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Fine-scale population structure and demographic history of British Pakistanis

Author

Listed:
  • Elena Arciero

    (Wellcome Sanger Institute)

  • Sufyan A. Dogra

    (Bradford Teaching Hospitals NHS Foundation Trust)

  • Daniel S. Malawsky

    (Wellcome Sanger Institute)

  • Massimo Mezzavilla

    (University of Trieste)

  • Theofanis Tsismentzoglou

    (University of Leeds
    University of Leeds)

  • Qin Qin Huang

    (Wellcome Sanger Institute)

  • Karen A. Hunt

    (Queen Mary University of London)

  • Dan Mason

    (Bradford Teaching Hospitals NHS Foundation Trust)

  • Saghira Malik Sharif

    (Leeds Teaching Hospitals NHS Trust)

  • David A. Heel

    (Queen Mary University of London)

  • Eamonn Sheridan

    (University of Leeds)

  • John Wright

    (Bradford Teaching Hospitals NHS Foundation Trust)

  • Neil Small

    (University of Bradford)

  • Shai Carmi

    (The Hebrew University of Jerusalem)

  • Mark M. Iles

    (University of Leeds
    University of Leeds)

  • Hilary C. Martin

    (Wellcome Sanger Institute)

Abstract

Previous genetic and public health research in the Pakistani population has focused on the role of consanguinity in increasing recessive disease risk, but little is known about its recent population history or the effects of endogamy. Here, we investigate fine-scale population structure, history and consanguinity patterns using genotype chip data from 2,200 British Pakistanis. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low recent effective population sizes (Ne), with some showing a decrease 15‒20 generations ago that has resulted in extensive identity-by-descent sharing and homozygosity, increasing the risk of recessive disorders. Our results from two orthogonal methods (one using machine learning and the other coalescent-based) suggest that the detailed reporting of parental relatedness for mothers in the cohort under-represents the true levels of consanguinity. These results demonstrate the impact of cultural practices on population structure and genomic diversity in Pakistanis, and have important implications for medical genetic studies.

Suggested Citation

  • Elena Arciero & Sufyan A. Dogra & Daniel S. Malawsky & Massimo Mezzavilla & Theofanis Tsismentzoglou & Qin Qin Huang & Karen A. Hunt & Dan Mason & Saghira Malik Sharif & David A. Heel & Eamonn Sherida, 2021. "Fine-scale population structure and demographic history of British Pakistanis," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27394-2
    DOI: 10.1038/s41467-021-27394-2
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    References listed on IDEAS

    as
    1. Severson, Alissa L. & Carmi, Shai & Rosenberg, Noah A., 2021. "Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population," Theoretical Population Biology, Elsevier, vol. 139(C), pages 50-65.
    2. Joseph K Pickrell & Jonathan K Pritchard, 2012. "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data," PLOS Genetics, Public Library of Science, vol. 8(11), pages 1-17, November.
    3. Vagheesh M. Narasimhan & Raheleh Rahbari & Aylwyn Scally & Arthur Wuster & Dan Mason & Yali Xue & John Wright & Richard C. Trembath & Eamonn R. Maher & David A. van Heel & Adam Auton & Matthew E. Hurl, 2017. "Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes," Nature Communications, Nature, vol. 8(1), pages 1-7, December.
    4. Dray, Stéphane & Dufour, Anne-Béatrice, 2007. "The ade4 Package: Implementing the Duality Diagram for Ecologists," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i04).
    5. Eric Vallabh Minikel & Konrad J. Karczewski & Hilary C. Martin & Beryl B. Cummings & Nicola Whiffin & Daniel Rhodes & Jessica Alföldi & Richard C. Trembath & David A. Heel & Mark J. Daly & Stuart L. S, 2020. "Evaluating drug targets through human loss-of-function genetic variation," Nature, Nature, vol. 581(7809), pages 459-464, May.
    6. David Reich & Kumarasamy Thangaraj & Nick Patterson & Alkes L. Price & Lalji Singh, 2009. "Reconstructing Indian population history," Nature, Nature, vol. 461(7263), pages 489-494, September.
    7. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    8. David W Clark & Yukinori Okada & Kristjan H S Moore & Dan Mason & Nicola Pirastu & Ilaria Gandin & Hannele Mattsson & Catriona L K Barnes & Kuang Lin & Jing Hua Zhao & Patrick Deelen & Rebecca Rohde &, 2019. "Associations of autozygosity with a broad range of human phenotypes," Nature Communications, Nature, vol. 10(1), pages 1-17, December.
    9. Peter K. Joshi & Tonu Esko & Hannele Mattsson & Niina Eklund & Ilaria Gandin & Teresa Nutile & Anne U. Jackson & Claudia Schurmann & Albert V. Smith & Weihua Zhang & Yukinori Okada & Alena Stančáková , 2015. "Directional dominance on stature and cognition in diverse human populations," Nature, Nature, vol. 523(7561), pages 459-462, July.
    10. Daniel John Lawson & Garrett Hellenthal & Simon Myers & Daniel Falush, 2012. "Inference of Population Structure using Dense Haplotype Data," PLOS Genetics, Public Library of Science, vol. 8(1), pages 1-16, January.
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    1. Cotter, Daniel J. & Severson, Alissa L. & Carmi, Shai & Rosenberg, Noah A., 2022. "Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating," Theoretical Population Biology, Elsevier, vol. 147(C), pages 1-15.

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