Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
Abstract Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer’s underlying biology, bringing hope to…
Andrew D. Cherniack
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…
Ancestry-specific predisposing germline variants in cancer
Abstract Background: Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses…
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…
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…
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…
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…
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
Abstract For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of…
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…
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Abstract DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide…