Fine-scale population structure and demographic history of British Pakistanis

Arciero, Elena; Dogra, Sufyan Abid; Malawsky, Daniel; Mezzavilla, Massimo; Tsismentzoglou, Theofanis; Huang, Qin Qin; Hunt, Karen A.; Mason, Dan; Sharif, Saghira Malik; Heel, David A. van; Sheridan, Eamonn; Wright, John; Small, Neil; Carmi, Shai; Iles, Mark M.; Martin, Hilary C.

doi:10.1038/s41467-021-27394-2

Cited by 24 publications

(22 citation statements)

References 77 publications

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“…Ethnicity was self-reported and the homogeneity of the WE group has been confirmed in previous genetic analyses within BIB (33). 93.2% of the included WEs were born in the British Isles (i.e., the UK, Republic of Ireland, Channel Islands or Isle of Man), with the majority in England (91.4%).…”

Section: Participant Selectionmentioning

confidence: 70%

Unique Metabolic Profiles Associate with Gestational Diabetes and Ethnicity in Low and High-Risk Women Living in the UK

Fuller

Iles

Moore

et al. 2022

Preprint

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Background: Gestational Diabetes Mellitus (GDM) is the most common pregnancy complication to occur worldwide, however prevalence varies substantially between ethnicities with South Asians experiencing up to 3-times the risk of the disease compared to white Europeans (WEs). Factors driving this discrepancy in prevalence and the pathogenesis of GDM are unclear, although the metabolome is of great importance due to the metabolic dysregulation characterised GDM. Objective: To characterise and distinguish the metabolic profiles of GDM in two distinct ethnic populations at < 28 weeks gestation. Design: 146 fasting serum metabolite values, quantified by nuclear magnetic resonance, from 2668 pregnant WE and 2671 pregnant Pakistani (PK) women from the Born in Bradford (BIB) cohort, were analysed using partial least squares discriminatory analyses (PLSDA). The presence of a linear relationships between metabolite values and post-oral glucose tolerance test measures of dysglycemia (fasting glucose and 2- hour post glucose) were also examined. Results: Seven metabolites were associated with GDM status in both ethnicities, while 6 additional metabolites associated with GDM only in WE women. Unique metabolic profiles were observed in healthy weight women who later developed GDM, with distinct metabolite patterns identified by ethnicity and BMI status. Of the 146 metabolite values analysed in relation to dysglycemia, quantities of lactate, histidine, apolipoprotein A1, HDL cholesterol, HDL2 cholesterol, and DHA, as well as the diameter of very low density lipoprotein particles (nm) were associated with dysglycemia in WE women; while in PK women albumin alone associated with dysglycemia. Conclusion: This is the first study to show that the metabolic risk profile for GDM differs between ethnicities and highlights a need for ethnically appropriate GDM prevention strategies.

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Section: Participant Selectionmentioning

confidence: 70%

Unique Metabolic Profiles Associate with Gestational Diabetes and Ethnicity in Low and High-Risk Women Living in the UK

Fuller

Iles

Moore

et al. 2022

Preprint

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“…In addition, the isolate with the highest level of long ROHs, which indicated recent endogamy (Arciero et al, 2021;Ceballos et al, 2018;McQuillan et al, 2008), is the also one with the highest level of Y and mitochondrial haplotype diversity (RTZ), where the one with reduced Y haplotype diversity respect to mitochondrial haplotype diversity (STC) is the one with lower level of isolation. Thus, the absence of long ROHs could result from a small sex-biased gene flow that disrupted the actual pattern of homozygosity but not the distribution of ancestral components.…”

Section: Discussionmentioning

confidence: 99%

Genetic characterization of two North Italian villages: A story of isolation, ancient admixture, and genetic drift

Mezzavilla

Cocca

Delser

et al. 2022

American Journal of Biological Anthropology

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Objectives Population isolates represent a focus of interest because of their particular genetic history and the possibility of mapping peculiar deleterious variants. Here we investigated the pattern of genetic variation in two North Italian villages: Rotzo (RTZ) and Stoccareddo (STC), in the Asiago plateau. Materials and methods We genotyped over 800 individuals for more than 600.000 markers. We investigated the isolation level by analyzing runs of homozygosity (ROH) and the level of population structure. Then we estimated the time of admixture and the relationship between ancient genomes and these two villages. Finally, we looked at the effect of genetic drift on deleterious variants. Results We highlighted a different isolation level between RTZ and STC; despite the average number of ROH being similar between the two villages, RTZ shows a higher level of total homozygosity. We estimated, from different sources, that the time of admixture for the ancestors of these two populations was between 113 and 88 generations ago. We discovered that a deleterious variant in MCUB gene (rs78025076), which is linked to several lipid traits, is entirely absent in RTZ and at 1%frequency in STC. In contrast, the risk allele frequency is 2% in Europe and 2.4% in North‐East Italy. Discussion These results show the importance of a genetic characterization of geographically isolated populations. Their vast array of past history could highlight specific events in the past and help describe deleterious variants and traits distribution in different regions.

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“…We suggest that spore will be a useful tool for researchers monitoring experimental (e.g., Ferrari et al, 2022 ; Frentiu & Chenoweth, 2008 ; Luzynski et al, 2021 ; Stockley et al, 2013 ), wild (e.g., Bonnet et al, 2019 ; Chen et al, 2019 ; Clutton‐Brock & Pemberton, 2003 ; Weinman et al, 2015 ), agricultural (e.g. McClure et al, 2018 ; Tortereau et al, 2017 ), and even some human (e.g., Arciero et al, 2021 ), populations with incomplete mating and birth tracking, potentially imperfect genotypes, and at least some autozygosity resulting from population history or recent mating between close relatives.…”

Section: Discussionmentioning

confidence: 99%

Parent‐offspring inference in inbred populations

Runge

König

Lindholm

et al. 2022

Molecular Ecology Resources

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Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obfuscate genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human datasets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called SPORE (Specific Parent-Offspring Relationship Estimation). SPORE is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. SPORE therefore fills an important void in the arsenal of pedigree inference tools.

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Fine-scale population structure and demographic history of British Pakistanis

Cited by 24 publications

References 77 publications

Unique Metabolic Profiles Associate with Gestational Diabetes and Ethnicity in Low and High-Risk Women Living in the UK

Unique Metabolic Profiles Associate with Gestational Diabetes and Ethnicity in Low and High-Risk Women Living in the UK

Genetic characterization of two North Italian villages: A story of isolation, ancient admixture, and genetic drift

Parent‐offspring inference in inbred populations

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