Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

(2015) Hoon Kim et al.   GENOME RESEARCH

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

(2015) Caryn S Ross-Innes et al.   NATURE GENETICS

Microenvironmental regulation of therapeutic response in cancer

(2015) Florian Klemm et al.   TRENDS IN CELL BIOLOGY

Tracking the Genomic Evolution of Esophageal Adenocarcinoma through Neoadjuvant Chemotherapy

(2015) N. Murugaesu et al.   Cancer Discovery

A systematic review and meta-analysis of somatic and germline DNA sequence biomarkers of esophageal cancer survival, therapy response and stage

(2014) J. M. Findlay et al.   ANNALS OF ONCOLOGY

Functional Heterogeneity of Genetically Defined Subclones in Acute Myeloid Leukemia

(2014) Jeffery M. Klco et al.   CANCER CELL

Favorable Prognostic Impact in Loss of TP53 and PIK3CA Mutations after Neoadjuvant Chemotherapy in Breast Cancer

(2014) Y.-Z. Jiang et al.   CANCER RESEARCH

Tumor Stage After Neoadjuvant Chemotherapy Determines Survival After Surgery for Adenocarcinoma of the Esophagus and Esophagogastric Junction

(2014) Andrew R. Davies et al.   JOURNAL OF CLINICAL ONCOLOGY

Concordance of Genomic Alterations between Primary and Recurrent Breast Cancer

(2014) F. Meric-Bernstam et al.   MOLECULAR CANCER THERAPEUTICS

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

(2014) Andy Rimmer et al.   NATURE GENETICS

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis

(2014) Jamie M J Weaver et al.   NATURE GENETICS

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

(2014) Marco Gerlinger et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

(2014) J. Zhang et al.   SCIENCE

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

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

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

(2014) Katia Nones et al.   Nature Communications

Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

(2014) Vanessa Almendro et al.   Cell Reports

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

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

(2013) Gro Nilsen et al.   BMC GENOMICS

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Factors associated with early recurrence and death after esophagectomy for cancer

(2013) Andrew R. Davies et al.   JOURNAL OF SURGICAL ONCOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Influence of tumour micro-environment heterogeneity on therapeutic response

(2013) Melissa R. Junttila et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

(2013) Austin M Dulak et al.   NATURE GENETICS

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma

(2013) Jessica Okosun et al.   NATURE GENETICS

Frequent truncating mutations of STAG2 in bladder cancer

(2013) David A Solomon et al.   NATURE GENETICS

Mechanisms of resistance to therapies targeting BRCA-mutant cancers

(2013) Christopher J Lord et al.   NATURE MEDICINE

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

Clonal evolution and devolution after chemotherapy in adult acute myelogenous leukemia

(2012) B. Parkin et al.   BLOOD

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

(2012) A. Schuh et al.   BLOOD

Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis

(2012) A. M. Dulak et al.   CANCER RESEARCH

Molecular Pathways: Microsatellite Instability in Colorectal Cancer: Prognostic, Predictive, and Therapeutic Implications

(2012) F. A. Sinicrope et al.   CLINICAL CANCER RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

The role of minor subpopulations within the leukemic blast compartment of AML patients at initial diagnosis in the development of relapse

(2012) C Bachas et al.   LEUKEMIA

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

(2012) Li Ding et al.   NATURE

Clonal Architecture of Secondary Acute Myeloid Leukemia

(2012) Matthew J. Walter et al.   NEW ENGLAND JOURNAL OF MEDICINE

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

EGFR-Mediated Reactivation of MAPK Signaling Contributes to Insensitivity of BRAF -Mutant Colorectal Cancers to RAF Inhibition with Vemurafenib

(2012) Ryan B. Corcoran et al.   Cancer Discovery

Comparative Genomic Analysis of Esophageal Adenocarcinoma and Squamous Cell Carcinoma

(2012) Nishant Agrawal et al.   Cancer Discovery

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling

(2011) Nikhil Wagle et al.   JOURNAL OF CLINICAL ONCOLOGY

High-frequency type I/II mutational shifts between diagnosis and relapse are associated with outcome in pediatric AML: implications for personalized medicine

(2010) C. Bachas et al.   BLOOD

How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine

(2010) M Gerlinger et al.   BRITISH JOURNAL OF CANCER

Preexistence and Clonal Selection of MET Amplification in EGFR Mutant NSCLC

(2010) Alexa B. Turke et al.   CANCER CELL

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

IntOGen: integration and data mining of multidimensional oncogenomic data

(2010) Gunes Gundem et al.   NATURE METHODS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS