An efficient and tunable parameter to improve variant calling for whole genome and exome sequencing data

Area of Science:

• Genomics
• Bioinformatics
• Next-Generation Sequencing

Background:

• Next-generation sequencing (NGS) is crucial in diverse fields, but platforms exhibit amplification bias affecting variant calls.
• Accurate variant detection is essential for understanding genetic variations in personal genomes.

Purpose of the Study:

• To evaluate the accuracy and vulnerability of Illumina and Ion Proton NGS platforms in GC-rich/poor regions.
• To compare variant calling performance between two major NGS platforms using whole genome and whole exome data.

Main Methods:

• Whole genomes and exomes from ten Korean individuals were sequenced using Illumina and Ion Proton platforms.
• Reads were analyzed using the BWA-GATK variant calling pipeline with VQSR and filtering strategies.
• Variants unique to each platform and common variants were validated using Sanger sequencing.

Main Results:

• Illumina sequencing demonstrated higher accuracy compared to Ion Proton for variant detection.
• The study identified platform-specific vulnerabilities in GC-rich and GC-poor genomic areas.
• High-quality variants were achieved through rigorous filtering and the VQSR tool.

Conclusions:

• Illumina offers superior accuracy for variant calling in personal genomes over Ion Proton.
• The developed filtering methods enhance the reliability of NGS data for large-scale population studies.
• These findings aid in selecting appropriate NGS platforms for complex disease research.