Summary
Mitochondrial diseases are caused by changes in both nuclear and mitochondrial DNA (mtDNA), but many genetic tests still miss mtDNA analysis. This can lead to missed or incomplete diagnoses. We performed analytic validation for an NGS assay combining nuclear genes and mtDNA within the same test and retrospectively reviewed 6,684 reports for patients tested with Blueprint Genetics gene panel.
- The mean read depth across the mitochondrial genome was 18,224X, and 100% of base pairs were covered at least 1,000X.
- The test detected all single-nucleotide variants (SNVs) and small insertions/deletions (INDELs) present at more than 10% heteroplasmy.
- Sensitivity remained high for lower-level variants: 93.3% for SNVs at 5–10% heteroplasmy and 88.9% for variants below 5%.
- The assay was also highly sensitive (99.7%) for simulated deletions between 500 base pairs and 5 kilobases, even when present at only 10% heteroplasmy.
- In a clinical cohort of 6,684 tested patients, a pathogenic or likely pathogenic mitochondrial DNA variant was identified in 76 individuals (1.1%).
- The most common variants were m.3243A>G (26 patients; MELAS) and m.1555A>G (15 patients; aminoglycoside- induced hearing loss).
These data show that including techinically robust mtDNA assay in routine NGS panels significantly improves genetic diagnosis in patients with complex phenotypes.
Authors:
Pernilla von Nandelstadh, Sari Tuupanen, Marta Gandia, Sanna Vattulainen-Collanus, Kati Kämpjärvi, Johanna Känsäkoski, Katja Merkkiniemi, Laura Sarantaus, Raquel Perez-Carro, Jonna Tallila, Ville Kytölä, Mikko Muona, Johanna Sistonen, Inka Saarinen, Juha Koskenvuo, Tero-Pekka Alastalo