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Open AccessGenomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer
Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitor...
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Article
High-throughput genetic clustering of type 2 diabetes loci reveals heterogeneous mechanistic pathways of metabolic disease
Type 2 diabetes is highly polygenic and influenced by multiple biological pathways. Rapid expansion in the number of type 2 diabetes loci can be leveraged to identify such pathways.
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Open AccessAuthor Correction: The repertoire of mutational signatures in human cancer
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Open AccessAuthor Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Article
Open AccessBiomarker correlates with response to NY-ESO-1 TCR T cells in patients with synovial sarcoma
Autologous T cells transduced to express a high affinity T-cell receptor specific to NY-ESO-1 (letetresgene autoleucel, lete-cel) show promise in the treatment of metastatic synovial sarcoma, with 50% overall ...
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Article
Genetic analysis of dietary intake identifies new loci and functional links with metabolic traits
Dietary intake is a major contributor to the global obesity epidemic and represents a complex behavioural phenotype that is partially affected by innate biological differences. Here, we present a multivariate ...
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Article
Open AccessGenetic determinants of daytime nap** and effects on cardiometabolic health
Daytime nap** is a common, heritable behavior, but its genetic basis and causal relationship with cardiometabolic health remain unclear. Here, we perform a genome-wide association study of self-reported dayt...
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Article
Open AccessAnalyses of non-coding somatic drivers in 2,658 cancer whole genomes
The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from ...
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Article
Open AccessThe repertoire of mutational signatures in human cancer
Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) C...
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Article
Open AccessA model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma
In metastatic urothelial carcinoma (mUC), predictive biomarkers that correlate with response to immune checkpoint inhibitors (ICIs) are lacking. Here, we interrogated genomic and clinical features associated w...
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Article
Open AccessScaling computational genomics to millions of individuals with GPUs
Current genomics methods are designed to handle tens to thousands of samples but will need to scale to millions to match the pace of data and hypothesis generation in biomedical science. Here, we show that hig...
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Article
Next-generation characterization of the Cancer Cell Line Encyclopedia
Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets...
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Article
Mutational processes shape the landscape of TP53 mutations in human cancer
Unlike most tumor suppressor genes, the most common genetic alterations in tumor protein p53 (TP53) are missense mutations1,2. Mutant p53 protein is often abundantly expressed in cancers and specific allelic vari...
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Article
Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
In the version of this article originally published, an asterisk was omitted from Fig. 1a. The asterisk has been added to the figure. Additionally, a “NOTCH2” label was erroneously included in Fig. 4a. The lab...
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Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
In the version of this article originally published, some text above the “Tri–nucleotide sequence motifs” label in Fig. 2a appeared incorrectly. The text was garbled and should have appeared as nucleotide codes.
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Article
Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B...
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Genomic Assessment of Muscle-Invasive Bladder Cancer: Insights from the Cancer Genome Atlas (TCGA) Project
Invasive bladder cancer is a major medical problem associated with metastatic disease and frequent mortality. Although previous studies had identified many genetic alterations in invasive bladder cancer, recen...
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Article
Open AccessMutational patterns in chemotherapy resistant muscle-invasive bladder cancer
Despite continued widespread use, the genomic effects of cisplatin-based chemotherapy and implications for subsequent treatment are incompletely characterized. Here, we analyze whole exome sequencing of matche...
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Open AccessScalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA,...
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Article
A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer
Paz Polak, Jaegil Kim, Lior Z. Braunstein and colleagues have identified patterns of genome-wide mutation in certain breast cancers that can be used to identify those with DNA-repair deficiencies that make the...
