Linkage analysis in Leber’s hereditary optic neuropathy (LHON): failure to locate significant loci in a very large family indicates a polygenic/environmental complex contribution to penetrance

Abstract

Purpose: Leber’s hereditary optic neuropathy (LHON) is due to homoplasmic mtDNA missense mutations affecting complex I, but penetrance is largely incomplete. The existence of nuclear modifying genetic variants is hypothesized.

Methods: We carried out linkage analysis in a very large LHON pedigree (SOA-BR family, 354 subjects) carrying the 11778/ND4 mutation on a haplogroup J background. In total we genotyped 43 subjects with HumanCytoSNP-12 arrays (~300.000 molecular markers). The weight of age, gender, smoke, alcohol and other toxins as covariates was determined in affected subjects and unaffected mutation carriers. In order to perform the linkage analysis, we splitted the big pedigree in 3 smallest ones using PEDCUT. The 3 selected pedigrees are the ones with the maximum numbers of genotyped and phenotyped individuals (the most informative). After the splitting, we performed both parametric and non-parametric linkage analysis on autosomes and X chromosome with MERLIN.

Results: Despite the informativeness of the families, genome wide analysis produced very low LOD scores with both parametric and non-parametric linkage. As possible explanations for this failure we considered the existence of covariates not included in the analysis and/or the involvement of more genes as modifying factors. The covariates of gender and smoke were clearly associated with the affected status in the SOA-BR family, as largely expected from the literature data and previous studies conducted in this family.

Conclusions: Failure to locate any significant loci under the assumption of a monogenic modifier strongly suggests that incomplete penetrance in LHON is a polygenic trait. Interestingly, the previously reported identification of significant loci in the X-chromosome in this family is not confirmed by the current analysis. Furthermore, important covariates like gender and smoke has to be taken into account for future analysis. Some of these covariates may be correlated.

Keywords: 536 gene modifiers • 613 neuro-ophthalmology: optic nerve • 600 mitochondria