Evaluation of gain in statistical power for kinship analysis using sequence-based versus length-based STR genotyping

Area of Science:

• Forensic Genetics
• Molecular Biology
• Statistical Genetics

Background:

• Traditional capillary electrophoresis (CE) genotyping relies on length-based analysis of short tandem repeat (STR) loci.
• Shortcomings exist in CE methods for capturing the full spectrum of genetic variation, potentially limiting statistical power in kinship analysis.
• Next-generation sequencing (MPS) technologies offer higher resolution, enabling the detection of sequence-level variations within STR loci and flanking regions.

Purpose of the Study:

• To evaluate the statistical power gain in likelihood ratio (LR) calculations using sequence-based MPS genotyping versus length-based CE genotyping for STR loci.
• To assess the impact of incorporating STR DNA sequence variations and flanking single nucleotide polymorphisms (SNPs) into LR calculations.
• To demonstrate the enhanced utility of MPS in complex kinship analyses, particularly for distant relationships.

Main Methods:

• Analysis of 137 pairwise relationships from 49 individuals across four Turkish families.
• Comparison of genotyping data obtained from the MPS Precision ID GlobalFiler NGS STR panel Kit and the CE GlobalFiler™ PCR Amplification Kit.
• Development of an alphanumeric allele re-coding system to integrate STR DNA sequence variants and flanking SNP data into LR calculations.

Main Results:

• MPS-based genotyping identified 37 STR DNA sequence variations and 26 flanking SNPs, compared to 150 unique alleles from CE.
• A significant increase in mean combined LR (cLR) was observed with MPS, ranging from a 78.08 to a 7,864,630.60-fold increase over CE.
• MPS-based cLR values were higher in 134 out of 137 pairwise relationships; mean cLR exceeded 1,000 for all relationship categories with MPS, including third-degree relationships (mean cLR 3,717.31 vs. 47.61 with CE).

Conclusions:

• Incorporating DNA sequence variation data from MPS-based genotyping leads to a statistically significant gain in cLR values for kinship analysis.
• MPS technology, when accounting for sequence-level variations, substantially improves the power of kinship determination, especially for second and third-degree relationships.
• The findings underscore the considerable potential of MPS for forensic kinship analysis, with further improvements expected from broader marker types and loci coverage.