Analyzing the mitochondrial genome of over 2500 patients with retinal disease

Abstract

Purpose : Mitochondrial diseases are a heterogeneous group of disorders that arise as a result of dysfunction of the mitochondrial respiratory chain. The circular 16.5-kb mitochondrial genome (mtDNA) contains 37 genes, which are essential for normal mitochondrial function. Mitochondrial dysfunction caused by pathogenic/likely pathogenic variants in the mtDNA has been associated with retinal disease and vision loss. The goal of the study was to evaluate mtDNA variants in >2500 patients with inherited retinal disease (IRD).

Methods : We developed a highly sensitive and clinically validated mtDNA assay based on hybridization-based capture of mtDNA and next-generation sequencing (NGS) that is able to detect very low heteroplasmy levels of SNVs, INDELs and deletions. The mean read depth for the mtDNA was 18,224x, and 100% of base pairs were covered with a sequencing depth of at least 1000x. Sensitivity to detect SNVs and INDELs with over 10% heteroplasmy was 100%. For SNVs with 5-10% and <5% heteroplasmy levels the sensitivity was 93.3% and 88.9%, respectively. The mtDNA assay was included in diagnostic sequencing of 2597 IRD patients.

Results : A diagnostic (pathogenic/likely pathogenic) mtDNA variant was identified in 22 patients, contributing to a diagnostic yield of 0.85%. The 22 diagnostic variants included one heteroplasmic large deletion (7542bp) and 21 SNVs. Five of the SNVs were homoplasmic and 16 were heteroplasmic (>7%). Homoplasmic variants were associated mainly with Leber hereditary optic neuropathy (LHON). Diagnostic variants were identified in 8 mtDNA genes: MT-ND1, MT-ND4, MT-ND6, MT-ATP6, MT-TN, MT-TH, MT-TL1, and MT-TV. The most common variant was the retinal disease-associated MT-TL1 m.3243A>G, identified in 11 individuals in whom the retinal disease was most often described as macular/ cone dystrophy. Additionally, we reported a mtDNA VUS, likely to contribute to the patient’s diagnosis, in 7 cases.

Conclusions : Adding mtDNA analysis to routine genetic diagnostic process of IRD patients can increase the diagnostic yield by >0.85%. Analyzing the full mtDNA is beneficial as several different variants in mtDNA have been associated with both syndromic and non-syndromic IRD.

This is a 2021 ARVO Annual Meeting abstract.