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Thread: ADMIXTURE test using 350K markers

  1. #1
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    Lightbulb ADMIXTURE test using 350K markers

    I recently incorporated a panel of about 450 Eurasian samples with calls for about 1.1 million SNPs into my existing dataset. It turned out that the panel had about 400K overlapping SNPs with the 23andMe V4 chip. I was able to get a total of about 550 samples from the merged dataset with a genotype rate of 99% at about 350,000 SNPs.

    The panel contained samples mostly from Central Asia, Siberia, NE & SE Europe, SE Asia, Indonesian/Phillipines Archipelago, and some W Asian samples.

    I figured I would do a few ADMIXTURE tests using the above since I had not seen one before using that many SNPs (not that I expected any significantly different results from tests that use 100K SNPs), although a test using 350K markers should theoretically be useful in distinguishing closely related populations.

    Keep in mind that at 350K with a 99% genotype rate, I have to work with what I have, which is about 550 samples (including project members), so I don't have coverage from all over the world.

    I did a few supervised tests ( they are time consuming because of the high number of markers), and settled on a K of about 13. I decided to use the following components for starters.

    Component references:

    1- Brunei - About 8 Brunei_Murut references. I also have 8 Brunei_Dusun samples.
    2- Papuan - 6 Papua_Koinanbe and Papua_Kosipe references
    3- Afghan Pashtun - 6 Afghan Pashtun references, since I have never had an Afghan Pashtun component in any of my calculators, and since there are some W, SC, and S Asians here.
    4- Central Asian - Uzbek and Turkemen references. Keep in mind that C Asian scores will be reduced because of Pashtun component.
    5- Burmese
    6- SE European - Albanian, Macedonian, and Kosovo references
    7- NE European - Estonian references
    8- Near Eastern - Saudi, Jordanian, and Israeli Arab references
    9- Indian - Some Indian tribals
    10- German - The NW European cluster is weak here since I am limited to 4 German samples from W Europe
    11- NE Asian - Sakha references
    12- Mongolian - Mongolian and Altaian references. Members who score a couple of % in this category and NE Asian will see reduced scores, due to the Central Asian component.
    13- SSA - Based on Mbuti and Congo Pygmies, since I do not have other SSA groups at this high SNP level, although member SSA scores don't seem to be affected by this.

    Will post member and pop results later today time permitting as they become available

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  3. #2
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    Never seen any central Asian component before, kinda hyped for the results!
    Deg Teg Fateh - Victory to Charity and Arms

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    Where was the dataset? any Uyghurs? I thought of them when I saw Uzbek mentioned.
    dp :-)
    Last edited by dp; 09-28-2016 at 08:30 PM.
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    Quote Originally Posted by MonkeyDLuffy View Post
    Never seen any central Asian component before, kinda hyped for the results!
    Right? I'm excited about the Uzbek and Turkmen! I wonder what Balq's results will be like. Can't wait to test her brother if this becomes a DIY.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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    Quote Originally Posted by khanabadoshi View Post
    Right? I'm excited about the Uzbek and Turkmen! I wonder what Balq's results will be like. Can't wait to test her brother if this becomes a DIY.
    I had uzbek in my we genes results, so kinda fingers crossed for it! Maybe it will finally show some central asian connection in my case
    Deg Teg Fateh - Victory to Charity and Arms

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    Quote Originally Posted by MonkeyDLuffy View Post
    I had uzbek in my we genes results, so kinda fingers crossed for it! Maybe it will finally show some central asian connection in my case
    The Central Asian component I created was an Uzbek-Turkmen hybrid, and since I have a Pashtun component also, only ancestry closely related to Uzbeks and Turkmens will show up as a non-zero score, especially since I am using 350,000 SNPs. If I did not have a Pashtun component, Central Asian scores would likely have been higher.

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    Quote Originally Posted by khanabadoshi View Post
    Right? I'm excited about the Uzbek and Turkmen! I wonder what Balq's results will be like. Can't wait to test her brother if this becomes a DIY.
    Due to the presence of the Pashtun component, not too many members scores any Central Asian. You and a few other S Asians did score. Yours was close to 7%. I could not include your relatives or anyone elses for that matter, because that skews results in ADMIXTURE. You would have to run them through the DIY. Others with similar scores were some Pathans, Kurds, Iranian, and Tajiks.

