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AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data.

Kimberly Sturk-Andreaggi1, Michelle A Peck1, Cecilie Boysen2

  • 1Armed Forces DNA Identification Laboratory, A Division of the Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD 20850, United States.

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PubMed
Summary

A new toolkit, AQME, streamlines mitochondrial DNA (mtDNA) analysis for forensics using next-generation sequencing (NGS) data. It automates profile generation and haplogroup estimation, improving efficiency and accuracy in forensic casework.

Keywords:
Data analysisForensicsHaplogroupMitochondrial DNANext-generation sequencing (NGS)

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Area of Science:

  • Forensic Science
  • Genetics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) has advanced mitochondrial DNA (mtDNA) genome sequencing capabilities.
  • Analyzing NGS-generated mtDNA data presents significant challenges for forensic applications.
  • Existing bioinformatics pipelines require specialized tools for forensic mtDNA analysis.

Purpose of the Study:

  • To develop and evaluate a custom toolkit, the AFDIL-QIAGEN mtDNA Expert (AQME), for analyzing forensic mtDNA data generated by NGS.
  • To enhance the efficiency and accuracy of mtDNA profile generation and haplogroup estimation in forensic casework.
  • To integrate forensic conventions and interpretation ranges into automated mtDNA data analysis.

Main Methods:

  • Development of the AQME toolkit for the CLC Genomics Workbench, integrating forensic conventions.
  • Application of AQME to analyze Illumina-generated mitogenome NGS data from 21 samples of varying quality.
  • Evaluation of AQME's automated variant calling, profile generation, haplogroup estimation, and reporting functionalities.

Main Results:

  • AQME successfully generated editable mtDNA profiles adhering to forensic conventions, with 211 automated edits applied.
  • Haplogroup estimation was accurate for 18 out of 19 samples, with a bug identified for partial data.
  • The toolkit facilitated the transition to NGS mitogenome methods, with AFMES-AFDIL implementing two validated NGS methods.

Conclusions:

  • AQME is a functional and reliable toolkit for the forensic analysis of mitogenome NGS data.
  • The toolkit simplifies the integration of NGS data into routine forensic casework by automating key analysis steps.
  • AQME supports broader adoption of mtDNA analysis in forensics, enhancing casework efficiency and data interpretation.