Genetic origins, singularity, and heterogeneity of Basques

Flores-Bello, André; Bauduer, Frédéric; Salaberria, Jasone; Oyharçabal, Bernard; Calafell, Francesc; Bertranpetit, Jaume; Comas, David

doi:10.1016/j.cub.2021.03.010

Cited by 15 publications

(13 citation statements)

References 51 publications

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“…Our result highlights other communities relevant to genetic mapping efforts, some that are well established in the literature such Orkney and Shetland ( 20 , 21 , 46 , 47 ) or the Basque ( 48 – 51 ) and some novel, e.g., the Channel Islands. The Channel Islands are an archipelago of isles off the northern coast of France and are a British dependency.…”

Section: Discussionsupporting

confidence: 64%

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank

Gilbert

Shanmugam

Cavalleri

2022

Proc. Natl. Acad. Sci. U.S.A.

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Haplotype-based analyses have recently been leveraged to interrogate the fine-scale structure in specific geographic regions, notably in Europe, although an equivalent haplotype-based understanding across the whole of Europe with these tools is lacking. Furthermore, study of identity-by-descent (IBD) sharing in a large sample of haplotypes across Europe would allow a direct comparison between different demographic histories of different regions. The UK Biobank (UKBB) is a population-scale dataset of genotype and phenotype data collected from the United Kingdom, with established sampling of worldwide ancestries. The exact content of these non-UK ancestries is largely uncharacterized, where study could highlight valuable intracontinental ancestry references with deep phenotyping within the UKBB. In this context, we sought to investigate the sample of European ancestry captured in the UKBB. We studied the haplotypes of 5,500 UKBB individuals with a European birthplace; investigated the population structure and demographic history in Europe, showing in parallel the variety of footprints of demographic history in different genetic regions around Europe; and expand knowledge of the genetic landscape of the east and southeast of Europe. Providing an updated map of European genetics, we leverage IBD-segment sharing to explore the extent of population isolation and size across the continent. In addition to building and expanding upon previous knowledge in Europe, our results show the UKBB as a source of diverse ancestries beyond Britain. These worldwide ancestries sampled in the UKBB may complement and inform researchers interested in specific communities or regions not limited to Britain.

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Section: Discussionsupporting

confidence: 64%

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank

Gilbert

Shanmugam

Cavalleri

2022

Proc. Natl. Acad. Sci. U.S.A.

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“…The two cohorts investigated here, although both Caucasian, were from different ethnic backgrounds with differences in the diet and culture. The Spanish cohort is predominantly from the Basque region, which in itself is culturally and genetically different from the main Spanish population . Although we do not have detailed genetic or dietary data for either of the cohorts, there is a reasonable expectation that there will be some systematic differences between the populations at the genetic and environmental/lifestyle levels. , Furthermore, there may also be differences in the range of severity of infection between the two patient groups, and so it is highly pertinent to question whether or not such diverse and largely uncontrolled groups can be cross-modeled in integrated data sets.…”

Section: Resultsmentioning

confidence: 99%

Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts

et al. 2021

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Quantitative plasma lipoprotein and metabolite profiles were measured on an autonomous community of the Basque Country (Spain) cohort consisting of hospitalized COVID-19 patients (n = 72) and a matched control group (n = 75) and a Western Australian (WA) cohort consisting of (n = 17) SARS-CoV-2 positives and (n = 20) healthy controls using 600 MHz 1H nuclear magnetic resonance (NMR) spectroscopy. Spanish samples were measured in two laboratories using one-dimensional (1D) solvent-suppressed and T2-filtered methods with in vitro diagnostic quantification of lipoproteins and metabolites. SARS-CoV-2 positive patients and healthy controls from both populations were modeled and cross-projected to estimate the biological similarities and validate biomarkers. Using the top 15 most discriminatory variables enabled construction of a cross-predictive model with 100% sensitivity and specificity (within populations) and 100% sensitivity and 82% specificity (between populations). Minor differences were observed between the control metabolic variables in the two cohorts, but the lipoproteins were virtually indistinguishable. We observed highly significant infection-related reductions in high-density lipoprotein (HDL) subfraction 4 phospholipids, apolipoproteins A1 and A2,that have previously been associated with negative regulation of blood coagulation and fibrinolysis. The Spanish and Australian diagnostic SARS-CoV-2 biomarkers were mathematically and biologically equivalent, demonstrating that NMR-based technologies are suitable for the study of the comparative pathology of COVID-19 via plasma phenotyping.

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“…ROHs were identified using PLINK v1.9b software [ 25 ] with the following non-default parameters: maximum gap between SNPs of 100 kb and a minimum threshold of 500 kb and 50 SNPs. This analysis was performed using a set of reference populations to enable an informative comparison: Spanish as representative of the general Iberian Peninsula context; Basque and Roma as examples of ancient and recent inbreeding, respectively [ 11 , 13 , 21 ]; CEU and YRI which represent the genetic diversity with and without the Out-of-Africa bottleneck, respectively. We performed Wilcoxon tests to assess whether the sum of ROH lengths between each pair of populations was statistically significant.…”

Section: Methodsmentioning

confidence: 99%

“…The Iberian Peninsula population has been analysed in many genetic studies, showing an internal heterogeneity with genetic geographic patterns following an east-to-west axis [ 6 ]. In addition, several population groups have stood out from this general context due to their particular demographic histories and genetic landscapes, as it is the case of Basque [ 11 ], Eivissa [ 12 ], and Spanish Roma populations [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

et al. 2021

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Background The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. Results Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. Conclusions This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.

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Genetic origins, singularity, and heterogeneity of Basques

Cited by 15 publications

References 51 publications

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank

Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts

The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

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