Experience using conventional compared to ancestry-based population descriptors in clinical genomics laboratories

The American Journal of Human Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(4)

Published: March 15, 2024

Abstract Summary Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for special challenges studies admixed populations. Here, we present admix-kit, an integrated toolkit pipeline analyses Admix-kit implements a suite methods to facilitate genotype phenotype simulation, association testing, architecture inference, polygenic scoring Availability implementation package is open-source available at https://github.com/KangchengHou/admix-kit. Additionally, users can use designed simulation https://github.com/UW-GAC/admix-kit_workflow.

Language: Английский

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Genes, culture, and scientific racism

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(48)

Published: Nov. 18, 2024

Quantitative studies of cultural evolution and gene-culture coevolution (henceforth “CE” “GCC”) emerged in the 1970s, aftermath “race intelligence quotient (IQ)” “human sociobiology” debates, as a counter to extreme hereditarian positions. These incorporated transmission its interaction with genetics contributing patterns human variation. Neither CE nor GCC results were consistent racist claims ubiquitous genetic differences between socially defined races. We summarize how data refute notion racial substructure for populations address naive interpretations race across biological sciences, including those related ancestry, health, intelligence, that help perpetuate ideas. A perspective can reductionist determinist while providing more inclusive multidisciplinary framework which interpret

Language: Английский

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Influence of Cytokine-Related genetic variants in TNF, IL6, IL1β, and IFNγ genes in the thalidomide treatment for Erythema nodosum leprosum in a Brazilian population sample

Human Immunology, Journal Year: 2025, Volume and Issue: 86(2), P. 111260 - 111260

Published: Feb. 16, 2025

Language: Английский

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Admixture Increases Genetic Diversity and Adaptive Potential in Australasian Killer Whales

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 28, 2025

Admixture is the exchange of genetic variation between differentiated demes, resulting in ancestry within a population coalescing multiple ancestral source populations. Low-latitude killer whales (Orcinus orca) populations typically have higher diversity than those more densely populated, high productivity and high-latitude regions. This has been hypothesized to be due episodic admixture with distinct backgrounds. We test this hypothesis by estimating local whole genome sequences from three genetically differentiated, low-latitude whale comparing them global variation. find 'Antarctic-like' tracts genomes southwestern Australia (SWA) including recent (within last 2-4 generations) admixture. Admixed individuals had, on average, shorter fewer runs homozygosity unadmixed increased effective size (Ne). Thus, connectivity demes results maintenance Ne relatively small at level comparable sum across demes. A subset admixed regions was inferred evolving under selection SWA population, suggesting that may contributing population's adaptive potential. study provides important rare empirical evidence can maintain sporadic different backgrounds promote long-term stability Ne.

Language: Английский

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Psychiatric genetics in the diverse landscape of Latin American populations

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Language: Английский

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Accurate identification of Helicoverpa armigera–Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance

Frontiers in Insect Science, Journal Year: 2024, Volume and Issue: 4

Published: Feb. 23, 2024

Helicoverpa armigera , the cotton bollworm moth, is one of world’s most important crop pests, and spreading throughout New World from its original range in Old World. In Brazil, invasive H. has been reported to hybridize with local populations zea . The correct identification armigera-H. hybrids understanding origin, spread future outlook for regions that are affected by outbreaks, given hybridization can potentially facilitate pesticide resistance host plant via introgression genes. Here, we present a genome admixture analysis high quality sequences generated two F1 different labs. Our pipeline predicts 48.8% 48.9% hybrids, confirming accuracy. Genome five were as part study show no evidence hybridization. Interestingly, four genomes previous predicted possess proportion genetic material. Using unsupervised clustering identify non-hybridized genomes, 8511 ancestry informative markers (AIMs) identified. Their relative frequencies consistent minor component however origin remains be established. We size genomic reference datasets critical accurate prediction. Consequently, discuss potential pitfalls suggest measures will improve such analyses.

Language: Английский

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FedGMMAT: Federated generalized linear mixed model association tests

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(7), P. e1012142 - e1012142

Published: July 24, 2024

Increasing genetic and phenotypic data size is critical for understanding the determinants of diseases. Evidently, establishing practical means collaboration sharing among institutions a fundamental methodological barrier performing high-powered studies. As sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct confounders that may bias results. On another front, due privacy concerns around Protected Health Information (PHI), information restrictively protected by according regulations Insurance Portability Accountability Act (HIPAA). This limits hampers efforts executing collaborative Federated approaches are promising alleviate issues performance, since sensitive never leaves local sites. Motivated these, we developed FedGMMAT, federated association testing tool utilizes approach efficient tests can confounding fixed additive polygenic random different collaborating Genetic shared sites, intermediate statistics encryption. Using simulated real datasets, demonstrate FedGMMAT achieve virtually same results pooled analysis under privacy-preserving framework with resource requirements.

Language: Английский

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Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 2, 2023

Abstract Summary Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for special challenges study admixed populations. Here, we present admix-kit, an integrated toolkit pipeline analyses Admix-kit implements a suite methods to facilitate genotype phenotype simulation, association testing, architecture inference, polygenic scoring Availability implementation package is open-source available at https://github.com/KangchengHou/admix-kit . Additionally, users can use designed simulation https://github.com/UW-GAC/admix-kit_workflow

Language: Английский

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Advanced median-based genetic similarity analysis in Kazakh Tazy dogs: A novel approach for breed conformity assessment

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 20, 2024

Abstract The breed conformity evaluation is crucial for the preservation of traits that characterise each dog breed. use genetic markers this purpose provides a precision and objectivity can surpass reliability phenotypic evaluations. In study, we present new simple algorithm assessing conformity. creates similarity matrix based on genotypic data then uses median to calculate percentage an individual has in relation diversity To validate proposed algorithm, applied it 18 microsatellites 43,691 single nucleotide polymorphisms (SNPs) Kazakh Tazy dog, great cultural historical importance Kazakhstan now threatened with extinction due crossbreeding. showed moderate correlation between microsatellite SNP genotyping methods, reflecting different aspects similarity. particular, SNP-based evaluations agreed better expert judgements, highlighting their potential accurate analysis easily interpretable results, flexible, adapts may provide mechanism situations where there no reference population, incomplete pedigrees, unidentified meta-founders high population. Author summary Our research was initiated by urgent concern possible deep roots significance Kazakhstan. Information at DNA level lead faster improvement than relying only pedigrees. Genotypic be processed valuable insights into diversity, relatedness ancestry. However, existing methods do not measure used assess how closely particular matches typical composition These challenges have led us propose approach overcomes limitations allows assessed genotypes. It median-based analyze been but also adapted other markers. This method results even absence defined complete pedigrees or identified meta-pedigrees during within breeders researchers tool maintain purity unique breeds.

Language: Английский

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