Application of a custom haplotype caller to analyze sequence-based data of 56 microhaplotypes

Kwon, Ye-Lim; Lee, Eun Young; Kim, Bo Min; Joo, Su Min; Jeong, Kyu Sik; Chun, Byung Won; Lee, Yang Han; Park, Ki Won; Shin, Kyoung Jin

doi:10.1016/j.fsigen.2022.102778

Cited by 4 publications

(3 citation statements)

References 28 publications

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“…The marker length and amplicon of the 50 MHs were 11–81 bp (average 65.58 bp) and 123–198 bp (average 156.02 bp), respectively, which were shorter than those of other panels. For example, the marker lengths of 60, 56, 40, 30, and 18 MHs have been reported as 20–116 [ 42 ], 17–218 [ 43 ], 8–114 [ 44 ], 63–423 [ 30 ], and 14–103 bp [ 45 ], respectively. The amplicons of 74, 56, 30, and 21 MHs have been reported as 157–325 [ 14 ], 115–263 [ 43 ], 63–423 (average 216) [ 30 ], and 125–375 bp [ 46 ], respectively.…”

Section: Discussionmentioning

confidence: 99%

“…For example, the marker lengths of 60, 56, 40, 30, and 18 MHs have been reported as 20–116 [ 42 ], 17–218 [ 43 ], 8–114 [ 44 ], 63–423 [ 30 ], and 14–103 bp [ 45 ], respectively. The amplicons of 74, 56, 30, and 21 MHs have been reported as 157–325 [ 14 ], 115–263 [ 43 ], 63–423 (average 216) [ 30 ], and 125–375 bp [ 46 ], respectively.…”

Section: Discussionmentioning

confidence: 99%

“…For example, Oldoni et al reported that the Het and A e of the 74 MHs were 0.51–0.78 [ 47 ] and 1.307–6.010 (median 2.706) [ 14 ], respectively. The A e of the 56, 40, and 30 MHs have been reported as 1.74–6.98 (average 3.45) [ 43 ], 2.62–4.41 (average 3.61) [ 44 ] and 3.91 [ 30 ], respectively. Studies have shown that Het > 0.4 and A e > 3.0 loci can be effectively used to analyze individual identification, kinship testing, degradation, mixtures, and ancestral inferences [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

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An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis

Zhang

Xue

Tan

et al. 2023

Genes

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Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.

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