Identifying rhesus macaque gene orthologs using heterospecific human CNV probes

Jillian Ng; Joseph N. Fass; Blythe Durbin-Johnson; David Glenn Smith; Sreetharan Kanthaswamy

doi:10.1016/j.gdata.2015.09.016

Identifying rhesus macaque gene orthologs using heterospecific human CNV probes

Jillian Ng, Joseph N. Fass, Blythe Durbin-Johnson, David Glenn Smith, Sreetharan Kanthaswamy

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

We used the Affymetrix^® Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

Original language	English (US)
Pages (from-to)	202-207
Number of pages	6
Journal	Genomics Data
Volume	6
DOIs	https://doi.org/10.1016/j.gdata.2015.09.016
State	Published - Dec 1 2015

Keywords

Copy number variation (CNV)
Heterospecific sequence map
Homo sapiens
Macaca mulatta

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Medicine
Genetics

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10.1016/j.gdata.2015.09.016

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title = "Identifying rhesus macaque gene orthologs using heterospecific human CNV probes",

abstract = "We used the Affymetrix{\textregistered} Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.",

keywords = "Copy number variation (CNV), Heterospecific sequence map, Homo sapiens, Macaca mulatta",

author = "Jillian Ng and Fass, {Joseph N.} and Blythe Durbin-Johnson and Smith, {David Glenn} and Sreetharan Kanthaswamy",

note = "Funding Information: This study was supported by the California National Primate Research Center base grant (No. RR000169-48 ), by an ARRA supplement awarded to S.K. and Nick Lerche, CNPRC (No. RR018144-07 ), NIH grants RR005090 and RR025871 to D.G.S., and the UC Davis Henry A. Jastro Graduate Research Award to J.N. Animals used in this research were managed in compliance with Institutional Animal Care and Use Committee (IACUC) regulations or in accordance with the National Institutes of Health guidelines or the US Department of Agriculture regulations prescribing the humane care and use of laboratory animals. Publisher Copyright: {\textcopyright} 2015 The Authors.",

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AU - Smith, David Glenn

AU - Kanthaswamy, Sreetharan

N1 - Funding Information: This study was supported by the California National Primate Research Center base grant (No. RR000169-48 ), by an ARRA supplement awarded to S.K. and Nick Lerche, CNPRC (No. RR018144-07 ), NIH grants RR005090 and RR025871 to D.G.S., and the UC Davis Henry A. Jastro Graduate Research Award to J.N. Animals used in this research were managed in compliance with Institutional Animal Care and Use Committee (IACUC) regulations or in accordance with the National Institutes of Health guidelines or the US Department of Agriculture regulations prescribing the humane care and use of laboratory animals. Publisher Copyright: © 2015 The Authors.

PY - 2015/12/1

Y1 - 2015/12/1

N2 - We used the Affymetrix® Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

AB - We used the Affymetrix® Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.

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Identifying rhesus macaque gene orthologs using heterospecific human CNV probes

Abstract

Keywords

ASJC Scopus subject areas

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