Ion torrent high throughput mitochondrial genome sequencing (HTMGS)

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Next-generation sequencing (NGS) has spurred the development of rapid whole mitochondrial genome sequencing techniques.
• Existing commercial methods often require extensive optimization for accurate mitochondrial genome amplification.

Purpose of the Study:

• To present an efficient and cost-effective NGS approach for sequencing human mitochondrial genomes.
• To detail a bioinformatics pipeline for streamlined variant calling in mitochondrial DNA.
• To introduce a high-throughput mitochondrial genome sequencing (HTMGS) methodology.

Main Methods:

• Utilized Ion Torrent PGM platform with Ion 316 chips for tandem sequencing of mitochondrial genomes.
• Developed a modified bioinformatics pipeline based on GATK best practices tailored for mitochondrial data.
• Incorporated dual-platform barcodes for compatibility with Illumina systems.

Main Results:

• The HTMGS method allows high sample multiplexing and uses alternative library preparation reagents at a lower cost (~1.7 times less per sample).
• Achieved robust mitochondrial sequencing data with >450X average coverage.
• Identified an average of ~30 variants per sample, with 572 variants observed across 315 samples.

Conclusions:

• Developed a high-throughput sequencing and analysis method for complete mitochondrial genomes.
• The HTMGS methodology is potentially platform-agnostic and adaptable to various study designs.
• This approach offers a cost-effective and efficient alternative for mitochondrial genome sequencing and variant analysis.