Fine-scale population structure and demographic history of British Pakistanis

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 Sheridan, John Wright, Neil Small, Shai Carmi, Mark M. Iles and Hilary C. Martin ()
Additional contact information
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
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
Hilary C. Martin: Wellcome Sanger Institute

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-27394-2

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