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Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases
Journal article   Peer reviewed

Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases

Erwen Huang, Changhui Liu, Jingjing Zheng, Xiaolong Han, Weian Du, Yuanjian Huang, Chengshi Li, Xiaoguang Wang, Dayue Tong, Xueling Ou, …
Scientific reports, Vol.8(1), pp.5553-6
04/03/2018
DOI: 10.1038/s41598-018-23888-0
PMID: 29615764
url
https://doi.org/10.1038/s41598-018-23888-0View
Published (Version of record) Open Access

Abstract

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 x 10-48 to 1.93 x 10-50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 x 10-47 and CEP = 0.999999999862. 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.
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