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Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits
BACKGROUND: We 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 biomedic...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494155/ https://www.ncbi.nlm.nih.gov/pubmed/26092298 http://dx.doi.org/10.1186/s12915-015-0152-2 |
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author | Huang, Yu S. Ramensky, Vasily Service, Susan K. Jasinska, Anna J. Jung, Yoon Choi, Oi-Wa Cantor, Rita M. Juretic, Nikoleta Wasserscheid, Jessica Kaplan, Jay R. Jorgensen, Matthew J. Dyer, Thomas D. Dewar, Ken Blangero, John Wilson, Richard K. Warren, Wesley Weinstock, George M. Freimer, Nelson B. |
author_facet | Huang, Yu S. Ramensky, Vasily Service, Susan K. Jasinska, Anna J. Jung, Yoon Choi, Oi-Wa Cantor, Rita M. Juretic, Nikoleta Wasserscheid, Jessica Kaplan, Jay R. Jorgensen, Matthew J. Dyer, Thomas D. Dewar, Ken Blangero, John Wilson, Richard K. Warren, Wesley Weinstock, George M. Freimer, Nelson B. |
author_sort | Huang, Yu S. |
collection | PubMed |
description | BACKGROUND: We 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. RESULTS: We 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. CONCLUSIONS: The 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0152-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4494155 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-44941552015-07-08 Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits Huang, Yu S. Ramensky, Vasily Service, Susan K. Jasinska, Anna J. Jung, Yoon Choi, Oi-Wa Cantor, Rita M. Juretic, Nikoleta Wasserscheid, Jessica Kaplan, Jay R. Jorgensen, Matthew J. Dyer, Thomas D. Dewar, Ken Blangero, John Wilson, Richard K. Warren, Wesley Weinstock, George M. Freimer, Nelson B. BMC Biol Research Article BACKGROUND: We 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. RESULTS: We 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. CONCLUSIONS: The 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0152-2) contains supplementary material, which is available to authorized users. BioMed Central 2015-06-20 /pmc/articles/PMC4494155/ /pubmed/26092298 http://dx.doi.org/10.1186/s12915-015-0152-2 Text en © Huang et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Huang, Yu S. Ramensky, Vasily Service, Susan K. Jasinska, Anna J. Jung, Yoon Choi, Oi-Wa Cantor, Rita M. Juretic, Nikoleta Wasserscheid, Jessica Kaplan, Jay R. Jorgensen, Matthew J. Dyer, Thomas D. Dewar, Ken Blangero, John Wilson, Richard K. Warren, Wesley Weinstock, George M. Freimer, Nelson B. Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title | Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title_full | Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title_fullStr | Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title_full_unstemmed | Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title_short | Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
title_sort | sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494155/ https://www.ncbi.nlm.nih.gov/pubmed/26092298 http://dx.doi.org/10.1186/s12915-015-0152-2 |
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