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Improved pairwise kinship analysis using massively parallel sequencing.

Ran Li1, Haixia Li1, Dan Peng1

  • 1Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong, People's Republic of China.

Forensic Science International. Genetics
|October 28, 2018
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Summary
This summary is machine-generated.

Sequence-based STR typing offers enhanced discrimination power for kinship analysis, identifying more alleles and improving likelihood ratios. SNP markers show advantages in paternity testing, especially with STR mutations.

Keywords:
ForenSeq™ DNA signature prep kitKinship analysisMassively parallel sequencing (MPS)Short tandem repeat (STR)Single nucleotide polymorphism (SNP)

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Area of Science:

  • Forensic genetics
  • Molecular biology
  • Human identification

Background:

  • Accurate pairwise kinship analysis is crucial in forensic science.
  • Short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers are widely used for human identification.
  • Sequence-based STR typing may offer advantages over length-based typing.

Purpose of the Study:

  • To evaluate the ForenSeq™ DNA Signature Prep Kit for pairwise kinship analysis.
  • To compare the efficacy of sequence-based versus length-based STR typing.
  • To assess the utility of STRs and SNPs in determining various familial relationships.

Main Methods:

  • Analysis of 67 individuals from two families for six types of pairwise relationships.
  • Calculation of likelihood ratios (LRs) using sequence-based (LRsequence) and length-based (LRlength) STR genotype data.
  • Simulation of 10,000 relationship pairs to estimate system powers of STRs and SNPs.

Main Results:

  • Sequence-based typing identified additional alleles for autosomal, Y-STRs, and X-STRs, including novel alleles.
  • LRs significantly increased for various relationships when using sequence-based STR data compared to length-based data.
  • SNP markers demonstrated superior discrimination for non-parent-offspring relationships compared to STRs.
  • High accuracy was achieved for parent-offspring and full sibling testing; moderate accuracy for second-degree relatives; lower accuracy for first cousins.

Conclusions:

  • Sequence-based STR typing enhances polymorphism and discrimination power for kinship testing.
  • SNP markers offer advantages in paternity testing, particularly in cases with STR mutations or related alleged parents.
  • The ForenSeq™ DNA Signature Prep Kit is effective for paternity and full sibling testing, with potential for second-degree relatives, but requires further refinement for first-cousin identification.