Computational protocol: Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer

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Protocol publication

[…] Array CGH was carried out by Oxford Gene Technology (Oxford, UK) on the Agilent SurePrint G3 Human Catalog 4x180k array CGH platform. Data analysis was carried out in-house using the Bioconductor packages snapCGH, DNAcopy and CGHcall. The arrays were median normalised and segmented using the circular binary segmentation algorithm (). Cellularity was assessed by histopathology and by probability analysis using CGHcall implemented in R. Amplification was defined as regions with a log ratio >1.5 and homozygous deletion as log ratio <−1.5. Array CGH data have been uploaded to the GEO database with accession number GSE21025. […]

Pipeline specifications

Software tools snapCGH, CGHcall, DNA copy
Application aCGH data analysis
Organisms Homo sapiens
Diseases Leukemia, Neoplasms, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, Leukemia, Myeloid, Acute