ArticleBMC biology2015
Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits.
Article in BMC biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Genetic characterization of a captive marmoset (Callithrix jacchus) colony using genotype-by-sequencing.American journal of primatology · 2024Article
- Evaluation of genetic demultiplexing of single-cell sequencing data from model species.Life science alliance · 2023Article
- Current advances in primate genomics: novel approaches for understanding evolution and disease.Nature reviews. Genetics · 2023Review
- Nonhuman primate genetic models for the study of rare diseases.Orphanet journal of rare diseases · 2023Review
- Epigenetic clock and methylation studies in vervet monkeys.GeroScience · 2022Article
- A Fine-Scale Genetic Map for Vervet Monkeys.Molecular biology and evolution · 2020Article
- Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models.BMC genomics · 2018Article
- Obesity and obesogenic growth are both highly heritable and modified by diet in a nonhuman primate model, the African green monkey (Chlorocebus aethiops sabaeus).International journal of obesity (2005) · 2018Article
- Neurodegenerative disease biomarkers AβBrain and behavior · 2018Article
- Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.Nature genetics · 2017Article
- Ancient hybridization and strong adaptation to viruses across African vervet monkey populations.Nature genetics · 2017Article
- Evolutionary insights from wild vervet genomes.Nature genetics · 2017Article
- Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation.BMC genomics · 2016Article
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Authors and funding
18 authors.
Funding
Abstract
backgroundWe report here the first genome-wide high-resolution polymorphism resource for non-human primate (NHP) association and linkage studies, constructed for the Caribbean-origin vervet monkey, or African green monkey (Chlorocebus aethiops sabaeus), one of the most widely used NHPs in biomedical research. We generated this resource by whole genome sequencing (WGS) of monkeys from the Vervet Research Colony (VRC), an NIH-supported research resource for which extensive phenotypic data are available.
resultsWe identified genome-wide single nucleotide polymorphisms (SNPs) by WGS of 721 members of an extended pedigree from the VRC. From high-depth WGS data we identified more than 4 million polymorphic unequivocal segregating sites; by pruning these SNPs based on heterozygosity, quality control filters, and the degree of linkage disequilibrium (LD) between SNPs, we constructed genome-wide panels suitable for genetic association (about 500,000 SNPs) and linkage analysis (about 150,000 SNPs). To further enhance the utility of these resources for linkage analysis, we used a further pruned subset of the linkage panel to generate multipoint identity by descent matrices.
conclusionsThe genetic and phenotypic resources now available for the VRC and other Caribbean-origin vervets enable their use for genetic investigation of traits relevant to human diseases.
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