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Enhanced Genetic Analysis of Single Human Bioparticles Recovered by Simplified Micromanipulation from Forensic ‘Touch DNA’ Evidence
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Forensic DNA phenotyping using Oxford Nanopore Sequencing system.

Veysel Sapan1, Sumeyye Zulal Simsek1, Gonul Filoğlu1

  • 1Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey.

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|May 25, 2024
PubMed
Summary

Oxford Nanopore Sequencing (ONT) offers promising results for forensic genetics, with ligation significantly improving genotyping accuracy for the HIrisPlex-S panel. Further optimization is needed to address error rates and enhance reliability.

Keywords:
HIrisPlex‐SOxford Nanopore Sequencingsingle nucleotide polymorphism

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Area of Science:

  • Forensic Genetics
  • Next-Generation Sequencing
  • Human Identification

Background:

  • Forensic science requires precise, consistent, and cost-effective methods for human identification.
  • Next-generation sequencing (NGS) technologies are being explored to meet these demands.
  • The HIrisPlex-S panel, comprising 41 single nucleotide polymorphism (SNP) markers, is crucial for predicting phenotypic traits like eye, hair, and skin color.

Purpose of the Study:

  • To investigate the potential of Oxford Nanopore Sequencing (ONT) Technology for analyzing the HIrisPlex-S panel.
  • To assess the accuracy and reliability of ONT-generated data by comparing it with conventional capillary electrophoresis (CE).
  • To evaluate the impact of ligation on ONT sequencing accuracy for forensic genetic analysis.

Main Methods:

  • Oxford Nanopore Sequencing (ONT) was used to analyze 18 samples for the HIrisPlex-S panel.
  • ONT data was basecalled using Guppy v6.1 and processed using Burrows-Wheeler Aligner, Samtools, BCFtools, and Python.
  • Genotyping accuracy was compared between ONT-unligated and ONT-ligated samples against capillary electrophoresis (CE) data.

Main Results:

  • ONT-unligated samples showed 62% correct SNP genotyping, with 36% allele dropout and 2% incorrect genotyping.
  • ONT-ligated samples demonstrated improved accuracy with 85% correct SNP genotyping, 10% allele dropout, and 5% incorrect genotyping.
  • Phenotype predictions based on ONT data showed varying but often high accuracy, indicating potential despite recognized error rates.

Conclusions:

  • ONT sequencing, especially with ligation, significantly enhances genotyping accuracy and coverage for the HIrisPlex-S panel in forensic genetics.
  • While ONT shows promise, challenges related to error rates necessitate further optimization and stringent quality control measures.
  • This study contributes to refining sequence read tuning and improving correction tools for ONT technology in forensic applications.