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Validation of novel forensic DNA markers using multiplex microhaplotype sequencing.

Neeru Gandotra1, William C Speed1, Wenyi Qin1

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A new assay enables multiplex sequencing of 90 microhaplotypes (MH), improving genetic variation analysis across diverse populations. This tool enhances forensic applications by detecting novel single nucleotide polymorphisms (SNPs) and visualizing haplotype data.

Keywords:
Diverse populationsForensicsMPSMassively parallel sequencingMicrohaplotypeSNPs

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Area of Science:

  • Genetics
  • Forensic Science
  • Bioinformatics

Background:

  • Microhaplotypes (MH), sets of single nucleotide polymorphisms (SNPs) within short genomic regions, offer powerful genetic markers.
  • Existing tools for MH analysis require improvement for broader application in diverse populations and forensic contexts.

Purpose of the Study:

  • To design and validate a novel assay for multiplex sequencing of 90 microhaplotypes (mMHseq).
  • To enhance the analysis of genetic variation and biogeographic ancestry using MH in various populations.

Main Methods:

  • Developed a multiplex assay (mMHseq) for 90 MH loci, including previously identified high-allele-count loci and novel ones from the 1000 Genomes Project.
  • Integrated a novel method for multiplex amplification from minimal DNA amounts and sequencing of 48 samples per run.
  • Evaluated assay performance in 156 individuals across seven global populations, with statistical analysis on 30 populations.

Main Results:

  • The mMHseq assay successfully detected MH variation, with a mean global average effective number of alleles (Ae) of 5.08 and mean informativeness for biogeographic variation (In) of 0.30 across 30 populations.
  • Identified 85 novel SNPs within 58 of the 90 microhaplotypes.
  • Developed open-source software for visualizing haplotype phase data.

Conclusions:

  • The multiplex microhaplotype sequencing assay (mMHseq) is a versatile and customizable tool for genetic analysis.
  • This approach significantly advances the application of microhaplotypes in population genetics and forensic science.
  • The developed assay and software facilitate broader and more efficient use of MH data.