Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light

Abstract

The expanding use of exome sequencing (ES) in diagnosis generates a huge amount of data, including untargeted mitochondrial DNA (mtDNA) sequences. We developed a strategy to deeply study ES data, focusing on the mtDNA genome on a large unspecific cohort to increase diagnostic yield. A targeted bioinformatics pipeline assembled mitochondrial genome from ES data to detect pathogenic mtDNA variants in parallel with the "in-house" nuclear exome pipeline. mtDNA data coming from offtarget sequences (indirect sequencing) were extracted from the BAM files in 928 individuals with developmental and/or neurological anomalies. The mtDNA variants were filtered out based on database information, cohort frequencies, haplogroups and protein consequences. Two homoplasmic pathogenic variants (m.9035T>C and m.11778G>A) were identified in 2 out of 928 unrelated individuals (0.2%): the *Christel Thauvin-Robinet and Yannis Duffourd contributed equally to this work. m.9035T>C (MT-ATP6) variant in a female with ataxia and the m.11778G>A (MT-ND4) variant in a male with a complex mosaic disorder and a severe ophthalmological phenotype, uncovering undiagnosed Leber's hereditary optic neuropathy (LHON).Seven secondary findings were also found, predisposing to deafness or LHON, in 7 out of 928 individuals (0.75%). This study demonstrates the usefulness of including a targeted strategy in ES pipeline to detect mtDNA variants, improving results in diagnosis and research, without resampling patients and performing targeted mtDNA strategies.

Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis

“…Although whole exome sequencing largely provides adequate coverage of nDNA protein coding exons, the average coverage of mtDNA is much lower (∼50×) and thus less sensitive when compared with WGS. 48 Whole exome sequencing of nDNA and mtDNA is performed in parallel and is subject to incomplete coverage and target enrichment bias during library preparation, when compared with WGS. Of further benefit, analysis of WGS provides more capability when identifying CNVs and SVs, which can be challenging when using targeted sequencing panels or whole exome sequencing.…”

The diagnostic rate of inherited metabolic disorders by exome sequencing in a cohort of 547 individuals with developmental disorders

“…ES was performed from DNA obtained from blood samples. A solo strategy was used in 506/547 individuals (92%), following protocols previously described [5] , [18] , [19] and American College of Medical Genetics and Genomics guidelines [20] . All candidate or pathogenic variants were verified by a second genetic technique, as well as familial segregation.…”

Clinical Heterogeneity in MT-ATP6 Pathogenic Variants: Same Genotype—Different Onset

“…For NC_012920.1(MT-ATP6):m.9035T>C, for example, this correlation does not hold true [15]. Indeed, in the literature, both patients with a more severe presentation during childhood consisting of cognitive developmental delay and progressive ataxia, and patients with a milder phe-notype characterized by an adult-onset spinocerebellar syndrome, displayed very high levels of heteroplasmy (90-100%) [12][13][14][15][16][17]. In our study as well, despite the different clinical presentation, the NC_012920.1(MT-ATP6):m.9035T>C pathogenic variant was found to be homoplasmic in the evaluated tissues of both patients.…”

“…Furthermore, it has also been associated with adult-onset ataxia [13]. Overall, only a few papers have reported on patients with NC_012920.1(MT-ATP6):m.9035T>C [5,8,[12][13][14][15][16][17] (see Table S1 for an overview of previously published cases).…”