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Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing.

Jiaming Xue1, Mengyu Tan1, Ranran Zhang1

  • 1Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.

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Summary

This study developed new microhaplotype (MH) panels, including InDels, for enhanced forensic kinship testing. Panel C demonstrated superior performance in identifying close and distant relatives, improving accuracy in complex cases.

Keywords:
InDelKinship analysisMicrohaplotype

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Area of Science:

  • Forensic genetics
  • Population genetics
  • Human identification

Background:

  • Microhaplotypes (MHs) are crucial in forensic genetics for kinship analysis.
  • Traditional MHs, based solely on SNPs, have limitations in complex kinship identification, especially for distant relatives.
  • Expanding MHs to include short insertions/deletions (InDels) can enhance their discriminatory power.

Purpose of the Study:

  • To develop novel microhaplotype (MH) markers, incorporating both SNPs and InDels, for improved kinship testing.
  • To evaluate the performance of newly developed MH panels in various familial relationship analyses.
  • To assess the utility of these MH panels in complex forensic scenarios, including disaster victim identification and criminal investigations.

Main Methods:

  • Genome-wide screening of the Chinese Southern Han population from the 1000 Genomes Project to identify MH markers (2 or more variants within 220 bp).
  • Development of a 67plex MH panel (Panel B) using next-generation sequencing (NGS) and population genetic data collection from 124 unrelated individuals.
  • Combination of Panel B with a previously published panel (Panel A) to create an 87plex panel (Panel C) for comprehensive kinship analysis.

Main Results:

  • A novel 67plex MH panel (Panel B) was developed, featuring 65 newly discovered MHs with high average effective number of alleles (Ae = 5.34) and heterozygosity (0.7352).
  • The combined 87plex panel (Panel C) showed superior performance in distinguishing various degrees of relatedness (parent-child to 5th-degree relatives) compared to other panels.
  • Panel C achieved a low false testing level (FTL) of 0.11% for simulated 2nd-degree relatives but higher FTLs for more distant relationships (8.99% for 3rd-degree). It effectively excluded unrelated pairs and close relatives in paternity testing.

Conclusions:

  • The developed microhaplotype panels, particularly Panel C, significantly enhance the power of kinship analysis in forensic genetics.
  • Incorporating InDels into MHs broadens their application and improves accuracy for complex familial relationship testing.
  • These MH panels offer valuable supplementary genetic markers for challenging forensic investigations requiring high discriminatory power.