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This results in somatic mutational profiles for 3,096 patients with mutations in 19,171 genes (mapped to the Entrez Genes).
To assess the clinical relevance of these genetic alterations in HER2+ cancer, copy number and mutational profiles for the genes ERBB2, and commonly mutated components of the PI3K (PIK3R1, PIK3R1, and PTEN) and MAPK cascades (BRAF, KRAS, HRAS, NRAS) were extracted from primary tumor genome sequence data in the Cancer Genome Atlas (TCGA) using cBioPortal.
We processed 107 samples using the Sequenom system, which provided us with complete mutational profiles for 85 samples to which the data reported here relate.
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All three cell lines are included in the Cancer Cell Line Encyclopedia (CCLE) 15; the CCLE includes a mutational profile for known oncogenes and drug response information for each cell line.
The panel of markers used in the mutational profiling for this study was selected based on substantial evidence supporting their involvement in pancreaticobiliary cancers.
More specifically, the study aimed to examine the added value of mutational profiling for detecting aggressive disease when first line testing by cytopathology was either negative or insufficient for diagnosis (i.e. atypical or indeterminate) of malignancy.
We introduce a new framework for uncovering cancer genes, differential mutation analysis, which compares the mutational profiles of genes across cancer genomes with their natural germline variation across healthy individuals.
The overall aim of the laboratory is to provide oncologists with detailed mutational profiles of their patients' tumors so that treatment for patients may be individually optimized--a process often referred to as personalized medicine.
Recently, efforts to establish mutational profiles of lung cancer have been undertaken and showed promising results for mutation-specific treatment, for example of tumour cells showing ras mutations, with an Hsp90 inhibitor [ 43].
Thus, mutational profiles of tumors can help prioritize anticancer therapy.
In contrast, the mutational profiles of young and old SCCs were similar (Supplementary Fig. 2b).
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