Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Abstract The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome…
Francisco Sanchez-Vega
Comprehensive molecular characterization of mitochondrial genomes in human cancers
Abstract Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome…
Divergent mutational processes distinguish hypoxic and normoxic tumours
Abstract Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular…
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Abstract Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles…
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
Abstract We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting…
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
Abstract Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may…
Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype
Abstract Background: The term CpG island methylator phenotype (CIMP) has been used to describe widespread DNA hypermethylation at CpG-rich genomic…