Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Cancer Genome Evolutionary Trajectories in Metastasis

(2020) Nicolai J. Birkbak et al.   CANCER CELL

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

Pan-cancer analysis of whole genomes

(2020)   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

A community effort to create standards for evaluating tumor subclonal reconstruction

(2020) Adriana Salcedo et al.   NATURE BIOTECHNOLOGY

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

(2020) Yulia Rubanova et al.   Nature Communications

Inferring structural variant cancer cell fraction

(2020) Marek Cmero et al.   Nature Communications

Pervasive lesion segregation shapes cancer genome evolution

(2020) Sarah J. Aitken et al.   NATURE

Characterizing the ecological and evolutionary dynamics of cancer

(2020) Nastaran Zahir et al.   NATURE GENETICS

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

Genomic characterization of metastatic breast cancers

(2019) François Bertucci et al.   NATURE

Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma

(2019) Jake June-Koo Lee et al.   CELL

A clonal expression biomarker associates with lung cancer mortality

(2019) Dhruva Biswas et al.   NATURE MEDICINE

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

(2018) Shadrielle Melijah G. Espiritu et al.   CELL

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Quantification of subclonal selection in cancer from bulk sequencing data

(2018) Marc J. Williams et al.   NATURE GENETICS

The long tail of oncogenic drivers in prostate cancer

(2018) Joshua Armenia et al.   NATURE GENETICS

Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust

(2018) Yupeng Cun et al.   Nature Protocols

Genomic patterns of progression in smoldering multiple myeloma

(2018) Niccolò Bolli et al.   Nature Communications

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

(2018) Clarissa Gerhauser et al.   CANCER CELL

Neutral tumor evolution?

(2018) Maxime Tarabichi et al.   NATURE GENETICS

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data

(2017) Nilgun Donmez et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

(2017) Christopher Abbosh et al.   NATURE

Between-region genetic divergence reflects the mode and tempo of tumor evolution

(2017) Ruping Sun et al.   NATURE GENETICS

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors

(2017) Jiqiu Cheng et al.   Nature Communications

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer

(2017) Soulafa Mamlouk et al.   Nature Communications

Principles of Reconstructing the Subclonal Architecture of Cancers

(2017) Stefan C. Dentro et al.   Cold Spring Harbor Perspectives in Medicine

Detecting truly clonal alterations from multi-region profiling of tumours

(2017) Benjamin Werner et al.   Scientific Reports

Palbociclib (PD-0332991), a selective CDK4/6 inhibitor, restricts tumour growth in preclinical models of hepatocellular carcinoma

(2016) Julien Bollard et al.   GUT

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

(2016) Andrew McPherson et al.   NATURE GENETICS

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F

(2016) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

Allele-Specific Quantification of Structural Variations in Cancer Genomes

(2016) Yang Li et al.   Cell Systems

BRAF Fusion Analysis in Pilocytic Astrocytomas: KIAA1549-BRAF 15-9 Fusions Are More Frequent in the Midline Than Within the Cerebellum

(2015) Claire Faulkner et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

(2015) Martin Peifer et al.   NATURE

Comprehensive genomic profiles of small cell lung cancer

(2015) Julie George et al.   NATURE

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Toward understanding and exploiting tumor heterogeneity

(2015) Ash A Alizadeh et al.   NATURE MEDICINE

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

(2015) Noemi Andor et al.   NATURE MEDICINE

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

The influence of subclonal resistance mutations on targeted cancer therapy

(2015) Michael W. Schmitt et al.   Nature Reviews Clinical Oncology

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

(2015) Nicholas McGranahan et al.   Science Translational Medicine

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

(2014) Niccolo Bolli et al.   Nature Communications

Critical limitations of consensus clustering in class discovery

(2014) Yasin Șenbabaoğlu et al.   Scientific Reports

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma

(2013) Edmund A. Mroz et al.   CANCER

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Beyond UV radiation: A skin under challenge

(2013) E. Dupont et al.   INTERNATIONAL JOURNAL OF COSMETIC SCIENCE

Reconstructing cancer genomes from paired-end sequencing data

(2012) Layla Oesper et al.   BMC BIOINFORMATICS

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

Cellular origin and pathophysiology of chronic lymphocytic leukemia

(2012) Marc Seifert et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Optimal Detection of Changepoints With a Linear Computational Cost

(2012) R. Killick et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma

(2012) Edmund A. Mroz et al.   ORAL ONCOLOGY

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation

(2011) Adam B. Olshen et al.   BIOINFORMATICS

Nearly unbiased variable selection under minimax concave penalty

(2010) Cun-Hui Zhang   ANNALS OF STATISTICS

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methods for merging Gaussian mixture components

(2010) Christian Hennig   Advances in Data Analysis and Classification

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA