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Hui Cai, Peter Nagy, Rando Allikmets; Mitochondrial DNA Heteroplasmy in Retinas of AMD Patients. Invest. Ophthalmol. Vis. Sci. 2013;54(15):6194.
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© ARVO (1962-2015); The Authors (2016-present)
Accumulation of somatic genetic variation (heteroplasmy) in mitochondrial genome has been implicated in age-related macular degeneration (AMD). We used deep sequencing of mitochondrial DNA samples from retinas (macular and peripheral regions) of donor eyes from AMD patients and age-matched controls to assess the extent of heteroplasmy acquired with age and disease.
In this pilot study we used genomic DNA isolated from retina tissue of donor eyes of ten AMD patients and ten age-matched controls. Samples were sequenced using mitochondrial DNA (mtDNA) deep sequencing technology with a minimum of 2000X coverage; i.e., the entire 16,569 bp of mitochondrial DNA in each sample was covered by at least 2000 sequence reads. Sequence data were annotated and genetic variation (heteroplasmy) was identified and analyzed by NextGene (SoftGenetics) software. Identified variants were compared to published mtDNA variants from the control region and coding & RNA regions [MITOMAP.org: A Human Mitochondrial Genome Database, 2012].
The minimum depth of the reliably observed heteroplasmy was set at 2%. In order to assess possible clinically meaningful variants, the more stringent heteroplasmy threshold was set at 40%. With these criteria seventy five variants were identified in 10 AMD samples compared to sixty five in 10 control samples. Among these, variants close to 99% heteroplasmy rates were seen at certain positions in single samples in 37 out of 75 variants. More variants were found in coding regions of mtDNA from AMD vs. control samples (43 vs. 35). In AMD samples, thirteen variants in mtDNA coding region were non-synonymous and were detected in NADH subunits 1, 2, 4 and 5, CYTB, COX1, and ATP6 genes. These genes are involved in the Krebs cycle and electron transport chain reaction of aerobic respiration in mitochondria. Four mutations had not been reported before and six mutations had been identified as associated with human diseases, e.g., AMD, LHON, Alzheimer and Parkinson Diseases.
Deep sequencing of mtDNA is an effective tool to identify heteroplasmy. While our sample size in this pilot study was small, we observed a real trend towards more heteroplasmy, both qualitatively and quantitatively, in AMD samples as compared to matched controls. Sequencing of a much larger cohort, which will allow substantial statistical power for definitive conclusions, is under way.
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