Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Tracking the Evolution of Non–Small-Cell Lung Cancer

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

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

(2017) Kajsa Ericson Lindquist et al.   Oncotarget

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group

(2016) Ariadne H.A.G. Ooms et al.   CLINICAL CANCER RESEARCH

Gain of 1q As a Prognostic Biomarker in Wilms Tumors (WTs) Treated With Preoperative Chemotherapy in the International Society of Paediatric Oncology (SIOP) WT 2001 Trial: A SIOP Renal Tumours Biology Consortium Study

(2016) Tasnim Chagtai et al.   JOURNAL OF CLINICAL ONCOLOGY

Association of Chromosome 1q Gain With Inferior Survival in Favorable-Histology Wilms Tumor: A Report From the Children’s Oncology Group

(2016) Eric J. Gratias et al.   JOURNAL OF CLINICAL ONCOLOGY

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

(2016) Faiyaz Notta et al.   NATURE

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

(2016) Ruli Gao et al.   NATURE GENETICS

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Rhabdomyosarcoma

(2016) Roshni Dasgupta et al.   Seminars in Pediatric Surgery

Rawcopy: Improved copy number analysis with Affymetrix arrays

(2016) Markus Mayrhofer et al.   Scientific Reports

Enrichment of Targetable Mutations in the Relapsed Neuroblastoma Genome

(2016) Olivia M. Padovan-Merhar et al.   PLoS Genetics

Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications

(2016) George D. Cresswell et al.   EBioMedicine

Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors

(2015) Amy L. Walz et al.   CANCER CELL

Mutations in the SIX1/2 Pathway and the DROSHA/DGCR8 miRNA Microprocessor Complex Underlie High-Risk Blastemal Type Wilms Tumors

(2015) Jenny Wegert et al.   CANCER CELL

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations

(2015) Thomas F Eleveld et al.   NATURE GENETICS

Mutational dynamics between primary and relapse neuroblastomas

(2015) Alexander Schramm et al.   NATURE GENETICS

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

(2015) Linda Holmquist Mengelbier et al.   Nature Communications

Mutational and gene fusion analyses of primary large cell and large cell neuroendocrine lung cancer

(2015) Anna Karlsson et al.   Oncotarget

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

(2014) Andriy Marusyk et al.   NATURE

A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations

(2014) Shinji Kohsaka et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector

(2014) Ami M. Kabadi et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

(2012) Jan J. Molenaar et al.   NATURE

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

The GPER1 Agonist G-1 Attenuates Endothelial Cell Proliferation by Inhibiting DNA Synthesis and Accumulating Cells in the S and G2 Phases of the Cell Cycle

(2011) Anders Holm et al.   JOURNAL OF VASCULAR RESEARCH

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

(2011) Markus Rasmussen et al.   GENOME BIOLOGY

Deletions of 16q in Wilms Tumors Localize to Blastemal-Anaplastic Cells and Are Associated with Reduced Expression of the IRXB Renal Tubulogenesis Gene Cluster

(2010) Linda Holmquist Mengelbier et al.   AMERICAN JOURNAL OF PATHOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Generation of trisomies in cancer cells by multipolar mitosis and incomplete cytokinesis

(2010) D. Gisselsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset

(2010) H. Caren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Classification of chromosome segregation errors in cancer

(2008) David Gisselsson   CHROMOSOMA

The International Neuroblastoma Risk Group (INRG) Classification System: An INRG Task Force Report

(2008) Susan L. Cohn et al.   JOURNAL OF CLINICAL ONCOLOGY

When the Genome Plays Dice: Circumvention of the Spindle Assembly Checkpoint and Near-Random Chromosome Segregation in Multipolar Cancer Cell Mitoses

(2008) David Gisselsson et al.   PLoS One

Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays

(2008) Johan Staaf et al.   GENOME BIOLOGY