Genomics and drug profiling of fatal TCF3-HLF−positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options

The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias

(2015) Anna K Andersson et al.   NATURE GENETICS

Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia

(2015) Xiaotu Ma et al.   Nature Communications

Image-based RNA interference screening reveals an individual dependence of acute lymphoblastic leukemia on stromal cysteine support

(2015) Jeannette Boutter et al.   Oncotarget

A novel integrated cytogenetic and genomic classification refines risk stratification in pediatric acute lymphoblastic leukemia

(2014) A. V. Moorman et al.   BLOOD

ABT-199 mediated inhibition of BCL-2 as a novel therapeutic strategy in T-cell acute lymphoblastic leukemia

(2014) S. Peirs et al.   BLOOD

Ras pathway mutations are prevalent in relapsed childhood acute lymphoblastic leukemia and confer sensitivity to MEK inhibition

(2014) J. Irving et al.   BLOOD

GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files

(2014) Björn Stade et al.   BMC GENOMICS

Reprogramming Committed Murine Blood Cells to Induced Hematopoietic Stem Cells with Defined Factors

(2014) Jonah Riddell et al.   CELL

Prostaglandin E2 Regulates Liver versus Pancreas Cell-Fate Decisions and Endodermal Outgrowth

(2014) Sahar Nissim et al.   DEVELOPMENTAL CELL

The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function

(2014) Sören Boller et al.   IMMUNOLOGICAL REVIEWS

Leucine-rich Repeat-containing G-protein-coupled Receptor 5 Marks Short-term Hematopoietic Stem and Progenitor Cells during Mouse Embryonic Development

(2014) Donghua Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reprogramming human endothelial cells to haematopoietic cells requires vascular induction

(2014) Vladislav M. Sandler et al.   NATURE

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

(2014) Elli Papaemmanuil et al.   NATURE GENETICS

Loss of Ikaros DNA-binding function confers integrin-dependent survival on pre-B cells and progression to acute lymphoblastic leukemia

(2014) Ila Joshi et al.   NATURE IMMUNOLOGY

Maturation Stage of T-cell Acute Lymphoblastic Leukemia Determines BCL-2 versus BCL-XL Dependence and Sensitivity to ABT-199

(2014) T. N. Chonghaile et al.   Cancer Discovery

Acute lymphoblastic leukaemia

(2013) Hiroto Inaba et al.   LANCET

VPREB1 deletions occur independent of lambda light chain rearrangement in childhood acute lymphoblastic leukemia

(2013) D S Mangum et al.   LEUKEMIA

An intragenic ERG deletion is a marker of an oncogenic subtype of B-cell precursor acute lymphoblastic leukemia with a favorable outcome despite frequent IKZF1 deletions

(2013) E Clappier et al.   LEUKEMIA

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The genomic landscape of hypodiploid acute lymphoblastic leukemia

(2013) Linda Holmfeldt et al.   NATURE GENETICS

The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

(2013) Elisa Laurenti et al.   NATURE IMMUNOLOGY

ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets

(2013) Andrew J Souers et al.   NATURE MEDICINE

Reconstructing targetable pathways in lung cancer by integrating diverse omics data

(2013) O. Alejandro Balbin et al.   Nature Communications

Structural Basis for LMO2-Driven Recruitment of the SCL:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets

(2013) Kamel El Omari et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Biphenotypic B-lymphoid/myeloid cells expressing low levels of Pax5: potential targets of BAL development

(2012) S. Simmons et al.   BLOOD

Crosstalk between ROR1 and the Pre-B Cell Receptor Promotes Survival of t(1;19) Acute Lymphoblastic Leukemia

(2012) Vincent T. Bicocca et al.   CANCER CELL

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

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

IKZF1 deletion is an independent predictor of outcome in pediatric acute lymphoblastic leukemia treated according to the ALL-BFM 2000 protocol

(2012) P. Dorge et al.   HAEMATOLOGICA

B-lineage transcription factors and cooperating gene lesions required for leukemia development

(2012) E Tijchon et al.   LEUKEMIA

Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics

(2012) Roland Schmitz et al.   NATURE

From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software

(2012) Michael Forster et al.   NUCLEIC ACIDS RESEARCH

Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas

(2012) A. G. Schepers et al.   SCIENCE

The Origin and Nature of Tightly Clustered BTG1 Deletions in Precursor B-Cell Acute Lymphoblastic Leukemia Support a Model of Multiclonal Evolution

(2012) Esmé Waanders et al.   PLoS Genetics

Xenografts of highly resistant leukemia recapitulate the clonal composition of the leukemogenic compartment

(2011) M. Schmitz et al.   BLOOD

Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group

(2011) J. Zhang et al.   BLOOD

Two novel germline KRAS mutations: expanding the molecular and clinical phenotype

(2011) Z Stark et al.   CLINICAL GENETICS

Ebf1orPax5haploinsufficiency synergizes with STAT5 activation to initiate acute lymphoblastic leukemia

(2011) Lynn M. Heltemes-Harris et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Prognostic impact of t(1;19)/TCF3–PBX1in childhood acute lymphoblastic leukemia in the context of Berlin–Frankfurt–Münster-based protocols

(2011) MarÍa S. Felice et al.   LEUKEMIA & LYMPHOMA

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Aberrant induction of LMO2 by the E2A-HLF chimeric transcription factor and its implication in leukemogenesis of B-precursor ALL with t(17;19)

(2010) K. Hirose et al.   BLOOD

Molecular response to treatment redefines all prognostic factors in children and adolescents with B-cell precursor acute lymphoblastic leukemia: results in 3184 patients of the AIEOP-BFM ALL 2000 study

(2010) V. Conter et al.   BLOOD

Detection of prognostically relevant genetic abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: recommendations from the Biology and Diagnosis Committee of the International Berlin-Frankfürt-Münster study group

(2010) Christine J. Harrison et al.   BRITISH JOURNAL OF HAEMATOLOGY

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers 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

Induction of autophagy-dependent necroptosis is required for childhood acute lymphoblastic leukemia cells to overcome glucocorticoid resistance

(2010) Laura Bonapace et al.   JOURNAL OF CLINICAL INVESTIGATION

Specific induction of CD33 expression by E2A–HLF: the first evidence for aberrant myeloid antigen expression in ALL by a fusion transcription factor

(2010) K Akahane et al.   LEUKEMIA

The E2A-HLF oncogenic fusion protein acts through Lmo2 and Bcl-2 to immortalize hematopoietic progenitors

(2010) J de Boer et al.   LEUKEMIA

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

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

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group

(2009) L. Hertzberg et al.   BLOOD

Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia

(2009) L. J. Russell et al.   BLOOD

A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study

(2009) Monique L Den Boer et al.   LANCET ONCOLOGY

Rearrangement of CRLF2 in B-progenitor– and Down syndrome–associated acute lymphoblastic leukemia

(2009) Charles G Mullighan et al.   NATURE GENETICS

LitInspector: literature and signal transduction pathway mining in PubMed abstracts

(2009) Matthias Frisch et al.   NUCLEIC ACIDS RESEARCH

Mutation of Genes Affecting the RAS Pathway Is Common in Childhood Acute Lymphoblastic Leukemia

(2008) M. Case et al.   CANCER RESEARCH

Human Chromosomal Translocations at CpG Sites and a Theoretical Basis for Their Lineage and Stage Specificity

(2008) Albert G. Tsai et al.   CELL

Instructive Role of the Transcription Factor E2A in Early B Lymphopoiesis and Germinal Center B Cell Development

(2008) Kyongrim Kwon et al.   IMMUNITY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS