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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics.

Hao Wu1, Ai-Cen Ji1,2, Yi-Cheng Liu1

  • 1National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.

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|August 10, 2020
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Summary

This study introduces a new next-generation sequencing panel for forensic STR analysis, significantly improving DNA matching probability and aiding in DNA mixture deconvolution.

Keywords:
Forensic geneticsNext-generation sequencingSTRStutter sequenceYunnan Bai population

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Area of Science:

  • Forensic Genetics
  • Molecular Biology
  • Genomics

Background:

  • Short tandem repeats (STRs) are crucial in forensic genetics for DNA profiling.
  • Traditional STR analysis relies on length-based genotyping.
  • Next-generation sequencing (NGS) offers enhanced capabilities for STR analysis, including sequence variation detection.

Purpose of the Study:

  • To develop and evaluate an in-house NGS-based panel for comprehensive forensic STR analysis.
  • To assess the performance of the panel in terms of sensitivity, data balance, and discriminatory power.
  • To investigate STR stutter patterns and their implications for DNA mixture deconvolution.

Main Methods:

  • Design and validation of a 29-plex NGS panel covering 28 autosomal STR loci and Amelogenin.
  • Evaluation of panel sensitivity using low DNA input amounts (as low as 62.5 pg).
  • Sequencing of 203 individuals from the Yunnan Bai population and comparative analysis of length-based vs. sequence-based data.

Main Results:

  • The panel demonstrated intralocus- and interlocus-balanced sequencing data.
  • High sensitivity was achieved, with reliable results from 62.5 pg of input DNA.
  • Sequence-based matching probability reached 2.37 × 10-29, a 23-fold increase over length-based data.
  • Analysis of STR stutter sequences revealed insights into repeat motif variations and co-existence of different stutter types.

Conclusions:

  • The developed NGS panel provides superior discriminatory power for forensic identification compared to traditional methods.
  • The findings enhance understanding of STR stutter mechanisms, crucial for complex DNA mixture analysis.
  • This panel offers a robust tool for forensic casework, particularly for DNA mixture deconvolution.