IA:I6545 2.2 Scotland_N:I26602 Narva_Lithuania: Donkalnis6

    Lactose persistance rs3213871 rs4988243

  2. #32
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    Quote Originally Posted by Donwulff View Post
    Original poster said, "so remove the Dalit SNPs using pre-processing & add some Aryan SNPs to make a statement. So they will be doing it."

    I really wanted to bite on that, because the idea of "Dalit SNPs"... The microarrays used in current ancestry testing are testing mostly for frequent variants, in fact the definition of SNP is something along the lines of frequency more than 1-2%. To become that common, they need to be tens of thousands years old - in other words, they were formed long before the populations they seek to measure. Unless the variant is very recent one, it's going to be shared a lot by geographically close populations, and has indepently occurred in geographically distant populations. Most modern ancestry estimation methods in fact use haplotype based approach due to these reasons, not individual markers. It's quite doubtful any "Dalit SNPs" exist, and the suggestion of them existing in itself sounds discriminatory.

    On the technical side though, I have bad news. Regardless of the method used for ancestry estimates, for an individual tester it would be as simple as copying raw data from someone of desired ethnicity (Many, many people have published their raw data) to run at a third party. Of course, why bother when you can just paintshop the results? As for the genetic genealogy companies itself, having developed the analysis of course they have the expertise to make changes to data to make it look any ethnicity desired. But as I noted early on, if they actually changed the raw data as was implied by the original poster, these people would no longer match their relatives in DNA relatives comparison.

    So basically, there are no "SNP's for specific ethnicity", and while tampering with the genetic data is a feasible feat, for the test-taker Photoshop is much more easy and straightforward, and if a testing company did it, it would be immediately obvious. Adjusting ancestry analysis results is well possible, but lacks motivation unless it can be shown that the party doing the analysis is of or getting paid by said ethnicity. Either way, it should be easy to provide specific proof of "Fraud and frequent preprocessing".
    This also seems oddly south asian specific with the use of these terms...
    I don't think this is possible without an inordinate amount of work.

    Which makes me wonder where any thought over its existence is coming from

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  4. #33
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    There was a discussion about 23andMe's methodology here:

    http://www.anthrogenica.com/showthre...l=1#post145261

    Quote:

    "23andMe's speculative mode greatly overestimates major components, and underestimates minor components. This is due to their methodology of snipping the genome into 100 SNP segments to compare against the limited references they have. So for example, if 60% of the segment indicates Middle Eastern, and 40% indicates South Asian, that segment is assigned 100% Middle Eastern. In effect 40% of the segment, which is South Asian is ignored, and the whole segment is assigned Middle-Eastern.

    Also, their methodology includes segment smoothing, which means if there are chunks of minor components in a segment, they are ignored.

    That is how Iranians and West Asians turn out 98-100% Middle Eastern, and folks in neighboring Pakistan turn out 98-100% South Asian in speculative mode.

    This naturally is unrealistic and uninformative, because you don't need a test to tell you that. Conservative mode is better with regards to inflation of major components and underestimation of minor components, but the trouble here is that people get 5-70% unassigned. This is where your minor components are hidden.

    The above translates to 23andMe being useless for figuring out your minor components to any degree of accuracy."

    ====

    But I don't think any other company is using the same "purifying methodology".
    Last edited by Tomenable; 04-09-2019 at 11:20 PM.

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  6. #34
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    Quote Originally Posted by Tomenable View Post
    There was a discussion about 23andMe's methodology here:

    http://www.anthrogenica.com/showthre...l=1#post145261

    Quote:

    "23andMe's speculative mode greatly overestimates major components, and underestimates minor components. This is due to their methodology of snipping the genome into 100 SNP segments to compare against the limited references they have. So for example, if 60% of the segment indicates Middle Eastern, and 40% indicates South Asian, that segment is assigned 100% Middle Eastern. In effect 40% of the segment, which is South Asian is ignored, and the whole segment is assigned Middle-Eastern.

    Also, their methodology includes segment smoothing, which means if there are chunks of minor components in a segment, they are ignored.

    That is how Iranians and West Asians turn out 98-100% Middle Eastern, and folks in neighboring Pakistan turn out 98-100% South Asian in speculative mode.

    This naturally is unrealistic and uninformative, because you don't need a test to tell you that. Conservative mode is better with regards to inflation of major components and underestimation of minor components, but the trouble here is that people get 5-70% unassigned. This is where your minor components are hidden.

