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U.S. population data for 94 identity informative SNP loci



Kevin Kiesler, Lisa Borsuk, Becky Steffen, Peter Vallone, Katherine Gettings


The U.S. National Institute of Standards and Technology analyzed a set of 1036 samples representing four major U.S. population groups (African American, Asian American, Caucasian, and Hispanic) with the ForenSeq DNA Signature Prep Kit, DNA primer mix B (DPMB) on the MiSeq FGx Sequencing System. In addition to the previously reported STR markers, DPMB includes amplification primers for single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs, n = 94), ancestry inference (aiSNPs, n = 56), and phenotype prediction (piSNPs, n = 22). In this report, resulting sequencing coverage information was interpreted for the 94 iiSNP markers. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data with an alternate informatic pipeline identified variants in the sequenced regions flanking the targeted SNPs in the assay. Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15 % over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 x 10-38 for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes.


Single nucleotide polymorphism, human identification, microhaplotype, next generation sequencing


Kiesler, K. , Borsuk, L. , Steffen, B. , Vallone, P. and Gettings, K. (2023), U.S. population data for 94 identity informative SNP loci, Genes, [online],, (Accessed May 25, 2024)


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Created May 15, 2023, Updated October 6, 2023