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The population genetics characteristics of a 90 locus panel of microhaplotypes

NCJ Number
HUMAN GENETICS Volume: 140 Dated: October 2021 Pages: 1753-1773
Andrew J. Pakstis; Neeru Gandotra; William C. Speed; Michael Murtha; Curt Scharfe ; Kenneth K. Kidd
Date Published
October 2021
21 pages

This study analyzed information for 90 microhaplotype loci in 4,009 individuals from 79 world populations in 6 major biogeographic regions. 


Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. The current study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3,485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1,337 occurred at frequencies > 5 percent in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions. (publisher abstract modified)

Date Published: October 1, 2021