Computational protocol: Prevalence and clinical significance of BRCA1/2 germline and somatic mutations in Taiwanese patients with ovarian cancer

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Protocol publication

[…] Raw sequence data were mapped to the human reference genome (hg19) using The Torrent Suite Server (v. 4.2). Variant calling was performed with the Torrent Suite Variant Caller plug-in (v. 4.2) and the Variant Effect Predictor (VEP) was used for annotation. Variants with a read count <25 and a variant frequency <5% were not analyzed further. Common single nucleotide polymorphisms (SNPs) were identified using the dbSNP (release 138), 1000 Genome (phase 1 data), and 5000 Exome data sets. Previously reported BRCA1/2 mutations were identified and classified with the BIC (Breast Cancer Information Core, http://research.nhgri.nih.gov/bic/), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/), LOVD (Leiden Open Variation Database, http://www.lovd.nl/3.0/home), ARUP (http://arup.utah.edu/database/BRCA/), and BRCA Share (http://www.umd.be/BRCA1/) data sets. A variant classified as “likely benign” or “likely pathogenic” by the ClinVar was considered as VUS. Variants were classified as pathogenic if 1) they were labeled as such in any of the data sets used for the study or 2) they were frameshift or stop mutations. Variants were considered as benign if they were unequivocally classified as such (i.e., without a concurrent classification either as VUS or pathogenic within the same database) in the consulted data sets. All of the previously unidentified variants that were not clearly benign or pathogenic were regarded as VUS. A pathogenic variant was considered as novel if it was absent in the abovementioned data sets as well as in the COSMIC database (version 70, http://cancer.sanger.ac.uk/cosmic). SIFT (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/index.shtml), and Grantham (http://asia.ensembl.org/info/genome/variation/predicted_data.html) were used to predict the functional impact of the detected variants (). Variants classified as “probably damaging” in PolyPhen2 were considered as pathogenic, whereas “possibly damaging” variants were classified as VUS. SNP data of 997 healthy subjects of the population-based project in Taiwan were downloaded for comparison (https://taiwanview.twbiobank.org.tw/index).In line with previous methodology [], LOH was determined by analyzing the frequency of the patient's SNPs within the mutated BRCA gene using the ADTEx tool. This method may also detect large genomic rearrangements. […]

Pipeline specifications

Software tools PolyPhen, ADTEx
Application WES analysis
Organisms Homo sapiens
Diseases Carcinoma, Neoplasms, Ovarian Neoplasms
Chemicals Formaldehyde, Poly Adenosine Diphosphate Ribose