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DYT-TUBB4A (DYT4 Dystonia): New Clinical and Genetic Observations.
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In: Neurology, vol. 96, no. 14, pp. e1887-e1897 (2021)
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Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry.
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In: Molecular psychiatry, vol 25, iss 10 (2020)
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Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry.
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In: Molecular psychiatry, vol 25, iss 10 (2020)
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Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula
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Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis.
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In: Human molecular genetics, vol 27, iss 24 (2018)
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Enrichment of genetic markers of recent human evolution in educational and cognitive traits.
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In: Scientific reports, vol 8, iss 1 (2018)
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Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.
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In: Nature genetics, vol 50, iss 7 (2018)
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Multi-Trait Analysis of GWAS and Biological Insights Into Cognition: A Response to Hill (2018).
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In: Twin research and human genetics : the official journal of the International Society for Twin Studies, vol 21, iss 5 (2018)
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Global genetic differentiation of complex traits shaped by natural selection in humans.
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In: Nature communications, vol. 9, no. 1, pp. 1865 (2018)
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GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium.
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In: Molecular psychiatry, vol 22, iss 3 (2017)
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AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.
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In: BMC bioinformatics, vol 18, iss 1 (2017)
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Abstract:
BackgroundInferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA.ResultsWe demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage.ConclusionsAD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.
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Keyword:
Admixture; Ancestry; Animals; Bears; Bioinformatics; Biological Sciences; Genetic; Genetic Speciation; Genetics; Genome; Human Genome; Humans; Hybridization; Information and Computing Sciences; Markov Chains; Mathematical Sciences; Polymorphism; Single Nucleotide; Software; Speciation; Ursidae
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URL: https://escholarship.org/uc/item/04j576r0
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| 12 |
A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. ...
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An ancient selective sweep linked to reproductive life history evolution in sockeye salmon
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An ancient selective sweep linked to reproductive life history evolution in sockeye salmon
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A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea
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Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.
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In: ISSN: 0099-2240 ; EISSN: 1098-5336 ; Applied and Environmental Microbiology ; https://hal-pasteur.archives-ouvertes.fr/pasteur-01421019 ; Applied and Environmental Microbiology, American Society for Microbiology, 2016, 82 (8), pp.2516-26. ⟨10.1128/AEM.03821-15⟩ (2016)
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Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan.
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In: Journal of human genetics, vol 61, iss 3 (2016)
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Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.
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In: Genetics, vol 204, iss 1 (2016)
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Dyslexia and language impairment associated genetic markers influence cortical thickness and white matter in typically developing children.
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In: Brain imaging and behavior, vol 10, iss 1 (2016)
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Dyslexia and language impairment associated genetic markers influence cortical thickness and white matter in typically developing children.
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In: Brain imaging and behavior, vol 10, iss 1 (2016)
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