Pan-cancer analysis of whole genomes

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Genomics: data sharing needs an international code of conduct

(2020) Mark Phillips et al.   NATURE

Butler enables rapid cloud-based analysis of thousands of human genomes

(2020) Sergei Yakneen et al.   NATURE BIOTECHNOLOGY

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

(2020) Bernardo Rodriguez-Martin et al.   NATURE GENETICS

Comprehensive molecular characterization of mitochondrial genomes in human cancers

(2020) Yuan Yuan et al.   NATURE GENETICS

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

(2020) Isidro Cortés-Ciriano et al.   NATURE GENETICS

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

The landscape of viral associations in human cancers

(2020) Marc Zapatka et al.   NATURE GENETICS

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

(2020) Wei Jiao et al.   Nature Communications

Inferring structural variant cancer cell fraction

(2020) Marek Cmero et al.   Nature Communications

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

(2020) Yiqun Zhang et al.   Nature Communications

Genomic footprints of activated telomere maintenance mechanisms in cancer

(2020) Lina Sieverling et al.   Nature Communications

The International Cancer Genome Consortium Data Portal

(2019) Junjun Zhang et al.   NATURE BIOTECHNOLOGY

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

DeTiN: overcoming tumor-in-normal contamination

(2018) Amaro Taylor-Weiner et al.   NATURE METHODS

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

(2018) David Tamborero et al.   Genome Medicine

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

Whole-genome landscape of pancreatic neuroendocrine tumours

(2017) Aldo Scarpa et al.   NATURE

Whole-genome landscapes of major melanoma subtypes

(2017) Nicholas K. Hayward et al.   NATURE

Systematic analysis of telomere length and somatic alterations in 31 cancer types

(2017) Floris P Barthel et al.   NATURE GENETICS

Precision oncology for acute myeloid leukemia using a knowledge bank approach

(2017) Moritz Gerstung et al.   NATURE GENETICS

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors

(2016) Candace D Middlebrooks et al.   NATURE GENETICS

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

The tandem duplicator phenotype as a distinct genomic configuration in cancer

(2016) Francesca Menghi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

A cell-based model system links chromothripsis with hyperploidy

(2015) B. R. Mardin et al.   Molecular Systems Biology

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

(2015) Martin Peifer et al.   NATURE

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

Chromothripsis from DNA damage in micronuclei

(2015) Cheng-Zhong Zhang et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

Variation in cancer risk among tissues can be explained by the number of stem cell divisions

(2015) C. Tomasetti et al.   SCIENCE

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

(2014) Caleb F. Davis et al.   CANCER CELL

The Architecture and Evolution of Cancer Neochromosomes

(2014) Dale W. Garsed et al.   CANCER CELL

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

(2014) Nishant Agrawal et al.   CELL

C. eleganswhole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency

(2014) Bettina Meier et al.   GENOME RESEARCH

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

(2014) E. Helman et al.   GENOME RESEARCH

Realizing the promise of cancer predisposition genes

(2014) Nazneen Rahman   NATURE

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

(2014) Valentí Moncunill et al.   NATURE BIOTECHNOLOGY

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

(2014) Serena Nik-Zainal et al.   NATURE GENETICS

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Trans-ancestry mutational landscape of hepatocellular carcinoma genomes

(2014) Yasushi Totoki et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

bam.iobio: a web-based, real-time, sequence alignment file inspector

(2014) Chase A Miller et al.   NATURE METHODS

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

(2014) J. M. C. Tubio et al.   SCIENCE

Processed pseudogenes acquired somatically during cancer development

(2014) Susanna L. Cooke et al.   Nature Communications

Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

(2013) Joachim Weischenfeldt et al.   CANCER CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

(2012) Y. Drier et al.   GENOME RESEARCH

Global estimates of cancer prevalence for 27 sites in the adult population in 2008

(2012) Freddie Bray et al.   INTERNATIONAL JOURNAL OF CANCER

Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions

(2012) Steven A. Roberts et al.   MOLECULAR CELL

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Prevalence of the Alternative Lengthening of Telomeres Telomere Maintenance Mechanism in Human Cancer Subtypes

(2011) Christopher M. Heaphy et al.   AMERICAN JOURNAL OF PATHOLOGY

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Temporal Dissection of Tumorigenesis in Primary Cancers

(2011) Steffen Durinck et al.   Cancer Discovery

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS