SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms

Abstract

Inherited genetic variation plays a critical but largely uncharacterized role in human differentiation. The completion of the International HapMap Project makes it possible to identify loci that may cause human differentiation. We have devised an approach to find such ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database. We selected ESNPs using the nearest shrunken centroid method (NSCM), and performed multiple tests for genetic heterogeneity and frequency spectrum on genes having ESNPs. The function and disease association of the selected SNPs were also annotated. This resulted in the identification of 100 736 SNPs that appeared uniquely in each ethnic group. Of these SNPs, 1009 were within disease-associated genes, and 85 were predicted as damaging using the Sorting Intolerant From Tolerant system. This study resulted in the creation of the SNP@Ethnos database, which is designed to make this type of detailed genetic variation approach available to a wider range of researchers. SNP@Ethnos is a public database of ESNPs with annotation information that currently contains 100 736 ESNPs from 10 138 genes, and can be accessed at and or directly at .

LCT 13910 C/T polymorphism, serum calcium, and bone mineral density in postmenopausal women

“…The polymerase chain reaction (PCR) mixture (20 μL) contained 1 μL genomic DNA (50 ng/μL), 0.18 μL primers (100 μmol/L; Sigma-Genosys, Woodlans, TX, USA), 0.04 μL probes (100 μmol/L; Applied Biosystems, Foster City, CA, USA), 10 μL of TaqMan Universal PCR Assay Mix (Applied Biosystems), and 8.56 μL ultrapure PCR water. In order to measure population stratification, rs1445398 C/T and rs7130656 A/G as ancestry-related polymorphisms were chosen from the Human1M-Duo Illumina Array and Ethnically Variant SNP database [17]. The genetic analyses of these polymorphisms were carried out by pre-designed TaqMan primer/probe sets (Applied Biosystems): the PCR mixture (20 μL) contained 1 μL genomic DNA (50 ng/μL), 0.50 μL 40× pre-designed TaqMan SNP Genotyping Assay (Applied Biosystems), 10 μL of TaqMan Universal PCR Assay Mix (Applied Biosystems), and 8.50 μL ultrapure PCR water.…”

Identification of Ancestry Informative Markers from Chromosome-Wide Single Nucleotide Polymorphisms Using Symmetrical Uncertainty Ranking

“…The chromosome-wide search for AIMs reveals that a set of SNPs that can lead to complete classification is not unique. In fact, the number of SNPs required to achieve this level of classification accuracy is much smaller than those reported in early works by Park et al [12], Paschou et al [6] and Zhou and Wang [13]. A summary of the numbers of required SNPs from the early works and the present study is given in Table II.…”

“…A summary of the numbers of required SNPs from the early works and the present study is given in Table II. Park et al [12] employ a nearest shrunken centroid method while Zhou and Wang [13] develop a modified t-test for SNP screening. Both approaches are filter-based attribute selection techniques where each SNP is prioritised by identifying its usefulness for separating all population classes from one another.…”

“…As a result, the search for SNP-based AIMs usually involves genome-wide SNP screening. Many measures including informativeness [11], t statistics [12], [13] and F statistics [13] have been proposed for SNP prioritisation. The screening is then carried out via a greedy search [11] or a ranking method [13].…”

“…The genome-wide SNP screening indicates that AIMs spread across the whole genome [6], [12], [13]. In fact, only 14 SNPs are required for the complete classification between the CEU (Utah residents with northern and western European ancestry), YRI (Yoruba in Ibadan, Nigeria) and combined JPT (Japanese in Tokyo) and CHB (Han Chinese in Beijing) samples in the HapMap data [6].…”