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, 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