    The above translates to 23andMe being useless for figuring out your minor components to any degree of accuracy."

    ====

    But I don't think any other company is using the same "purifying methodology".
    Yeah but this is very different than "aryan" and "dalit" SNPs. This sounds more like a south asian specific accusation, as in certain users/people "doctor" their results to appear more "aryan".

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    Quote Originally Posted by tipirneni View Post
    I was also thinking in same lines. May be some unseen money pot is investing in few urban hotspots where few disgruntled upper caste people trying to erase all other people from their genome history.
    Where have you seen this? I'm legitimately curious as to where this is coming from.

  9. #36
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    Quote Originally Posted by 26284729292 View Post
    Yeah but this is very different than "aryan" and "dalit" SNPs. This sounds more like a south asian specific accusation, as in certain users/people "doctor" their results to appear more "aryan".
    Well, dalits do tend to have slightly more of indigenous South Asian DNA.

    Anyway as for that methodology:

    I don't think doing that is "wrong" or "right", but people should understand 23andMe shows recent and geographical (not deep or ethnic / "racial") ancestry.

    That's why they claim what they do about the timeframe (that their test goes only a few centuries back, to Early Modern Era).

    So what Maciamo claims on Eupedia (that 23andMe goes back even thousands of years ago, and he uses their data in his "racial admixture maps") is wrong.

    See what I'm talking about: https://www.eupedia.com/europe/autos....shtml#23andMe

    E.g. map of "Italian admixture": https://www.eupedia.com/images/conte...Me_Italian.png

    ^^^
    Less than 1% Italian DNA in Britain and in much of France and Iberia, which is almost certainly wrong considering how significant was Roman impact there:

    http://science.sciencemag.org/content/363/6432/1230

    ^^^
    This study detected high Italian admix only in Iberia, but brace yourselves: future aDNA studies about France and Southern Britain will also find Roman DNA. Reich lately suggested Roman impact in Southern England. And I claimed this back in 2015/2016 on forums (that South English have some Italian admix). There is also no way that all of France (Gaul) started speaking Latin and building advanced Roman-type cities without large influx of actual Roman settlers.
    Last edited by Tomenable; 04-10-2019 at 12:07 AM.

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    Quote Originally Posted by Tomenable View Post
    Well, dalits do tend to have slightly more of indigenous South Asian DNA.

    Anyway as for that methodology:

    I don't think doing that is "wrong" or "right", but people should understand 23andMe shows recent and geographical (not deep or ethnic / "racial") ancestry.

    That's why they claim what they do about the timeframe (that their test goes only a few centuries back, to Early Modern Era).

    So what Maciamo claims on Eupedia (that 23andMe goes back even thousands of years ago, and he uses their data in his "racial admixture maps") is wrong.

    See what I'm talking about: https://www.eupedia.com/europe/autos....shtml#23andMe

    E.g. map of "Italian admixture": https://www.eupedia.com/images/conte...Me_Italian.png

    ^^^
    Less than 1% Italian DNA in Britain and in much of France and Iberia, which is almost certainly wrong considering how significant was Roman impact there:

    http://science.sciencemag.org/content/363/6432/1230

    ^^^
    This study detected high Italian admix only in Iberia, but brace yourselves: future aDNA studies about France and Southern Britain will also find Roman DNA. Reich lately suggested Roman impact in Southern England. And I claimed this back in 2015/2016 on forums (that South English have some Italian admix). There is also no way that all of France (Gaul) started speaking Latin and building advanced Roman-type cities without large influx of actual Roman settlers.
    I don't disagree with your claim. But again I don't 'think he's referring so much to the 23andme interpretation as to doctoring the SNP's themselves in anticipation of how admix calculators work. E.g. an individual who is 35% south indian on harappa world (35% "dalit" for instance) altering his SNP's to replace some of the "south indian" SNPs with "caucasian/ne euro (other groups on harappa)" SNPs, making themselves appear more aryan and hence distanced from other local groups/castes.

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    how in the world do you alter/change SNP data?

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    Quote Originally Posted by JerryS. View Post
    how in the world do you alter/change SNP data?
    It is a text file that assigns each SNP an allele A/T, or C/G and all you have to do is to change the assigned A to T or C to G etc, afaik.

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