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Thread: Worldwide ROH paper (Pemberton et al.)

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    Worldwide ROH paper (Pemberton et al.)

    While discussing Runs of Homozygosity (ROH) with a friend, I discovered a study published in 2010 that analysed the HapMap and HGDP-CEPH datasets for them. I have attached below the image I deemed to be the most immediately interpretable in this context. As a rough guide, please note the horizontal white lines and vertical black lines/length of the violin plots represent the median and 25-75% range of ROHs per ethnic group respectively.

    Within West Eurasia (Europe, Middle-East, South-Central Asia) the results do seem to match one's preconceptions with respect to each tested group's individual geography and history (e.g. Bedouin and Basque sample having larger ROHs than Uyghurs).

    What did catch my attention was the situation in South-Central Asia. Despite coming from neighbouring regions, the Kalash and Burusho are on completely different levels. The Kalash and Balochi have the largest median ROH scores. This lends support to the ideas expressed in this thread regarding their infamous reputation as being particularly light-pigmented as partially being the result of over-expression of recessive features given their endogamous status accompanying the over-reporting of said features.

    Genomic Patterns of Homozygosity in Worldwide Human Populations
    Trevor J. Pemberton, Devin Absher, Marcus W. Feldman, Richard M. Myers, Noah A. Rosenberg, Jun Z. Li

    Quote Originally Posted by Abstract
    Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classesóshort, intermediate, and longówith a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.
    [Link]


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    Quote Originally Posted by DMXX View Post
    While discussing Runs of Homozygosity (ROH) with a friend, I discovered a study published in 2010 that analysed the HapMap and HGDP-CEPH datasets for them. I have attached below the image I deemed to be the most immediately interpretable in this context. As a rough guide, please note the horizontal white lines and vertical black lines/length of the violin plots represent the median and 25-75% range of ROHs per ethnic group respectively.

    Within West Eurasia (Europe, Middle-East, South-Central Asia) the results do seem to match one's preconceptions with respect to each tested group's individual geography and history (e.g. Bedouin and Basque sample having larger ROHs than Uyghurs).

    What did catch my attention was the situation in South-Central Asia. Despite coming from neighbouring regions, the Kalash and Burusho are on completely different levels. The Kalash and Balochi have the largest median ROH scores. This lends support to the ideas expressed in this thread regarding their infamous reputation as being particularly light-pigmented as partially being the result of over-expression of recessive features given their endogamous status accompanying the over-reporting of said features.

    Genomic Patterns of Homozygosity in Worldwide Human Populations
    Trevor J. Pemberton, Devin Absher, Marcus W. Feldman, Richard M. Myers, Noah A. Rosenberg, Jun Z. Li



    [Link]

    I'm a bit rusty on my maths(crap at it). But don't pathans have more people with Longer ROHs. *Edit: Nvm stupid question.
    Last edited by Arbogan; 04-16-2014 at 02:23 AM.

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    Quote Originally Posted by Baibars View Post
    I'm a bit rusty on my maths(crap at it). But don't pathans have more people with Longer ROHs. *Edit: Nvm stupid question.
    I think I understand the basis of your question - Please correct me if I'm wrong about that after the sentences below.

    Some populations shown have exceptionally long violin plot shapes. Particularly the Bedouins, Druze, Palestinians, Makrani, Brahui, Pathans and the North American groups. A larger length means a population has longer ROH segments. The form taken at the ends indicate the extent to which that population has these long segments.

    Using the Pathans as an example relative to other South-Central Asians, the median white line and vertical black lines are both well within the norm formed in the region. However, the pencil-shaped peak indicates a minority of the Pathan sample have exceptionally large ROHs. As we know they're from the Kurram valley, I suppose this represents either consanguinity or a very localised form of endogamy among some there. I don't think they're remarkable in this regard; we see a somewhat similar shape in the Druze and probably among other West-South Asians with a similar background. Some Iranian villages might produce that sort of shape as well.

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    Quote Originally Posted by DMXX View Post
    I think I understand the basis of your question - Please correct me if I'm wrong about that after the sentences below.

    Some populations shown have exceptionally long violin plot shapes. Particularly the Bedouins, Druze, Palestinians, Makrani, Brahui, Pathans and the North American groups. A larger length means a population has longer ROH segments. The form taken at the ends indicate the extent to which that population has these long segments.

    Using the Pathans as an example relative to other South-Central Asians, the median white line and vertical black lines are both well within the norm formed in the region. However, the pencil-shaped peak indicates a minority of the Pathan sample have exceptionally large ROHs. As we know they're from the Kurram valley, I suppose this represents either consanguinity or a very localised form of endogamy among some there. I don't think they're remarkable in this regard; we see a somewhat similar shape in the Druze and probably among other West-South Asians with a similar background. Some Iranian villages might produce that sort of shape as well.
    I don't know if i'm confusing math concepts here... but the diagram has two median lines.

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    Interesting - have any of you used : http://www.math.mun.ca/~dapike/FF23utils/roh.php

    Also did anyone do the TGAC analysis at Ethnoancestry a few years ago ? ( now Scotland DNA )
    Last edited by LUKE33; 04-17-2014 at 11:56 PM.

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