Computational protocol: CHEK2 contribution to hereditary breast cancer in non-BRCA families

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Protocol publication

[…] For each missense variant, prediction of the impact of the mutation on the protein was assessed by calculating the SIFT (Sorting Intolerant From Tolerant), Align-GVGD and PolyPhen-2 (Polymorphism Phenotyping v2) software tool scores [-]. Align-GVGD predictions and SIFT score were computed using the ortholog alignment of exons 2 to 14 of CHEK2 derived by using Alamut software (Interactive Biosoftware, Rouen, France) []. Included were human (Homo sapiens) [GenBank:NP_009125.1], chimpanzee (Pan troglodytes) [GenBank:XP_001172759.1], macaque (Macaca) [GenBank:XP_001101658.1], rat (Rattus norvegicus) [GenBank:NP_446129.1], mouse (Mus musculus) [GenBank:NP_057890.1], dog (Canis lupus familiaris) [GenBank:XP_543464.2], cow (Bos taurus) [GenBank:NP_001029703.1], chicken (Gallus gallus) [GenBank:XP_001232074.1], frog (Xenopus tropicalis) [GenBank:NP_001119996.1] and pufferfish (Tetraodon nigroviridis) [UniProtKB/TrEMBL:Q4TI84], all extracted from the Ensembl Compara database []. PolyPhen-2 score was calculated online using default settings and accession numbers [UniProtKB/Swiss-Prot:O96017] [,]. The potential impact on splicing was studied using SpliceSiteFinder, MaxEntScan and GeneSplicer prediction software [-]. […]

Pipeline specifications

Software tools SIFT, Align-GVGD, PolyPhen, MaxEntScan, GeneSplicer
Databases UniProt
Application WGS analysis
Organisms Homo sapiens
Diseases Breast Neoplasms