Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA

Lao, Oscar; Vallone, Peter M.; Coble, Michael D.; Diegoli, Toni M.; Oven, Mannis van; Gaag, Kristiaan J. van der; Pijpe, Jeroen; Knijff, Peter de; Kayser, Manfred

doi:10.1002/humu.21366

Cited by 83 publications

(58 citation statements)

References 65 publications

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“…Fifty-two ancestry informative marker (AIM) single nucleotide polymorphisms (SNPs) and 76 MS SNPs were genotyped using the TaqMan OpenArray genotyping technology (Life Technologies, Carlsbad, CA). AIM SNPs were selected from previously published studies [22][23][24][25][26][27] to cover all chromosomes. MS SNPs were selected from the latest GWAS 8 and meta-analysis.…”

Section: Resultsmentioning

confidence: 99%

Genetic risk variants in African Americans with multiple sclerosis

et al. 2013

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Objectives: To assess the association of established multiple sclerosis (MS) risk variants in 3,254African Americans (1,162 cases and 2,092 controls).Methods: Human leukocyte antigen (HLA)-DRB1, HLA-DQB1, and HLA-A alleles were typed by molecular techniques. Single nucleotide polymorphism (SNP) genotyping was conducted for 76 MS-associated SNPs and 52 ancestry informative marker SNPs selected throughout the genome. Self-declared ancestry was refined by principal component analysis of the ancestry informative marker SNPs. An ancestry-adjusted multivariate model was applied to assess genetic associations. Results:The following major histocompatibility complex risk alleles were replicated: HLA- Genome-wide association studies (GWAS) have contributed considerably to the understanding of multiple sclerosis (MS) susceptibility through the identification of genetic variants influencing risk and quantitation of their effects. To date, the results of 9 GWAS 1-9 and 2 metaanalyses 10,11 have been reported, generating a roster of nearly 60 candidate genes in support of a polygenic model of pathogenesis 12,13 driven primarily by relatively common alleles. Most noteworthy is a recent multicenter GWAS 8 that replicated nearly all of the previously GWASsuggested associations together with the identification of 29 novel susceptibility loci. Immunologically relevant genes, including epistatic signals across the major histocompatibility complex (MHC) region, dominate the genomic signature of this disease. Invariably, all reported MS GWAS focused on high-prevalence datasets of European descent.14 The transferability of these results to other ancestral groups remains to be addressed.

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Section: Resultsmentioning

confidence: 99%

Genetic risk variants in African Americans with multiple sclerosis

et al. 2013

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“…By default, genetic studies of US population samples categorize individuals as European American, African American, Hispanic, or Asian (42,51,74,94,105). In Ibero-America, such categorization of research subjects is not standard, but studies of this type have been performed for some urban population samples (particularly in Brazil) (70,72,93,101) and for certain historic isolates (e.g., African-derived Brazilian Quilombos) (79).…”

Section: Genetic Ancestry In European Americans and African Americansmentioning

confidence: 99%

The Genetic Diversity of the Americas

Adhikari

Chacón-Duque

Mendoza‐Revilla

et al. 2017

Annu. Rev. Genom. Hum. Genet.

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The history of the Americas involved the encounter of millions of Native Americans, Europeans, and Africans. A variable admixture of these three continental groups has taken place between them throughout the continent, influenced by demography and a range of social factors. These events have had a major influence on the genetic makeup of populations across the continent. Here, we summarize the demographic history of the region, highlight some social factors that affected historical admixture, and review major patterns of diversity across the Western Hemisphere based on genetic data.2

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“…1B). structure analysis (Pritchard et al 2000) of DNA samples from HEMn-LP and HEMn-DP cells using 24 ancestry-informative autosomal SNPs together with a worldwide reference data set (HGDP-CEPH) (Lao et al 2010) revealed a probable European and a probable Sub-Saharan African genetic origin of the respective cell donors (Supplemental Fig. S1).…”

Section: Characterization and Suitability Of The Melanocyte Cell Systemmentioning

confidence: 99%

“…Genotypes of rs7164220, rs7497270, rs58843292, rs72625136, and rs79494067 were determined by restriction digestion of PCR fragments. To infer the geographic origin/genetic ancestry of the cell-line donors, 24 autosomal SNPs sensitive to detect continental ancestry were genotyped via two SNaPshot (Applied Biosystems) multiplex reactions as described elsewhere (Lao et al 2010). The continental ancestry of the samples was recovered by performing a structure analysis (Pritchard et al 2000) in which data from the HGDP-CEPH panel served as reference, as described elsewhere (Lao et al 2010).…”

Section: Genotypingmentioning

confidence: 99%

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

Visser

Kayser²,

Palstra³

2012

Genome Res.

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Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of the pigment gene OCA2, and the region surrounding rs12913832 is highly conserved among animal species. However, the exact functional role of HERC2 rs12913832 in human pigmentation is unknown. Here we demonstrate that the HERC2 rs12913832 region functions as an enhancer regulating OCA2 transcription. In darkly pigmented human melanocytes carrying the rs12913832 T-allele, we detected binding of the transcription factors HLTF, LEF1, and MITF to the HERC2 rs12913832 enhancer, and a long-range chromatin loop between this enhancer and the OCA2 promoter that leads to elevated OCA2 expression. In contrast, in lightly pigmented melanocytes carrying the rs12913832 C-allele, chromatin-loop formation, transcription factor recruitment, and OCA2 expression are all reduced. Hence, we demonstrate that allelic variation of a common noncoding SNP located in a distal regulatory element not only disrupts the regulatory potential of this element but also affects its interaction with the relevant promoter. We provide the key mechanistic insight that allele-dependent differences in chromatin-loop formation (i.e., structural differences in the folding of gene loci) result in differences in allelic gene expression that affects common phenotypic traits. This concept is highly relevant for future studies aiming to unveil the functional basis of genetically determined phenotypes, including diseases.

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Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA

Cited by 83 publications

References 65 publications

Genetic risk variants in African Americans with multiple sclerosis

Genetic risk variants in African Americans with multiple sclerosis

The Genetic Diversity of the Americas

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

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