J Korean Med Sci.  2023 Sep;38(36):e297. 10.3346/jkms.2023.38.e297.

Comparison of Two Variant Analysis Programs for Next-Generation Sequencing Data of Whole Mitochondrial Genome

• Lee SE
• Kim GE
• Kim H
• Chung DH
• Lee SD
• Kim MY

• KMID: 2545787
• DOI: http://doi.org/10.3346/jkms.2023.38.e297

Abstract

Background
With advance of next-generation sequencing (NGS) techniques, the need for mitochondrial DNA analysis is increasing not only in the forensic area, but also in medical fields.
Methods
Two commercial programs, Converge Software (CS) and Torrent Variant Caller for variant calling of NGS data, were compared with a considerable amount of sequence data of 50 samples with a homogeneous ethnicity.
Results
About 2,300 variants were identified and the two programs showed about 90% of consistency. CS, a dedicated analysis program for mitochondrial DNA, showed some advantages for forensic use. By additional visual inspection, several causes of discrepancy in variant calling results were identified. Application of different notation rules for mitochondrial sequence and the minor allele frequency close to detection threshold were the two most significant reasons.
Conclusion
With prospective improvement of each program, researchers and practitioners should be aware of characteristics of the analysis program they use and prepare their own strategies to determine variants.

Keyword

Mitochondrial DNA; DNA Sequence Analysis; Next-Generation Sequencing

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