Leber Hereditary Optic Neuropathy (LHON) - Targeted Testing for 3 Common Pathogenic Variants

Leber hereditary optic neuropathy (LHON) is an inherited mitochondrial disease that results from respiratory chain dysfunction in the retinal ganglion cells, ultimately leading to progressive bilateral loss of vision (Yu-Wai-Man and Chinnery. 2021. PubMed ID: 20301353; Moster et al. 2016. PubMed ID: 27459664). Vision loss may be sequential; patients may initially be affected in only one eye, but the second may develop vision loss within ~8 weeks (Riordan-Eva et al. 1995. PubMed ID: 7735876). Onset may occur at any age, but for males often peaks in the second or third decade of life (Riordan-Eva et al. 1995. PubMed ID: 7735876; Lopez Sanchez et al. 2021. PubMed ID: 34670133).

The prevalence of LHON with a molecularly-confirmed diagnosis due to one of the three most common pathogenic variants has been estimated to be ~1:45,000 in European populations (Mascialino et al. 2012. PubMed ID: 21928272). LHON variants may display significant incomplete penetrance, but the exact percentage may vary from family to family and also over generational time, possibly due to other contributing genetic or environmental factors (Lopez Sanchez et al. 2021. PubMed ID: 34670133; Kirkman et al. 2009. PubMed ID: 19525327). A gender bias has been reported, with males affected more often than females, although the cause of this is not yet understood (Lopez Sanchez et al. 2021. PubMed ID: 34670133; Puomila et al. 2007. PubMed ID: 17406640; Yu-Wai-Man and Chinnery. 2021. PubMed ID: 20301353; Piotrowska-Nowak et al. 2020. PubMed ID: 32740724). Some large cohort studies estimate the overall lifetime risk of vision loss among males with a pathogenic LHON variant as ~17-27%, and females with a pathogenic LHON variant as ~5-8% (Lopez Sanchez et al. 2021. PubMed ID: 34670133; Puomila et al. 2007. PubMed ID: 17406640). Previous estimates, however, were as high as ~50-60% in males and 10-20% in females (Yu-Wai-Man and Chinnery. 2021. PubMed ID: 20301353).

Currently, there are no approved treatments for individuals with LHON, although research into effective drug or gene therapies is ongoing (Hage and Vignal-Clermont. 2021. PubMed ID: 34122299).

LHON, a maternally-inherited disorder, is caused by pathogenic variants in the mitochondrial genome, with three specific missense variants accounting for ~90% of cases worldwide (Mackey et al. 1996. PubMed ID: 8755941; Yu-Wai-Man and Chinnery. 2021. PubMed ID: 20301353): MT-ND1 m.3460G>A (p.Ala52Thr), MT-ND4 m.11778G>A (p.Arg340His), and MT-ND6 m.14484T>C (p.Met64Val). These three variants are located in three different genes that encode for subunits of the mitochondrial complex I (Kirches et al. 2011. PubMed ID: 21886454).

Clinical sensitivity for this test is expected to be high as these three variants (MT-ND1 m.3460G>A (p.Ala52Thr), MT-ND4 m.11778G>A (p.Arg340His), and MT-ND6 m.14484T>C (p.Met64Val)) have been documented to account for ~90% of LHON cases worldwide (Mackey et al. 1996. PubMed ID: 8755941; Yu-Wai-Man and Chinnery. 2021. PubMed ID: 20301353). The majority of LHON cases (~85%) have been shown to harbor a homoplasmic pathogenic variant that is stable across most tested tissues; however, heteroplasmic variants have been reported (Yu-Wai-Man et al. 2003. PubMed ID: 12518276; Phasukkijwatana et al. 2006. PubMed ID: 17072496).

Acceptable specimen types for this test are: whole blood, fresh/frozen tissue, or DNA extracted from whole blood or fresh/frozen tissue. 

This test utilizes long-range polymerase chain reaction followed by Sanger sequencing. To mitigate allele dropout, two separate PCR primer sets are used to amplify the entire mtDNA genome, resulting in two separate fragments for analysis. Only MT-ND1 m.3460G>A (p.Ala52Thr), MT-ND4 m.11778G>A (p.Arg340His), and MT-ND6 m.14484T>C (p.Met64Val) are included in this analysis. While the vast majority of these variants are identified as homoplasmic variants in affected individuals, heteroplasmic variation has been known to occur (Yu-Wai-Man et al. 2003. PubMed ID: 12518276; Phasukkijwatana et al. 2006. PubMed ID: 17072496). Due to technical limitations, variants <20% heteroplasmy may fall below the limit of detection for Sanger sequencing.

Human Genome Variation Society (HGVS) recommendations are used to name sequence variants (Human Genome Variation Society). mtDNA sequence variants are interpreted utilizing a combination of resources, including recommendations from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (Richards et al. 2015. PubMed ID: 25741868), which was primarily developed for interpretation of variants in nuclear genes; as well as recommendations from the MSeqDR consortium (McCormick et al. 2020. PubMed ID: 32906214) and Baylor College of Medicine (Wong et al. 2020. PubMed ID: 31965079), which were developed specifically for mtDNA variant interpretation.