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Thread: SAPDA geneplaza

  1. #1
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    SAPDA geneplaza

    I'm struggling to see what's so wonderful about this .


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    It shows many people in South Asia have high West Eurasia drift. I am getting following


    W Eurasia 70.6%
    E Eurasia 16.1
    Siberian 13.3

    Deep ancestry takes W Eurasia to 75.2%
    Y: H1a1a4b3b1a8 Yfull id-> YF83218
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    mtDNA:U2a1a2
    G25 Ancients Dist 1.0 IRN_Shahr_I_Sokhta_BA2 88.4 MAR_Taforalt 2.6NPL_Mebrak 5
    VK2020_SWE_Gotland_VA 4 Hidden Content

    Lactose Persistence rs3213871 rs4988243 rs4988183 rs3769005 rs2236783
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  5. #3
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    Let's hope it's just for entertainment.
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  7. #4
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    I don't believe this to be just for entertainment, though it is thinking outside the box of many of the other techniques that often are discussed here. Being curious, I ran my family group through this test. I will attempt to explain what I am seeing in case anyone else has run the test. It may take more than one post.

    This test is using a limited number of SNPs that are considered to be very informative and in very limited, very broad sets of continental-based categories. Every SNP is assigned as West Eurasian, East Eurasian, West African, East African, or Siberian-American. So, it is a bit like a K=5 type of test. Within each of the five categories, the SNPs are defined as "Deep Ancestral", meaning that this is an old mutation that could be shared with other categories to some extent because the the SNP was set before a possible "split", such as between West and East Eurasian, and "Ancestral", meaning this is a more recent mutation and may indicate a more recent admixture event. In this type of low K test, it wouldn't be unusual, for example, for a European to have some East Eurasian and Siberian/Amerindian SNPs because these would exist and show up because of the nature of the test.

    For starters, you get an "Ancestral" admixture report based on just the limited SNPs that are being tested. Here is what we get:

    Me:

    MeAdmixture.png

    Dad:

    DadAdmixture.png

    Mom:

    MomAdmixture.png

    Wife:

    WifeAdmixture.png

    Father in law:

    FILAdmixture.png
    Last edited by randwulf; 12-17-2019 at 04:09 AM.

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  9. #5
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    Further into the report, you get the Ancestral admixture report repeated, as well as a different admixture report that uses the SNPs classified as Deep Ancestral. Here is my admixture report highlighting each separate Deep Ancestral category, so the percentage of each is displayed:

    With this, you can see my Deep Ancestral admixture results are the following:

    West Eurasian 93.90%
    East Eurasian 3.10%
    Siberian-American 1.70%
    East African 0.80%
    West African 0.50%

    Here are the pictures:

    MeDeepAncestralWEuro.png

    MeDeepAncestralEastAsian.png

    MeDeepAncestralSibAmerind.png

    MeDeepAncestralEastAfrican.png

    MeDeepAncestralWestAfrican.png
    Last edited by randwulf; 12-17-2019 at 05:29 AM.

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  11. #6
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    Just below the initial Ancestral Admixture Report, you get an interactive report of the actual SNPs of each type that you match on each chromosome. You select the type you want to see by clicking on the category in the initial Ancestral Admixture Report (East African, West Eurasian, East Eurasian, Siberian-American, West African). By hovering over any of the red triangles, you get a listing of the SNPs that you match at that location (one to many). Sometimes this is just one SNP and sometimes you get a list of SNPs, such as this:

    DadEastEurasianChrReport.png

    My father has several extensive non-European chromosome sections that can be seen in any chromosome painting utility, such as can be found at Gedmatch. Many of these show up on this test, too. Another way this can show up is that you can get several red triangles in close proximity, each with one to many SNPs at the location, such as you can see on this West African display for my father (see chromosome 13 where there is a cluster of red triangles):

    DadWestAfricanChrReport.png

    My thinking is that sections like this, especially when repeatedly reinforced by evidence from other targeted chromosome types of tests, may indicate fairly recent admixture (still, it may be a few generations back). Where there are many un-clustered, single SNPs, the overall percentage is reinforced, but it may be a little less conclusive on age of the admixture event.
    Last edited by randwulf; 12-17-2019 at 05:08 AM.

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  13. #7
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    Following this, you get a SNP-level report of each SNP of the type that you match in the category that you have highlighted. On the top part of the report, each SNP is displayed and when you hover over it with the mouse, you get the SNP name and the allele (value) that you have at that location that matches the category. Here, you can see that my father has one copy of the "A" allele for SNP RS78725400:

    DadSNPEastEurasian.png

    If you hover over the same SNP in the second half of this report, you get frequencies of that allele in various populations so you get some idea how "exclusive" this allele is to the category. In the case of RS78725400, you can see that East Asians have this value almost 62% of the time, southeast Asians 55+% of the time, Siberian/Amerinds and Europeans 1% to 3% of the time, and Africans 0%.

    DadSNPEastEurasian2.png

    I don't see any way to tell which SNPs are classified as Ancestral vs. Deep Ancestral, though, which would have been a nice feature.
    Last edited by randwulf; 12-17-2019 at 05:06 AM.

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  15. #8
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    Lastly, you get a "GSI" report, showing how similar you are to each category with regards to the set of informative SNPs in both the Deep Ancestral and Ancestral types for the category. The intent is that you can see some type of "flow", such as reduced similarity to West Eurasians or increased similarity to East Eurasians over time. I would imagine this could be most helpful for historical admixture events (invasion of Europe or West Asia from the east). It may be a little bit different for recent genealogical admixture between the category groups, which may require a bit of different interpretation (where one may get both Deep Ancestral and Ancestral alleles from the genealogical ancestor outside of the majority, I mean). At any rate, here are some pictures while hovering over my father's various GSI reports.

