Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM

Area of Science:

• Forensic Genetics
• Molecular Biology
• Genomics

Background:

• Shortcomings of traditional STR markers in forensic genetics, including high mutation rates and limited multiplexing.
• Emerging potential of Massively Parallel Sequencing (MPS) for high-throughput SNP genotyping.
• Need for validated SNP panels for forensic applications.

Purpose of the Study:

• To design and evaluate a custom SNP panel for forensic identity testing using MPS.
• To assess genotyping precision, sequence coverage, sensitivity, and SNP performance.
• To develop an automated data analysis tool for quality control.

Main Methods:

• Design of a 273-SNP panel from various databases and studies.
• Genotyping using the Ion Torrent PGM platform.
• Validation against Sanger sequencing and analysis of control samples and a Chinese HAN population cohort.
• DNA dilution series testing for sensitivity.

Main Results:

• High concordance with Sanger sequencing, with minimal missing calls due to low coverage.
• Balanced coverage across most loci, with minor issues in 16 SNPs.
• Extensive sequence coverage for most SNPs, with three Y-SNPs showing mean coverage below 1000.
• Reproducible results down to 1ng of DNA input.
• Demonstrated polymorphism and independence of SNP targets in the Chinese HAN population.

Conclusions:

• MPS technology is well-suited for forensic SNP analysis.
• The custom SNP panel demonstrates high sensitivity, accuracy, and genotyping performance.
• The developed assay provides a straightforward workflow for forensic casework, aiding individual identification and kinship analysis.