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

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

(2014) S. M. Dewhurst et al.   Cancer Discovery

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

Cancer statistics, 2013

(2013) Rebecca Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

(2013) C.-Z. Zhang et al.   GENES & DEVELOPMENT

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

(2013) A. Malhotra et al.   GENOME RESEARCH

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

Management of non-small-cell lung cancer: recent developments

(2013) Martin Reck et al.   LANCET

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Acquired Resistance and Clonal Evolution in Melanoma during BRAF Inhibitor Therapy

(2013) H. Shi et al.   Cancer Discovery

CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation

(2012) Maria Ortiz-Estevez et al.   BIOINFORMATICS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The landscape of cancer genes and mutational processes in breast cancer

(2012) Philip J. Stephens et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding 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

Chromosomal Instability Confers Intrinsic Multidrug Resistance

(2011) A. J. X. Lee et al.   CANCER RESEARCH

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

(2010) Henrik Bengtsson et al.   BMC BIOINFORMATICS

Mad2-induced chromosome instability leads to lung tumour relapse after oncogene withdrawal

(2010) Rocio Sotillo et al.   NATURE

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

Diverse somatic mutation patterns and pathway alterations in human cancers

(2010) Zhengyan Kan et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS 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

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6

(2009) Henrik Bengtsson et al.   BIOINFORMATICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Erin D. Pleasance et al.   NATURE

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE