Genomic tools in acute myeloid leukemia: From the bench to the bedside

Significance of expression of ITGA5 and its splice variants in acute myeloid leukemia: A report from the children's oncology group

(2013) Roland B. Walter et al.   AMERICAN JOURNAL OF HEMATOLOGY

Next generation sequencing in cancer research and clinical application

(2013) Derek Shyr et al.   BIOLOGICAL PROCEDURES ONLINE

CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype

(2013) R. Masetti et al.   BLOOD

Patterns of missplicing due to somatic U2AF1 mutations in myeloid neoplasms

(2013) B. Przychodzen et al.   BLOOD

Clinical impact of DNMT3A mutations in younger adult patients with acute myeloid leukemia: results of the AML Study Group (AMLSG)

(2013) V. I. Gaidzik et al.   BLOOD

Cancer heterogeneity: implications for targeted therapeutics

(2013) R Fisher et al.   BRITISH JOURNAL OF CANCER

Advances for studying clonal evolution in cancer

(2013) Li Ding et al.   CANCER LETTERS

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Genotyping of 25 Leukemia-Associated Genes in a Single Work Flow by Next-Generation Sequencing Technology with Low Amounts of Input Template DNA

(2013) J. Rinke et al.   CLINICAL CHEMISTRY

Spliceosome mutations exhibit specific associations with epigenetic modifiers and proto-oncogenes mutated in myelodysplastic syndrome

(2013) S. A. Mian et al.   HAEMATOLOGICA

Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture

(2013) N Conte et al.   LEUKEMIA

Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

(2013) M J Walter et al.   LEUKEMIA

DNMT3A mutation is a poor prognosis biomarker in AML: Results of a meta-analysis of 4500 AML patients

(2013) Velizar Shivarov et al.   LEUKEMIA RESEARCH

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Identification of Circulating MicroRNAs as Potential Biomarkers for Detecting Acute Myeloid Leukemia

(2013) Feng Zhi et al.   PLoS One

Lessons from next-generation sequencing analysis in hematological malignancies

(2013) E Braggio et al.   Blood Cancer Journal

Are Results of Targeted Gene Sequencing Ready to Be Used for Clinical Decision Making for Patients with Acute Myelogenous Leukemia?

(2013) Arati V. Rao et al.   Current Hematologic Malignancy Reports

Molecular genetics of AML

(2012) Daniel C. Link   BEST PRACTICE & RESEARCH CLINICAL HAEMATOLOGY

Mutations affecting mRNA splicing define distinct clinical phenotypes and correlate with patient outcome in myelodysplastic syndromes

(2012) F. Damm et al.   BLOOD

Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia

(2012) A. F. T. Ribeiro et al.   BLOOD

SF3B1 haploinsufficiency leads to formation of ring sideroblasts in myelodysplastic syndromes

(2012) V. Visconte et al.   BLOOD

Chromatin accessibility, p300, and histone acetylation define PML-RAR  and AML1-ETO binding sites in acute myeloid leukemia

(2012) S. Saeed et al.   BLOOD

Genome-wide methylation profiling in decitabine-treated patients with acute myeloid leukemia

(2012) P. Yan et al.   BLOOD

GATA2 zinc finger 1 mutations associated with biallelic CEBPA mutations define a unique genetic entity of acute myeloid leukemia

(2012) P. A. Greif et al.   BLOOD

Mutations in the spliceosome machinery, a novel and ubiquitous pathway in leukemogenesis

(2012) H. Makishima et al.   BLOOD

Sequential gain of mutations in severe congenital neutropenia progressing to acute myeloid leukemia

(2012) R. Beekman et al.   BLOOD

CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia

(2012) M. E. McNerney et al.   BLOOD

Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing

(2012) A. Dolnik et al.   BLOOD

ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2-Mediated Gene Repression

(2012) Omar Abdel-Wahab et al.   CANCER CELL

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique

(2012) Jaroslav Jelinek et al.   Epigenetics

Next-generation sequencing for minimal residual disease monitoring in acute myeloid leukemia patients with FLT3-ITD or NPM1 mutations

(2012) Felicitas Thol et al.   GENES CHROMOSOMES & CANCER

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies

(2012) K. Gronbaek et al.   HAEMATOLOGICA

Splicing factor mutations in myelodysplasia

(2012) Seishi Ogawa   INTERNATIONAL JOURNAL OF HEMATOLOGY

Age-Related Prognostic Impact of Different Types ofDNMT3AMutations in Adults With Primary Cytogenetically Normal Acute Myeloid Leukemia

(2012) Guido Marcucci et al.   JOURNAL OF CLINICAL ONCOLOGY

Validation of a Prognostic Model and the Impact of Mutations in Patients With Lower-Risk Myelodysplastic Syndromes

