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Integrative Genomics Viewer
The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.
The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
The results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents and the generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens.
The Genotype-Tissue Expression (GTEx) project
The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
The Somatic Genomic Landscape of Glioblastoma
MicroRNA expression profiles classify human cancers
A new, bead-based flow cytometric miRNA expression profiling method is used to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers, and finds the miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours.
Mutational heterogeneity in cancer and the search for new cancer-associated genes
Michael S. Lawrence*, Petar Stojanov*, Paz Polak*, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Chip Stewart, Craig H. Mermel, Steven A. Roberts, Adam Kiezun, Peter S.…
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
MuTect is presented, a method that applies a Bayesian classifier to detect somatic mutations with very low allele fractions, requiring only a few supporting reads, followed by carefully tuned filters that ensure high specificity.
Inferring tumour purity and stromal and immune cell admixture from expression data
A method that uses gene expression signatures to infer the fraction of stromal and immune cells in tumour samples and prediction accuracy is corroborated using 3,809 transcriptional profiles available elsewhere in the public domain.
Analysis of protein-coding genetic variation in 60,706 humans
The aggregation and analysis of high-quality exome (protein-coding region) sequence data for 60,706 individuals of diverse ethnicities generated as part of the Exome Aggregation Consortium (ExAC) provides direct evidence for the presence of widespread mutational recurrence.