Fine-scale population structure and demographic history of British Pakistanis

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.

Performing Hybridity or Deflecting Islamophobia? Adaptable Identity Management amongst Young British Pakistani Muslims

This article engages with issues of identity construction and maintenance as expressed by a group of young British Pakistanis living in the North-West of England. Drawing on primary data from a qualitative study, we examine the ways in which Muslim identities are maintained, negotiated, and protected in relation to everyday situated cultural experiences. Nested within a context in which Islamophobia is pervasive, we discuss four salient processes of identity management articulated by participants: cherry picking; strategic adaption; ambassadorship and active resistance. Whilst these processes are to be considered as porous rather than mutually exclusive, our analysis elucidates evidence of both nimble and creative individual identity management and also an entrenchment of collective pride. We posit that, for the participants in this study, such practices constitute a grounded, pragmatic response to living in an environment in which their religious beliefs, political values and cultural commitments are frequently questioned within public life, the media and the political sphere.

Harnessing the power of polygenic risk scores to predict type 2 diabetes and its subtypes in a high-risk population of British Pakistanis and Bangladeshis in a routine healthcare setting

Background: Type 2 diabetes is a heterogeneous condition highly prevalent in British Pakistanis and Bangladeshis (BPB). The Genes & Health (G&H) cohort offers means to explore genetic determinants of disease in BPBs, combining genetic and lifelong health record data. Methods: We assessed whether common genetic loci associated with type 2 diabetes in European-ancestry individuals (EUR) replicate in G&H. We constructed a type 2 diabetes polygenic risk score (PRS) and combined it with a clinical risk instrument (QDiabetes) to build a novel, integrated risk tool (IRT). We compared IRT performance using net reclassification index (NRI) versus QDiabetes alone. We assessed the ability of the PRS to predict type 2 diabetes following gestational diabetes (GDM). We compared PRS distribution between type 2 diabetes subgroups identified by clinical features at diagnosis. Findings: Accounting for power, we replicated fewer loci associated with type 2 diabetes in G&H (n = 76/338, 22%) than would be expected if all EUR-ascertained loci were transferable (n = 95, 28%) (binomial p value = 0.01). In 13,648 patients free from type 2 diabetes followed up for 10 years, NRI was 3.2% for IRT versus QDiabetes (95% confidence interval 2.0 - 4.4%). IRT performance was best in reclassification of young adults deemed low risk by QDiabetes as high risk. PRS was independently associated with progression to type 2 diabetes after GDM (p = 0.028). Mean type 2 diabetes PRS differed between phenotypically-defined type 2 diabetes subgroups (p = 0.002). Interpretation: The type 2 diabetes PRS has broad potential clinical application in BPB, improving identification of type 2 diabetes risk (especially in the young), and characterisation of type 2 diabetes subgroups at diagnosis. Funding: Wellcome Trust, MRC, NIHR, and others. Full funding disclosed within.

Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistanis and Bangladeshis

Background: Individuals with South Asian ancestry have higher risk of heart disease than other groups in Western countries; however, most genetic research has focused on European-ancestry (EUR) individuals. It is unknown whether reported genetic loci and polygenic scores (PGSs) for cardiometabolic traits are transferable to South Asians, and whether PGSs have utility in clinical settings. Methods: Using data from 22,000 British Pakistani and Bangladeshi individuals with linked electronic health records from the Genes & Health cohort (G&H), we conducted genome-wide association studies (GWAS) and characterised the genetic architecture of coronary artery disease (CAD), body mass index (BMI), lipid biomarkers and blood pressure. We applied a new technique to assess the extent to which loci from GWAS in EUR samples were transferable. We tested how well existing findings from EUR studies performed in genetic risk prediction and Mendelian randomisation in G&H. Results: Trans-ancestry genetic correlations between G&H and EUR samples for the tested traits were not significantly lower than 1, except for BMI (rg=0.85, p=0.02). We found evidence for transferability for the vast majority of loci from EUR discovery studies that were sufficiently powered to replicate in G&H. PGSs showed variable transferability in G&H, with the relative accuracy compared to EUR (ratio of incremental r2/AUC) ≥0.95 for HDL-C, triglycerides, and blood pressure, but lower for BMI (0.78) and CAD (0.42). We observed significant improvement in categorical net reclassification in G&H (NRI=3.9%; 95% CI 0.9-7.0) when adding a previously developed CAD PGS to clinical risk factors (QRISK3). We used transferable loci as genetic instruments in trans-ancestry Mendelian randomisation and found evidence of an increased CAD risk for higher LDL-C and BMI, and for lower HDL-C in G&H, consistent with our findings for EUR samples. Conclusions: The genetic loci for CAD and its risk factors are largely transferable from EUR studies to British Pakistanis and Bangladeshis, whereas the transferability of PGSs varies greatly between traits. Our analyses suggest clinical utility for addition of PGS to existing clinical risk prediction tools for this population.

Reflections on the contribution of Muhammad Anwar to the study of sociology and racial politics

Muhammad Anwar passed away on 11 June 2019, at the age of 75 after 50 years of research and policy development in the area of race and ethnic studies. In this article, I explore his numerous contributions, including his important work, The Myth of Return: Pakistanis in Britain, published in 1979. His interest in politics and, in particular, participation, and representation within it, led to Race and Elections, published in 1994. His subsequent works on identifying the intergenerational differences among British Pakistanis, who also happen to represent a significant proportion of British Muslims, developed into his final major book, Between Cultures, published in 1998. I explore the nature of his contribution, the impact that it had in the field of race and ethnic studies, and the research openings generated for other scholars to expand on his social anthropological and sociological emphasis on better understanding the experiences of racial and ethnic minorities and the need to better develop policies to alleviate ethnic and racial disadvantage.

Fine-scale population structure and demographic history of British Pakistanis

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 genetic and questionnaire data from >4,000 British Pakistani individuals, mostly with roots in Azad Kashmir and Punjab. We reveal strong recent population structure driven by the biraderi social stratification system. We find that all subgroups have had low effective population sizes (Ne) over the last 50 generations, with some showing a decrease in Ne 15-20 generations ago that has resulted in extensive identity-by-descent sharing and increased homozygosity. Using new theory, we show that the footprint of regions of homozygosity in the two largest subgroups is about twice that expected naively based on the self-reported consanguinity rates and the inferred historical Ne trajectory. These results demonstrate the impact of the cultural practices of endogamy and consanguinity on population structure and genomic diversity in British Pakistanis, and have important implications for medical genetic studies.

HFE GENE MUTATIONS

Objectives: To determine the frequency of two common HFE Gene Mutations(C282Y & H63D) in an immigrant population (British Pakistanis) in UK. Study Design: Crosssectional study. Setting: University of Lincoln UK. Duration: Duration of study was 12 monthsfrom 01/09/2012 to 31/08/2013. Material and Methods: Two hundred immigrant Pakistani (BP)chromosomes (100 samples; 50 male and 50 female) from major cities of UK and 200 ancestralorigin Pakistani chromosomes (100 samples; 50 male and 50 female) were analysed by PCRRFLPfor the presence of the H63D and C282Y mutations. Results: Eight individuals were foundto be heterozygous for the H63D mutation and one individual was found to be homozygousfor the H63D mutation, therefore, the H63D mutation was observed to have a frequency of 8%in immigrant Pakistani (BP) population sample and similar results were observed in ancestralorigin population from Pakistan. The C282Y mutation was not detected at all. Conclusion: Wefound that our results are close to Saudi-Arabian and Indian population (8.5% & 9.1% H63Dmutation, respectively) and in accordance with the global spread of the H63D mutation.