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Evidence for selection at HIV host susceptibility genes in a West Central African human population

Kai Zhao1, Yasuko Ishida1, Taras K Oleksyk2, Cheryl A Winkler3 and Alfred L Roca14*

Author Affiliations

1 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Il, 61801, USA

2 Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico , 00681

3 Basic Research Laboratory, Center for Cancer Research, NCI, SAIC-Frederick, Frederick National Laboratory for Cancer Research, Frederick, , MD, 21702, USA

4 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, , IL, 61801, USA

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BMC Evolutionary Biology 2012, 12:237  doi:10.1186/1471-2148-12-237

Published: 6 December 2012

Additional files

Additional file 1:

Table S1. Proportion of autosomes showing signatures of selection for pairs of populations. Description: “New” selection indicates selection after the divergence of the two populations. “Old” selection occurred prior to the divergence of the two populations. Proportions are based on physical size (bp not cM) of the genome. The method of Oleksyk and colleagues (2008) [19] was applied to the human genome diversity panel African populations. Table S2. Locations and descriptions of HIV associated host genes. Description: Genomic locations listed are based on UCSC Genome Browser build hg18 [73]. Table S3. Human genes associated with HIV-1 (HGAHs) and HIV dependency factors (HDFs) under potential selection in Biaka, when Biaka and Mbuti genomes are compared. Description: HDFs and HGAHs that overlapped with genomic regions found under putative selection by applying the method of Oleksyk et al. [19] were sorted by the type of selection (recent in Biaka, recent in both Biaka and Mbuti, or old in Biaka and Mbuti) then ranked by the strength of selection measured by the product of the λ values that were used to assign the type of selection (as noted in methods). Genes that are HGAHs are in boldface. Table S4. Genes from GWAS studies in regions of selection. Table S5. Human genes associated with HIV-1 (HGAHs) and HIV dependency factors (HDFs) among genes previously reported as under putative selection in the Biaka. Table S6. SNPs in genes sequenced in Pygmies. Table S7. Oligonucleotide primers used for PCR or sequencing of genes. Figure S1. Geographic distribution of chimpanzee subspecies and phylogenetic relationship of strains of immunodeficiency viruses. Figure S2. Identification of types of selection based on genomic patterns. Figure S3. Length in kb of genomic regions under putative selection, with number of SNPs and genes within each region. Figure S4. List of all HGAHs and HDFs found in regions with signatures of selection for all pairwise comparisons. (PDF 2979 kb)

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