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 × 10–48 to 1.93 × 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 × 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.
Highlights
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability
When the threshold of minor allele frequencies (MAF) was set at ≥0.38–0.44, the number of shared SNPs ranged from 3881 to 21
It caught our attention that in the panel of MAF ≥0.35, only one SNP was shared by the SNPforID5212, and only seven were shared by the IISNP panel composed of 92 SNPs developed in the Kidd Lab[13,17] (Table S1)
Summary
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. 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. In 134 tested Han samples, of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with. 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. The 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels. The advantages of SNP characteristics serving as forensic markers include: (1) much higher density interspersing in the whole genome[1,2], providing more selectable loci to offset the defect of only two alleles at each locus. (3) Lower mutation rate, endowing them with superiority in paternity and immigration testing4,5. (4) Faster and cheaper high-throughput approaches available for genotyping[6,7,8]
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