    If I remove the Pashtun component, C Asian scores would rise.

    Everything looks reasonable, but I am hesitating a little right now in posting results, because I am trying to figure out why my 2 Iraqi Kurd samples had one of the highest Pashtun scores in the run (about 10% higher than the other Kurds). I would like to verify with another run or two (each run takes about 5 hours).

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    Double post
    Last edited by Kurd; 09-29-2016 at 03:47 AM.

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    Quote Originally Posted by David Powell View Post
    Where was the dataset? any Uyghurs? I thought of them when I saw Uzbek mentioned.
    dp :-)
    The run has varying samples from the following populations:

    Albanians
    Altaians
    Arabs_Israel
    Assyrians
    Azerbaijanis
    Belarusians
    Bengali
    Bengali_Dhaka
    Bosnian
    Brahmin
    Brunei_Dusun
    Brunei_Murut
    Burmese
    Chuvashes
    Circassians
    Congo-pygmies
    Cossacks
    Cossacks_Kuban
    Croats
    Druze
    Estonians
    Finnish
    Georgians
    Germans
    Hungarians
    India_Asur
    India_Gond
    India_Gupta
    India_Ho
    India_Kapu
    India_Kol
    India_Kurmi
    India_Marwadi
    India_Mpradesh
    India_Orissa
    India_Santhal
    India_Thakur
    Indian_Balija
    Indonesia_Bajo
    Indonesia_Lebbo
    Iran_Kermani
    Iranians
    Jordanians
    Kosovo
    Kryashen-Tatars
    Kshatriya
    Kumyks
    Kyrgyz
    Kyrgyz_Tajikstan
    Latvians
    Lebanese
    Lezgins
    Lithuanians
    Macedonian
    Malayan
    Mbuti.DG
    Mishar-Tatars
    Moldavians
    Mongolians
    Montenegran
    Mordvins
    Mota
    Motala12
    Nepal_Tamang
    Nepali_Brahmin
    North-Ossetians
    Papua_Koinanbe
    Papua_Kosipe
    Pashtun_Afghan
    Philippines_Batak
    Philippines_Igorot
    Philippines_Luzon
    Philippines_Vizayan
    PhilippinesAeta
    PhilippinesAgta
    Poles
    Punjab
    Russia_Avars
    Russia_Balkar
    Russia_Bashkir
    Russia_Ingrians
    Russia_Kabardins
    Russia_Karelians
    Russia_Kazakhs
    Russia_Kets
    Russia_Khantys
    Russia_Komi
    Russia_Mansi
    Russia_Mari
    Russia_Vepsas
    Russians
    Russians-Central
    Russians-North
    Russians-West
    Saami
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    Tuvinians
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    Ukrainians_east
    Ukrainians_north
    Ukrainians_west
    Ust_Ishim
    Uygurs
    Uzbek
    Vietnamese_central
    Vietnamese_north
    Vietnamese_south
    Yakuts

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    Quote Originally Posted by Kurd View Post
    Due to the presence of the Pashtun component, not too many members scores any Central Asian. You and a few other S Asians did score. Yours was close to 7%. I could not include your relatives or anyone elses for that matter, because that skews results in ADMIXTURE. You would have to run them through the DIY. Others with similar scores were some Pathans, Kurds, Iranian, and Tajiks.

    If I remove the Pashtun component, C Asian scores would rise.

    Everything looks reasonable, but I am hesitating a little right now in posting results, because I am trying to figure out why my 2 Iraqi Kurd samples had one of the highest Pashtun scores in the run (about 10% higher than the other Kurds). I would like to verify with another run or two (each run takes about 5 hours).
    I realize that ADMIXTURE skews if relatives are in the mix. Last time you kept my sister in the runs -- .Hanif -- just thought I should let you know that maybe you should remove her in case you forgot she is my sister.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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