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Pipeline publication

[…] b't success., Written informed consent was obtained from the patient in the Hospitaux Universitaires de Geneve \xe2\x80\x98Analyse de la reponse immunologique contre les tumeurs cerebrales\xe2\x80\x99 translational approved protocol IRB 03-126. Tumour material was analysed under the UCL-Cancer Institute and Pathology biobank (UCLHRTB 10/H1306/42). The patient provided written informed consent to tumour sequencing analysis within a compassionate setting. The study was conducted according to the provisions of the Declaration of Helsinki and the Good Clinical Practice Guidelines of the International Conference on Harmonization., WGS was carried out by Illumina, UK. Mutation calling and filtering was carried out using VarScan2 as described [], annotation of coding mutations were carried out using ANNOVAR []. Structural variant (SV) breakpoint mechanism classification was carried out according to the criteria defined in Yang et al. []. Reconstruction of the putative double-minute chromosomes was carried out as described in Sanborn et al. [] and breakpoints mapping to the focal amplifications were validated by PCR and Sanger Sequencing. Copy-number variation (CNV) analysis was carried out on the WGS data. Purity, ploidy and allele-specific copy-number estimates were obtained with Sequenza []. Clonal analysis was carried out as described in Bolli et al. [], estimating the cancer cell fraction (CCF) by integrating variant allele frequency estimates with copy number, purity and ploidy estimates. Single-sample and multi-sample Dirichlet process clustering was carried out using the DPpackage R package []. In this work, mutations are referred to as \xe2\x80\x98sub-clonal\xe2\x80\x99 if their CCF indicates they are present in only a subset of cancer cells within a given sample (CCF <1). Mutations present in all cancer cells of a given sample (CCF \xe2\x88\xbc 1) are referred to as \xe2\x80\x98clonal\xe2\x80\x99. Genome doubling (GD) was determined from the comparison of the sequencing of the grade II and the grade IV regions' […]

Pipeline specifications

Software tools VarScan, ANNOVAR, Sequenza
Organisms Homo sapiens
Diseases Central Nervous System Neoplasms, Nervous System Neoplasms, Brain Diseases, Neoplasms, Nerve Tissue, Neoplasms, Germ Cell and Embryonal, Neoplasms, Glandular and Epithelial, Neoplasms, Genomic Instability