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Thread: Interpretome POPRES: European

  1. #1
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    Interpretome POPRES: European

    I was looking through the various PCA tools on this site http://www.interpretome.com and was trying different combinations on the POPRES: European tool and found a combination that seemed quite useful/intuitive.

    1. After you load up your genome results (click "Begin Exploring" in the upper right corner to upload them)
    2. Choose PCA
    3. Select POPRES: European
    4. Select 74,000 (v3)
    5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
    6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"
    6. Click visualize
    7. Reverse the y axis so that the Northern Europeans are at the top and the Southern Europeans are at the bottom of the graph.
    8. Click on the all the country initials at the bottom to turn them off and then turn on only the ones you want to see. This helps to unclutter the graph and to see what populations you fall within.

    This particular PC combination seemed to do the best job in clustering the country results and placing them in relation to each other.

    I loaded my parents and my 23andme genome results into the graph and here are some of the results for countries that we fit into (British, German, Irish, Dutch, Belgian). Besides these 5 we also were are the Northern edge of France, the Western edge of Poland, and the Northwestern edge of Austria. I'm the upper right square, my mom is in between, and dad is lower left.

    Interpretome-POPRES-Euro-V3-PC5-PC1-British.gifInterpretome-POPRES-Euro-V3-PC5-PC1-German.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Irish.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Dutch.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Belgian.gif
    Last edited by MitchellSince1893; 03-08-2014 at 07:15 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    35% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 5% Ireland, 3% Nordic, 2% French/Dutch, 1% India
    Hidden Content

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  3. #2
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    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    35% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 5% Ireland, 3% Nordic, 2% French/Dutch, 1% India
    Hidden Content

  4. #3
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    Although not your target audience, I attempted your steps to see what the result was. My result landed me somewhere between the North and Central European areas. This does actually agree with my ADMIXTURE scores on certain project runs (e.g. more North_European than Atlantic_Med on Dodecad K12b). Great share!

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     MitchellSince1893 (03-08-2014)

  6. #4
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    Quote Originally Posted by MitchellSince1893 View Post
    I was looking through the various PCA tools on this site http://www.interpretome.com and was trying different combinations on the POPRES: European tool and found a combination that seemed quite useful/intuitive.

    1. After you load up your genome results (click "Begin Exploring" in the upper right corner to upload them)
    2. Choose PCA
    3. Select POPRES: European
    4. Select 74,000 (v3)
    5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
    6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"
    6. Click visualize
    7. Reverse the y axis so that the Northern Europeans are at the top and the Southern Europeans are at the bottom of the graph.
    8. Click on the all the country initials at the bottom to turn them off and then turn on only the ones you want to see. This helps to unclutter the graph and to see what populations you fall within.

    This particular PC combination seemed to do the best job in clustering the country results and placing them in relation to each other.

    I loaded my parents and my 23andme genome results into the graph and here are some of the results for countries that we fit into (British, German, Irish, Dutch, Belgian). Besides these 5 we also were are the Northern edge of France, the Western edge of Poland, and the Northwestern edge of Austria. I'm the upper right square, my mom is in between, and dad is lower left.

    Interpretome-POPRES-Euro-V3-PC5-PC1-British.gifInterpretome-POPRES-Euro-V3-PC5-PC1-German.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Irish.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Dutch.gifInterpretome-POPRES-Euro-V3-PC5-PC1-Belgian.gif
    thanks

    for your step 8 , why don't you just use mouse to highlight your block which then brings up the zoomed version.

    as for my results.........they are the same , circled by french, italian and swiss flags with a single portuguese flag also......

    it states to use PCA1 and PCA4 to match info below
    http://www.ncbi.nlm.nih.gov/pubmed/18760391

    If I use PCA4 instead of your recommended PCA5 , the portuguese flag drops off...the rest remain
    Last edited by vettor; 03-08-2014 at 09:34 PM.


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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     MitchellSince1893 (03-08-2014)

  8. #5
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    (14.0, –53.65)

    Pretty much in the Alps, overlapping Austria, France, Switzerland. Italy is slightly too far south, Germany too far north, and Spain too far west, but all barely miss.

    My mother ends up at (14.0, –61.175) in a fairly solid UK cluster, or put another way, within that mythical spot where Ireland and Belgium meet.
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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  10. #6
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    Quote Originally Posted by vettor View Post
    ...why don't you just use mouse to highlight your block which then brings up the zoomed version.

    http://www.ncbi.nlm.nih.gov/pubmed/18760391

    If I use PCA4 instead of your recommended PCA5 , the portuguese flag drops off...the rest remain
    I find that by not zooming in and only showing one or 2 countries (at least turn off the UK with covers up many other results); it's easier to see where one fit into the bigger picture for a group.

    Yes I saw that PC 4 comment, but when I read that the PC 5 showed a North/South European cline, I found that this PC along with PC 1, and reversing the Y axis, put the nationalities in a configuration similar to European geography. Ireland to the Northwest, Scandinavian countries at the top, Iberian countries to the southwest, Poland and Baltic countries to the Northeast etc.
    Last edited by MitchellSince1893; 03-08-2014 at 11:01 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    35% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 5% Ireland, 3% Nordic, 2% French/Dutch, 1% India
    Hidden Content

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  12. #7
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    Quote Originally Posted by MitchellSince1893 View Post
    I find that by not zooming in and only showing one or 2 countries (at least turn off the UK with covers up many other results); it's easier to see where one fit into the bigger picture for a group.

    Yes I saw that PC 4 comment, but when I read that the PC 5 showed a North/South European cline, I found that this PC along with PC 1, and reversing the Y axis, put the nationalities in a configuration similar to European geography. Ireland to the Northwest, Scandinavian countries at the top, Iberian countries to the southwest, Poland and Baltic countries to the Northeast etc.
    ok , mine is below......I still had to zoom because it was congested between FRA, ITA and CH ( swiss)

    Uploaded with ImageShack.us


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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     MitchellSince1893 (03-08-2014)

  14. #8
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    France France Bretagne
    I'm closer to German than French!
    Attachment 1587

    Below: France, UK, Germany, Ireland, Italy, Spain:
    Attachment 1588

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  16. #9
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    Quote Originally Posted by DMXX View Post
    Although not your target audience, I attempted your steps to see what the result was. My result landed me somewhere between the North and Central European areas. This does actually agree with my ADMIXTURE scores on certain project runs (e.g. more North_European than Atlantic_Med on Dodecad K12b). Great share!
    Would you mind posting your location? Interestingly, out of the populations from the region (excluding the Italians), my spot would probably be most near to the average for the Greeks (and even the Albanians, and perhaps Bulgarians), rather than the Turks or Cypriots.

     

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  18. #10
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    Quote Originally Posted by Humanist View Post
    Would you mind posting your location?
    Most certainly. Please see the attached. I'm basically in the centre of the Swiss cluster and the southern part of the British one.

    MyPOPRESEuroMitchellinstruction.jpg

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