Computational protocol: Mitochondrial DNA Sequence Variation and Haplogroup Distribution in Chinese Patients with LHON and m.14484T>C

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Protocol publication

[…] We evaluated the penetrance rate of LHON in the pedigrees based on our previous criterion . Namely, we excluded the following family members from the analysis: (a) the first generation, (b) spouses of the matrilineal members, and (c) children of the male member in each family. Sequence variations in each proband mtDNA sequence were scored relative to the revised Cambridge Reference Sequence (rCRS) . We followed the recently updated version of East Asian mtDNA tree and the PhyloTree.org database (http://www.phylotree.org) [mtDNA tree Build 10; 10 Aug 2009] to classify each sample . Potential sequence abnormalities that were identified by using the phylogenetic approach , , as performed manually and/or automatically by the MitoTool (http://www.mitotool.org; this software was designed by ourselves), were rechecked for the original sequencing electropherograms or resequencing. We defined the uniqueness of mtDNA variant(s) in certain matriline by an exhaustive database search following the available guidelines . A schematic tree was reconstructed to show the relationship among these mtDNAs. Evolutionary conservation analysis for certain mtDNA variant was performed using the same approach as described in our previous study , . Statistical analysis was performed using the SPSS statistical package (version 11.5), and statistical significance was established at P<0.05. […]

Pipeline specifications

Software tools MitoTool, SPSS
Databases PhyloTree.org
Applications Miscellaneous, Phylogenetics
Organisms Homo sapiens
Diseases Optic Atrophy, Hereditary, Leber, Genetic Diseases, Inborn