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The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

Qiaoping Yuan1, Zhifeng Zhou1, Stephen G Lindell1, J Dee Higley2, Betsy Ferguson3, Robert C Thompson4, Juan F Lopez5, Stephen J Suomi6, Basel Baghal1, Maggie Baker1, Deborah C Mash7, Christina S Barr1* and David Goldman1*

Author Affiliations

1 Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, 20892, USA

2 Laboratory of Clinical and Translational Studies, NIAAA, Bethesda, MD, 20892, USA

3 Oregon National Primate Research Center, Oregon Health and Sciences University, 505 NW 185th Ave, Beaverton, OR, 97006, USA

4 Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48104, USA

5 Mental Health Research Institute, University of Michigan Medical Center, 3064 NSL, 1103 East Huron Street, Ann Arbor, MI, 48104, USA

6 Laboratory of Comparative Ethology, National Institute of Child Health and Human Development, NIH, Poolesville, MD, 20837, USA

7 Department of Neurology, University of Miami School of Medicine, Miami, FL, 33136, USA

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BMC Genetics 2012, 13:52  doi:10.1186/1471-2156-13-52

Published: 29 June 2012

Additional files

Additional file 1:

Table S1. Ancestry assay for rhesus macaque samples used in this study*. Table S2. Putative SNPs covered with sequence reads from ChIPseq and/or RNAseq. Table S3. SNPs from 1000 Genomes Project Pilot 2. Table S4. The average nucleotide heterozygosity from 1000 Genomes Project Pilot 2. Figure S1: A: RNAseq correlation between human vs macaque. Data points: mean of normalized gene expression level (log2). B: H3K4me3 ChIPseq correlation between human vs macaque. Data points mean of normalized area under curve (log10) of covered reads within 1Kb of TSS. C. Sequencing coverage (H3K4me3 ChIPseq and RNAseq) in NPY genic region. Figure S2: Human cSNPs identified in 1000 Genomes Project Pilot 2 samples and this study. C or CEU: CEU trio from 1000 Genomes Project Pilot 2; Y or YRI: YRI trio from 1000 Genomes Project Pilot 2; M or Miami: 14 samples from Miami dataset in this study. Figure S3: SNPs shared between individuals in 1000 Genomes Project Pilot 2.

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