Computational protocol: Cystic Echinococcoses in Mongolia: Molecular Identification, Serology and Risk Factors

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Protocol publication

[…] Genomic DNA was extracted from 43 ethanol-fixed samples from hepatic CE patients () using a DNeasy tissue kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The extracted DNA was kept at −20°C until further analysis could be performed. DNA obtained was used as templates for polymerase chain reaction (PCR). The complete or partial mitochondrial cytochrome c oxidase subunit I (cox 1) gene was amplified by PCR as reported previously –. PCR products were treated with illustra ExoStar (GE Healthcare) to remove excess primers and dNTPs, and directly sequenced with a BigDye Terminator v3.1 and a 3500 DNA sequencer (Life Technologies). Obtained sequences were edited using Geneious Pro version 7.0.4 (created by Biomatters, available from http://www.geneious.com), and multiple alignments of each cox1 haplotype were made by the program MAFFT with the homologous sequences of other Echinococcus species available in the GenBank database. A phylogenetic tree was constructed using the neighbour-joining method and Kimura's two-parameter model in Phylogenetic Analysis Using Parsimony (PAUP) version 4.0b . The robustness of the phylogenetic tree was tested by bootstrapping with 1000 replicates. For tree construction, Versteria mustelae was used as an outgroup because it is a sister to all members of the genus Echinococcus . […]

Pipeline specifications

Software tools Geneious, MAFFT, PAUP*
Application Phylogenetics
Organisms Echinococcus granulosus, Echinococcus canadensis, Camelus dromedarius, Homo sapiens
Diseases Echinococcosis, Chemical and Drug Induced Liver Injury