Finally, the average microhap heterozygosity globally should be greater than any of the SNPs alone can achieve. Over the past decade we have accumulated SNP genotype data at multiple genomic regions for 50+ Selisistat mw populations. In many of those regions the SNPs are densely packed with many SNPs within the targeted expanse. We used these genotypes already available on our set of 40+ populations as pilot data. Based on these analyses we then applied an average heterozygosity of >0.4 as an additional criterion when screening the Human Genome Diversity Project dataset [29] and the HapMap integrated (phases 1 + 2 + 3) dataset [30] for candidate microhaps.

These searches identified many candidate microhap loci; we have subsequently genotyped a few of the most promising of these as individual SNPs by TaqMan and statistically phased the genotype data into haplotypes. Those with the highest global average heterozygosity have been included in this study. During the course of our studies Nakahara et al. [28] presented a set of microhaps identified and studied in Japanese. We tested

one of them (COG2) and found it met our global criteria for the current panel; we have not tested the others. Sirolimus solubility dmso We note that while the ultimate objective is a panel of microhaplotypes for typing by sequencing, this initial characterization and selection of candidate loci is more efficiently and economically done with individual SNP typings, using preexisting data and new typings by TaqMan. The 54 populations studied, organized by geographical region of the world, are listed in Supplemental Table S1 along with

the sample size for each and the Sample UID in ALFRED [19] for additional information. These are the same population samples used in multiple publications [1], [2], [6], [17], [24], [31] and [32]. Collectively, these populations originate from most major regions of the world and include Megestrol Acetate a total of 2530 individuals of which 349 constitute about a third of the HGDP panel of around 1000 individuals. Table S1.   The 54 populations studied organized by geographical region. Column ABBREV shows the 3-character abbreviation employed in some figures and tables. Column Population UID holds the unique population identifier in ALFRED; Column Sample UID has the unique sample identifier in ALFRED. The DNA used has been extracted from lymphoblastoid cell lines. All individuals were typed with TaqMan assays from the Applied Biosystems Assays on Demand catalog. Typing was done in 3 μl reactions in 384-well plates using the manufacturer’s protocol. Following PCR in separate thermocyclers the plates were read using an AB7900 and the SDS software. Failed reactions were repeated once. In general, data were complete for >96% of individuals for each of the 66 SNPs (on average 98.9% complete).