Comparison of mitochondrial DNA variants detection using short- and long-read sequencing

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Short-read sequencing excels at single nucleotide variants but struggles with complex genomic regions.
• Long-read sequencing technologies promise to resolve structural variations, copy number variations, and homologous repeats.
• Long-read sequencing exhibits higher rates of random errors, including deletions, insertions, and single nucleotide errors.

Purpose of the Study:

• To compare the genotyping accuracy of long-read and short-read sequencing for mitochondrial DNA variants.
• To evaluate the suitability of long-read sequencing for accurate variant detection in complex genomic regions.

Main Methods:

• Genotyping of three DNA samples using PacBio Sequel long-read sequencing.
• Genotyping of the same three DNA samples using Illumina HiSeqX10 short-read sequencing.
• Comparative analysis of variant calls and error profiles between the two sequencing platforms.

Main Results:

• Long-read sequencing accuracy for genotyping short nuclear variants is comparable to short-read sequencing.
• Random error distribution in long reads allows for accurate variant correction at lower coverage.
• Approximately 37 reads of long-read data are sufficient for reliable genotyping of short variants.

Conclusions:

• Long-read sequencing is a viable alternative to short-read sequencing for genotyping short nuclear variants.
• The random nature of long-read errors enhances accuracy and reduces coverage requirements for variant detection.
• Advancements in long-read technology provide powerful tools for resolving complex genomic structures and variations.