Computational protocol: Mitochondrial DNA mutation m.10680G > A is associated with Leber hereditary optic neuropathy in Chinese patients

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Protocol publication

[…] The entire mitochondrial genomes of probands with m.10680G > A were amplified and sequenced by using primers and methods described in our previous study []. Sequences were handled by the DNASTAR program (DNAS Inc, Madison, WI, USA). We classified each patient into accurate haplogroup relative to the updated East Asian mtDNA tree and PhyloTree [-]. The novelty of variants/mutations was defined according to the available guidelines described by Bandelt et al. []. We presented mtDNA sequence variations in probands sequenced in this study, together with two reported LHON mtDNAs with m.10680G > A (family Le1107 reported by Zou et al. [] and LHON family reported by Yang et al. []) in a mtDNA tree. This phylogenetic approach has been demonstrated to be powerful to recognize private variants and haplogroup-specific variants in each lineage []. Evolutionary conservation analysis of m.10680G > A was performed by using the MitoTool (http://www.mitotool.org) [].To discern the frequency of m.10680G > A in reported mtDNAs across world, we collected 9277 complete (and/or incomplete) mtDNA sequences from PhyloTree (mtDNA Tree Build 12, 20 Jul 2011) [] and the MitoTool data set [] and excluded those data of Chinese LHON patients. The ten reported Chinese patients with suspected LHON in our recent study [] were aggregated with the patients screened in this study. Two tailed Fisher Exact test was used to evaluate the difference of m.10680G > A frequency between Chinese patients with suspected LHON and the reported data. A P value less than 0.05 was considered as significant. […]

Pipeline specifications

Software tools MitoTool
Databases nextstrain
Application Phylogenetics
Organisms Homo sapiens
Diseases Mitochondrial Diseases, Optic Atrophy, Hereditary, Leber