(2012) Rafael Bejar et al.   JOURNAL OF CLINICAL ONCOLOGY

Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data

(2012) David H. Spencer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Mutations in the DNMT3A exon 23 independently predict poor outcome in older patients with acute myeloid leukemia: a SWOG report

(2012) F Ostronoff et al.   LEUKEMIA

Prognostic significance of DNA methyltransferase 3A mutations in cytogenetically normal acute myeloid leukemia: a study by the Acute Leukemia French Association

(2012) A Renneville et al.   LEUKEMIA

ASXL1 exon 12 mutations are frequent in AML with intermediate risk karyotype and are independently associated with an adverse outcome

(2012) S Schnittger et al.   LEUKEMIA

Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia

(2012) Eric J Duncavage et al.   MODERN PATHOLOGY

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

(2012) Li Ding et al.   NATURE

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Clonal Architecture of Secondary Acute Myeloid Leukemia

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

Prognostic Relevance of Integrated Genetic Profiling in Acute Myeloid Leukemia

(2012) Jay P. Patel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

Genome Wide Analysis of Acute Myeloid Leukemia Reveal Leukemia Specific Methylome and Subtype Specific Hypomethylation of Repeats

(2012) Marwa H. Saied et al.   PLoS One

New Fusion Transcripts Identified in Normal Karyotype Acute Myeloid Leukemia

(2012) Hongxiu Wen et al.   PLoS One

Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

(2012) M. Jan et al.   Science Translational Medicine

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

PathScan: a tool for discerning mutational significance in groups of putative cancer genes

(2011) Michael C. Wendl et al.   BIOINFORMATICS

Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms

(2011) L. Malcovati et al.   BLOOD

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype

(2011) V. Grossmann et al.   BLOOD

ASXL1 mutations identify a high-risk subgroup of older patients with primary cytogenetically normal AML within the ELN Favorable genetic category

(2011) K. H. Metzeler et al.   BLOOD

Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness

(2011) D. Rossi et al.   BLOOD

TP53 alterations in acute myeloid leukemia with complex karyotype correlate with specific copy number alterations, monosomal karyotype, and dismal outcome

(2011) F. G. Rucker et al.   BLOOD

TET2 deletions are a recurrent but rare phenomenon in myeloid malignancies and are frequently accompanied by TET2 mutations on the remaining allele

(2011) Ulrike Bacher et al.   BRITISH JOURNAL OF HAEMATOLOGY

Genomics of Acute Myeloid Leukemia

(2011) Timothy A. Graubert et al.   CANCER JOURNAL

TET Family Proteins and Their Role in Stem Cell Differentiation and Transformation

(2011) Luisa Cimmino et al.   Cell Stem Cell

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Clinical Implications of Novel Mutations in Epigenetic Modifiers in AML

(2011) Omar Abdel-Wahab et al.   HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA

Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML

(2011) Daniel C. Link   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene

(2011) John S. Welch   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Strategy for Robust Detection of Insertions, Deletions, and Point Mutations in CEBPA, a GC-Rich Content Gene, Using 454 Next-Generation Deep-Sequencing Technology

(2011) Vera Grossmann et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Identification of recurring tumor-specific somatic mutations in acute myeloid leukemia by transcriptome sequencing

(2011) P A Greif et al.   LEUKEMIA

SF3B1 mutations in myelodysplastic syndromes: clinical associations and prognostic implications

(2011) F Damm et al.   LEUKEMIA

Landscape of TET2 mutations in acute myeloid leukemia

(2011) S Weissmann et al.   LEUKEMIA

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

(2011) Timothy A Graubert et al.   NATURE GENETICS

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

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

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

(2011) Weixin Wang et al.   Scientific Reports

Comparison of solution-based exome capture methods for next generation sequencing

(2011) Anna-Maija Sulonen et al.   GENOME BIOLOGY

Genomics of AML: Clinical Applications of Next-Generation Sequencing

(2011) J. S. Welch et al.   Hematology-American Society of Hematology Education Program

Genetics of Myelodysplastic Syndromes: New Insights

(2011) T. Graubert et al.   Hematology-American Society of Hematology Education Program

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Complete characterization of the microRNAome in a patient with acute myeloid leukemia

(2010) G. Ramsingh et al.   BLOOD

Next-generation sequencing of the TET2 gene in 355 MDS and CMML patients reveals low-abundance mutant clones with early origins, but indicates no definite prognostic value

(2010) A. E. Smith et al.   BLOOD

Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations

(2010) D. T. Starczynowski et al.   BLOOD

The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to 2-Hydroxyglutarate

(2010) Patrick S. Ward et al.   CANCER CELL

Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

(2010) Maria E. Figueroa et al.   CANCER CELL

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing screen reveals novel, transforming RAS mutations in myeloid leukemia patients

(2008) J. W. Tyner et al.   BLOOD

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS