Open AccessGenome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases
Author(s) -
Erwen Huang,
Changhui Liu,
Jingjing Zheng,
Han Xia,
Weian Du,
Yuesheng Huang,
Chengshi Li,
Xiaoguang Wang,
Dayue Tong,
Xueling Ou,
Hongyu Sun,
Zhaoshu Zeng,
Chao Liu
Publication year - 2018
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/s41598-018-23888-0
Subject(s) - international hapmap project , single nucleotide polymorphism , linkage disequilibrium , minor allele frequency , genetics , snp , snp genotyping , tag snp , biology , population , allele frequency , genome wide association study , allele , genotype , medicine , gene , environmental health
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10–48 to 1.93 × 10–50 and cumulative exclusion probability (CEP) ranged from 0.6653 to 0.45. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10–47 and CEP = 0.862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.