    DadGSIWestEuroDeepAnc.png

    DadGSIWestEuroAnc.png

    DadGSIEastAsianDeepAnc.png

    DadGSIEastAsianAnc.png

    DadGSISibAmerDeepAnc.png

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  17. #9
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    My result:
    GSI
    West Eurasian 61.20 Deep Ancestral and 38.30 Ancestral,
    Siberian-Amerindian 1.10 Deep Ancestral and 0.90 Ancestral,
    East asian 0.80 Deep Ancestral
    1.png2.png4.png
    Last edited by CelticGerman; 12-17-2019 at 08:07 AM.
    Known ancestry: 92.6% German (66.8% North German), 4.7% Danish, 1.8% Czech, 0.8% Austrian, 0.1% Swiss.
    EUROGENES K13: N German, N Dutch, DNK, SWE, NOR. Ancestry: Germanic 75%, Sweden 13%, Norway 11%, Baltic 1%. LM: NOR, DNK, NLD, N-DEU, SWE.
    23andMe: NW Europe 82.5% (French/German 50.2%, Scandinavian 9.1%, British/Irish 3.2%), East Europe 11.5%, South Europe 1.5%. DNAL: NW Euro 81%, NE Euro 11%, Med 6.5%
    Y-DNA: R1b/U152/Z36/CTS4333, Thuringia 1634, probably Alsace 1552, -- mt-DNA: H

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  19. #10
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    Quote Originally Posted by randwulf View Post
    Just below the initial Ancestral Admixture Report, you get an interactive report of the actual SNPs of each type that you match on each chromosome. You select the type you want to see by clicking on the category in the initial Ancestral Admixture Report (East African, West Eurasian, East Eurasian, Siberian-American, West African). By hovering over any of the red triangles, you get a listing of the SNPs that you match at that location (one to many). Sometimes this is just one SNP and sometimes you get a list of SNPs, such as this:

    DadEastEurasianChrReport.png

    My father has several extensive non-European chromosome sections that can be seen in any chromosome painting utility, such as can be found at Gedmatch. Many of these show up on this test, too. Another way this can show up is that you can get several red triangles in close proximity, each with one to many SNPs at the location, such as you can see on this West African display for my father (see chromosome 13 where there is a cluster of red triangles):

    DadWestAfricanChrReport.png

    My thinking is that sections like this, especially when repeatedly reinforced by evidence from other targeted chromosome types of tests, may indicate fairly recent admixture (still, it may be a few generations back). Where there are many un-clustered, single SNPs, the overall percentage is reinforced, but it may be a little less conclusive on age of the admixture event.

    I am unable to save a picture of a list of the snps as the list disappears when the cursor is moved. With the Siberian however I get one red triangle on chr 5 with

    Chr 5


    SNP Reference Allele Your Genotype
    ► rs77396005 T AT
    ► rs12173045 A CA
    ► rs78160752 T CT
    ► rs75961115 G AG
    ► rs76325941 T CT
    ► rs76705284 C TC
    ► rs79117061 G AG
    ► rs115203787 T CT
    ► rs75912834 A GA
    ► rs117817346 G CG
    ► rs79064345 G AG
    ► rs76776380 C AC
    ► rs117659274 G AG
    ► rs74463034 G AG
    ► rs77773812 A CA
    ► rs77790534 A TA
    ► rs117052705 A GA
    ► rs143480344 T GT
    ► rs77770306 T AT
    ► rs75034511 C TC
    ► rs116991923 C AC
    ► rs74353580 A GA
    ► rs77839562 G AG
    ► rs116795813 T CT
    ► rs76822738 C TC
    ► rs79013245 C TC
    ► rs76546364 A TA
    ► rs76635192 G CG
    ► rs79630023 T CT
    ► rs76396881 T CT
    ► rs74757826 G AG


    chr5:30,850,106

    chr 4 east eurasian 2 triangles not near each other 2=

    SNP Reference Allele Your Genotype
    ► rs76045183 C GC
    ► rs79843887 A TA
    ► rs76858092 T CT
    ► rs77066409 G AG
    ► rs79179278 T CT
    ► rs78896908 T AT
    ► rs140894866 A GA
    ► rs117750285 A GA
    ► rs79423134 C GC
    ► rs138923178 T CT
    ► rs79583284 A TA
    ► rs56944320 G CG
    ► rs75500593 G AG
    ► rs77291059 C TC
    ► rs74974094 T CT
    ► rs77920954 A TA
    ► rs76800405 G AG
    ► rs77514234 A CA
    ► rs74835253 C GC
    ► rs1391338 T CT
    ► rs75541456 C GC
    ► rs1497940 C GC
    ► rs2322579 C AC


    chr4:167,021,263


    chr 12 East Eurasian 1 red triangle

    SNP Reference Allele Your Genotype
    ► rs12582011 A GA
    ► rs79345295 T GT
    ► rs77841517 C TC
    ► rs12578915 C TC
    ► rs17032823 C TC
    ► rs58773246 T GT
    ► rs77592218 T CT
    ► rs17032833 C TC
    ► rs12580299 A GA
    ► rs57580368 A GA

    chr12:102,935,991



    chr 20 East Eurasian 2 red triangles not near each other . 1st =

    SNP Reference Allele Your Genotype
    ► rs6140125 A CA
    ► rs73602146 A GA
    ► rs6140149 G AG
    ► rs73602147 C TC
    ► rs6140182 C TC
    ► rs6140215 A CA

    chr20:745,547
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