Performance Comparison of Massively Parallel Sequencing (MPS) Instruments Using Single-Nucleotide Polymorphism (SNP)...

Area of Science:

• Forensic Genetics
• Genomic Sequencing Technologies

Background:

• The Precision ID Ancestry Panel uses 165 single-nucleotide polymorphisms (SNPs) for ancestry prediction.
• Early workflows with the Ion Torrent Personal Genome Machine (PGM) were semiautomated and labor-intensive.
• Newer automation with the Ion Chef robot and Ion S5 sequencer streamlines the process.

Purpose of the Study:

• To compare the performance of two massively parallel sequencing systems: PGM and S5.
• To evaluate if workflow automation impacts ancestry prediction accuracy.
• To assess changes in sequencing quality metrics.

Main Methods:

• Mock forensic samples (n=16) were used to prepare libraries.
• Libraries were templated using either the Ion OneTouch 2 system (for PGM) or the Ion Chef robot (for S5).
• Massively parallel sequencing was performed on both systems.

Main Results:

• Ion sphere particle performance metrics were comparable between the two systems.
• The Ion S5 system demonstrated higher total coverages per SNP and improved SNP quality.
• Ancestry predictions were concordant between the PGM and S5 systems.

Conclusions:

• Automating the workflow with the Ion Chef system significantly reduces labor.
• The automated workflow enhances sequencing quality.
• The transition to the automated Ion S5 system maintains accurate ancestry predictions.