Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

Abstract

The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.

The population genetics characteristics of a 90 locus panel of microhaplotypes

“…Those six clusters are the ones that correspond to “continental” clusters when representatives of all “continents” are present: Sub-Sahara Africa; North Africa, Southwest Asia, and Europe; South Central Asia; East Asia; the Pacific; and the Americas. These six are the commonly seen clusters from many studies based on SNPs (Soundararajan et al 2016 ; Li et al 2016 ; Cherni et al 2016 ; Santos et al 2016 ; Fondevila et al 2017 ; Pakstis et al 2017 ; Pakstis et al 2019 ;Xavier et al 2020 ), on studies of microhaplotypes (Kidd et al 2017 , 2018a ; Bulbul et al 2018 ; Gandotra et al 2020 ; Puente et al 2020b ; Staadig and Tillmar 2021 ), and on studies combining single SNPs and MHs (Phillips et al 2019 ; Kidd et al 2021 ). K = 6 provides a convenient basis for summarizing aspects of the data such as the MHs with the highest regional A e values.…”

“…Their desirable characteristics include multiple alleles with high heterozygosity and low mutation rates. Since then, MHs have been studied by many researchers with clear demonstration of their potential for forensic, medical, and anthropologic applications (Bulbul et al 2018 ; Chen et al 2018 ; Kidd et al 2018a , 2021 ; Cheung et al 2019 ; Phillips et al 2019 ; Puente et al 2020a ; Puente et al 2020b ), but they have not yet been incorporated into routine forensic casework.…”

“…While MPS was not used in these exploratory studies, it was clear that the existence of MPS was what made study of microhaplotypes relevant. Now, there have been several studies that have used MPS successfully to study panels of microhaplotypes on multiple individuals and/or populations (Turchi et al 2019 ; Chen et al 2018 ; Oldoni et al 2019 ; Bennett et al 2019 ; Gandotra et al 2020 ; Puente et al 2020a ; Puente et al 2020b ; Kureshi et al 2020 ; Wu et al 2021a ; Wu et al 2021b ).…”

A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures

“…The microhaplotype was defined as an assembly of SNPs within 200-300 bp forming multiple alleles and detected by MPS [4]. It theoretically combines the advantages of both STRs and single nucleotide polymorphisms (SNPs), and could be applied in multiple forensic scenarios [4][5][6][7]. Notably, free of stutter artifacts, shorter length, and larger multiplex capacities on the MPS platform make MH promising for DNA mixture analysis.…”

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures

“…MHs present some advantages over standard STRs: (1) a multiallelic nature and the absence of STR structures, which prevents Taq polymerase slippage and stutter peak generation; (2) balanced PCR amplification due to the similar lengths of MH amplicons (preferential PCR amplification for shorter alleles commonly occurs with STRs); and (3) lower mutation rates than STRs. Since Kidd proposed this powerful new type of genetic marker in 2013 [26], an increasing number of studies have primarily focused on the following aspects: (1) finding and evaluating more MHs with higher effective number of alleles (A e ) to yield low random match probabilities (RMPs) and high probabilities of enhancing deconvolution performance [27,28]; (2) expanding the forensic application scenarios of MHs (e.g., biogeographic ancestry inference [28][29][30][31][32][33][34][35][36][37][38][39][40], analysis of degraded samples [41][42][43][44], human and missing-person identification [27,38,[45][46][47][48][49][50], and relationship testing [51][52][53][54][55][56][57][58]); and (3) deconvoluting two-person and more-than-two-person DNA mixtures by different probabilistic models [42,…”