SONiCS: PCR stutter noise correction in genome-scale microsatellites

Area of Science:

• Genomics
• Bioinformatics
• Population Genetics

Background:

• Massively parallel capture of short tandem repeats (STRs) enables high-resolution population genomic and demographic analyses.
• High Polymerase Chain Reaction (PCR) cycle numbers in target capture experiments introduce genotyping noise via PCR stutter.

Purpose of the Study:

• To develop a computational solution for correcting PCR stutter in STR genotyping.
• To validate the accuracy and success rate of the developed stutter correction method.

Main Methods:

• Developed SONiCS (Stutter mONte Carlo Simulation), a tool simulating PCR and capture conditions for stutter correction.
• Genotyped a 2499-marker STR panel in humpback dolphins using target capture.
• Validated SONiCS using capillary-based genotypes for five STR markers.

Main Results:

• SONiCS demonstrated a 99.1% accuracy rate and a 98.2% genotyping success rate in 110 comparisons.
• The tool accurately genotyped STRs, with minimal errors in low-coverage markers.
• SONiCS successfully identified and handled problematic markers.

Conclusions:

• SONiCS effectively corrects PCR stutter, significantly improving the reliability of STR genotyping from target capture data.
• The simulation approach provides a robust method for enhancing genetic analyses in population studies.
• SONiCS is freely available, facilitating its adoption in genomic research.