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Identifying rhesus macaque gene orthologs using heterospecific human CNV probes.

Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S - Genom Data (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.

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.

No MeSH data available.


General conserved synteny of (a) Indian rhesus macaque (rheMac2) and (b) Chinese rhesus macaque (rheMac3) reference genome chromosomal segments relative to human (hg19) chromosomes. The colored bands (above) show orthologous rhesus macaque chromosome segments, with each color corresponding to a different rhesus macaque chromosome, and how they distribute across the human genome represented with G-banded chromosomes (below).
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f0025: General conserved synteny of (a) Indian rhesus macaque (rheMac2) and (b) Chinese rhesus macaque (rheMac3) reference genome chromosomal segments relative to human (hg19) chromosomes. The colored bands (above) show orthologous rhesus macaque chromosome segments, with each color corresponding to a different rhesus macaque chromosome, and how they distribute across the human genome represented with G-banded chromosomes (below).

Mentions: A total of 230,973 CNV markers on the Affymetrix® Genome-Wide Human SNP Array 6.0 were successfully mapped to both human (hg19) and Indian rhesus macaque (rheMac2) genomes. Seven hundred and nine of these markers mapped to multiple sites within the rheMac2 genome. The chromosomal distribution of the markers across both human and Indian rhesus macaque genomes is summarized in Table 1 and the generalized synteny of Indian rhesus macaque chromosomal segments relative to human chromosomes is shown in Fig. 1a. Though the majority of the human markers were mapped to the rhesus macaque chromosome orthologs that Rogers et al. [23] identified using STRs, suggesting generally conserved synteny across the genomes, a few markers did not (the single colored bands within the larger colored blocks), which could indicate genomic rearrangement. From the 230,973 human markers that mapped to the Indian rhesus macaque, 109,044 mapped to 30,642 unique NCBI RefSeq accession numbers and 14,466 unique annotated genes in human, and 24,666 markers mapped to 3809 unique accession numbers and 3782 genes in Indian rhesus macaque.


Identifying rhesus macaque gene orthologs using heterospecific human CNV probes.

Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S - Genom Data (2015)

General conserved synteny of (a) Indian rhesus macaque (rheMac2) and (b) Chinese rhesus macaque (rheMac3) reference genome chromosomal segments relative to human (hg19) chromosomes. The colored bands (above) show orthologous rhesus macaque chromosome segments, with each color corresponding to a different rhesus macaque chromosome, and how they distribute across the human genome represented with G-banded chromosomes (below).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664757&req=5

f0025: General conserved synteny of (a) Indian rhesus macaque (rheMac2) and (b) Chinese rhesus macaque (rheMac3) reference genome chromosomal segments relative to human (hg19) chromosomes. The colored bands (above) show orthologous rhesus macaque chromosome segments, with each color corresponding to a different rhesus macaque chromosome, and how they distribute across the human genome represented with G-banded chromosomes (below).
Mentions: A total of 230,973 CNV markers on the Affymetrix® Genome-Wide Human SNP Array 6.0 were successfully mapped to both human (hg19) and Indian rhesus macaque (rheMac2) genomes. Seven hundred and nine of these markers mapped to multiple sites within the rheMac2 genome. The chromosomal distribution of the markers across both human and Indian rhesus macaque genomes is summarized in Table 1 and the generalized synteny of Indian rhesus macaque chromosomal segments relative to human chromosomes is shown in Fig. 1a. Though the majority of the human markers were mapped to the rhesus macaque chromosome orthologs that Rogers et al. [23] identified using STRs, suggesting generally conserved synteny across the genomes, a few markers did not (the single colored bands within the larger colored blocks), which could indicate genomic rearrangement. From the 230,973 human markers that mapped to the Indian rhesus macaque, 109,044 mapped to 30,642 unique NCBI RefSeq accession numbers and 14,466 unique annotated genes in human, and 24,666 markers mapped to 3809 unique accession numbers and 3782 genes in Indian rhesus macaque.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.

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.

No MeSH data available.