The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”

Somatic mutation, copy number and transcriptomic profiles of primary and matched metastatic estrogen receptor-positive breast cancers

(2016) D. Fumagalli et al.   ANNALS OF ONCOLOGY

PlasmaESR1Mutations and the Treatment of Estrogen Receptor–Positive Advanced Breast Cancer

(2016) Charlotte Fribbens et al.   JOURNAL OF CLINICAL ONCOLOGY

Divergent clonal selection dominates medulloblastoma at recurrence

(2016) A. Sorana Morrissy et al.   NATURE

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

(2016) Faiyaz Notta et al.   NATURE

A community-based model of rapid autopsy in end-stage cancer patients

(2016) Kathryn Alsop et al.   NATURE BIOTECHNOLOGY

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

(2016) Ruli Gao et al.   NATURE GENETICS

Trace elements: Innovative biopsy programs map how cancer spreads

(2016) Jeanne Erdmann   NATURE MEDICINE

Extending Aromatase-Inhibitor Adjuvant Therapy to 10 Years

(2016) Paul E. Goss et al.   NEW ENGLAND JOURNAL OF MEDICINE

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures

(2016) Mohammed El-Kebir et al.   Cell Systems

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

(2015) S. Legare et al.   CANCER RESEARCH

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

(2015) Matthew T Chang et al.   NATURE BIOTECHNOLOGY

In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer

(2015) Michalina Janiszewska et al.   NATURE GENETICS

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Pertuzumab, Trastuzumab, and Docetaxel in HER2-Positive Metastatic Breast Cancer

(2015) Sandra M. Swain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

(2015) Matthew K.H. Hong et al.   Nature Communications

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer

(2015) Muhammed Murtaza et al.   Nature Communications

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing

(2015) Noushin Niknafs et al.   PLoS Computational Biology

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers

(2014) Félix Sanchez-Garcia et al.   CELL

Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity

(2014) Andriy Marusyk et al.   NATURE

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor

(2014) Dejan Juric et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

APOBEC-Mediated Cytosine Deamination Links PIK3CA Helical Domain Mutations to Human Papillomavirus-Driven Tumor Development

(2014) Stephen Henderson et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer

(2013) Weiyi Toy et al.   NATURE GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Long-term effects of continuing adjuvant tamoxifen to 10 years versus stopping at 5 years after diagnosis of oestrogen receptor-positive breast cancer: ATLAS, a randomised trial

(2012) Christina Davies et al.   LANCET

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

(2011) Adam B. Olshen et al.   BIOINFORMATICS

Chromosomal Instability Confers Intrinsic Multidrug Resistance

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

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

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

(2010) Henrik Bengtsson et al.   BMC BIOINFORMATICS

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

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

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

(2008) Johan Staaf et al.   BMC BIOINFORMATICS