Sparse windows extending more than 1 cM were found not to be present in the genomes, con sistent with previous selleckchem Ganetespib analyses of the HGDP genomes. Applying the method of Oleksyk et al. three values were calculated for each window, median multilo cus heterozygosity for each of two populations and the multilocus variance of FST between them. The distribu tions of multilocus values were then evaluated against distributions of ten million multilocus values created by the unrestricted random sampling of SNP windows within the same chromosome, for each size of the sam pling window. The quantiles resulting from the compari son with the resampled distribution were calculated for each of the 33 multilocus window sizes, and the most extreme quantile value across windows of different sizes centered on each SNP was reported, along with the corresponding window size, as described elsewhere in detail.
Only genomic regions with heterozygosity or FST in the most extreme 2. 5% tail of their randomized distributions were further examined. The multilocus windows of different sizes were placed in the candidate list of selection if two of the three scores for a window exceeded the 2. 5% cutoff. Windows centered on SNPs where at least two of the three scores were in the top 2. 5% were concatenated with overlap ping or adjacent windows fulfilling the same criteria. The type of se lection was inferred as follows, if median heterozy gosity in one population and variance of FST were both in the top 2. 5%, then a signature of new selection was inferred for the population. If the threshold of being in the top 2.
5% of genomic values was exceeded by median heterozygosity in both populations, and was exceeded also for the variance in FST, then a signature of new se lection was inferred for both populations. If the thresh old of being in the top 2. 5% of genomic values was exceeded by median heterozygosity in both populations, but was not exceeded by the variance in FST, then a sig nature of old selection was inferred. Since factors other than selection can sometimes affect these calculations, and since the history of African pygmies is not well characterized, we did not exclude genes identified as under old selection, although the focus was on genes under new selection in the Biaka. Host genes associated with HIV, and HIV dependency factors Previous studies have identified a set of host genes as being associated with an HIV phenotype.
A total of 45 genes clustering at 26 loci have been identi fied as human genes associated with HIV 1 in published research reports, these are listed in Additional file 1, Table S2. These 45 genes had been found using candidate gene or GWAS studies. Carfilzomib For GWAS studies, only those with genome wide significance of p 5 �� 10 8 were further considered, in order to minimize the num ber of false positives, as suggested by.
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