MHC genotyping from rhesus macaque exome sequences.
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ABSTRACT:
PROVIDER: PRJEB33995 | ENA |
REPOSITORIES: ENA
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Project description:MHC genotyping from rhesus macaque exome sequences
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Project description:Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.
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Project description:Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations.
2011-05-11 | GSE19881 | GEO
Project description:Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations. a custom designed Agilent array-based comparative genomic hybridization (aCGH) platform, which comprises 950,843 unique 60-mer oligonucleotide probes specific to the rhesus macaque reference genome (rheMac2), to compare the genomic DNAs of 17 unrelated rhesus macaques of Indian origin to the genome of an unrelated sample from the same species.
2011-05-11 | E-GEOD-19881 | biostudies-arrayexpress
Project description:The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. Keywords: cross hybridization
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