Accurate Genotyping and Tissue-Specific Expression Analysis of the Human Mitochondrial Genome integrating whole genome and direct long-read RNA sequencing data

This study introduces an integrated and scalable framework combining whole-genome sequencing (WGS) and direct long-read RNA sequencing (dRNA-seq) for high-resolution characterization of the human mitochondrial genome. A key innovation is MitSorter, a methylation-aware tool that distinguishes mtDNA from NUMTs, overcoming short-read limitations. Analysis of 73 samples across 15 tissues enabled accurate genotyping and tissue-specific expression profiling. Long-read RNA sequencing allows direct investigation of full-length transcripts, RNA processing, and post-transcriptional modifications. Integrating DNA and RNA variant data links mitochondrial genetic variation to transcriptional output, revealing tissue-specific regulatory signatures.