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Optimized variant calling for estimating kinship.

August E Woerner1, Sammed Mandape2, Kapema Bupe Kapema2

  • 1Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA.

Forensic Science International. Genetics
|October 7, 2022
PubMed
Summary
This summary is machine-generated.

Whole genome sequencing offers improved kinship estimation in forensic genetics. New bioinformatic pipelines using DeepVariant and BCFtools demonstrate similar performance after optimized filtering for accurate sample attribution.

Keywords:
Genetic genealogyGenomicsKinshipMassively parallel sequencingWhole genome sequencing

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Area of Science:

  • Forensic genetics
  • Genomics
  • Bioinformatics

Background:

  • Sample attribution is a key goal in forensic genetics, often relying on DNA profile comparison.
  • Limited genetic markers may lack resolution for accurate relationship determination.
  • Whole genome techniques offer greater potential for resolving familial relationships.

Purpose of the Study:

  • To introduce and evaluate bioinformatic pipelines for kinship estimation using whole genome sequencing data in a forensic context.
  • To compare the performance of different variant callers (BCFtools and DeepVariant) for forensic kinship analysis.
  • To optimize filters and thresholds for accurate relationship determination from whole genome data.

Main Methods:

  • Massively parallel sequencing of whole genomes was employed.
  • Two variant callers, BCFtools and DeepVariant, were utilized.
  • Bioinformatic pipelines were developed and evaluated using a titration series, with kinship estimation via the KING-robust algorithm.

Main Results:

  • Both BCFtools and DeepVariant pipelines performed similarly after filter optimization.
  • DeepVariant generally produced more accurate genotypes.
  • Inaccuracies from DeepVariant slightly impacted overall relatedness estimates.

Conclusions:

  • Optimized whole genome sequencing pipelines can effectively estimate kinship for forensic sample attribution.
  • The choice of variant caller impacts genotype accuracy, with implications for relationship estimation.
  • Further refinement of bioinformatic approaches is valuable for advancing forensic genetic analysis.