Toxicogenomics and Cancer Susceptibility: Advances with Next-Generation Sequencing

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data

(2013) Nameeta Shah et al.   BMC GENOMICS

Whole transcriptome RNA-Seq allelic expression in human brain

(2013) Ryan M Smith et al.   BMC GENOMICS

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2

(2013) Tú Nguyen-Dumont et al.   BMC Medical Genomics

Red and processed meat intake and risk of colorectal adenomas: a systematic review and meta-analysis of epidemiological studies

(2013) Dagfinn Aune et al.   CANCER CAUSES & CONTROL

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

miRNA expression profiling in a human stem cell-based model as a tool for developmental neurotoxicity testing

(2013) Giorgia Pallocca et al.   CELL BIOLOGY AND TOXICOLOGY

Influence of ambient air pollution on global DNA methylation in healthy adults: A seasonal follow-up

(2013) Sofie De Prins et al.   ENVIRONMENT INTERNATIONAL

Analysis of the transcriptome in molecular epidemiology studies

(2013) Cliona M. McHale et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny

(2013) S.T. Williams et al.   GENE

mRNA and miRNA expression patterns associated to pathways linked to metal mixture health effects

(2013) M. Martínez-Pacheco et al.   GENE

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

(2013) D. R. Winter et al.   GENOME RESEARCH

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform

(2013) Wiriya Rutvisuttinunt et al.   JOURNAL OF VIROLOGICAL METHODS

RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib

(2013) H Lilljebjörn et al.   LEUKEMIA

Targeted cancer exome sequencing reveals recurrent mutations in myeloproliferative neoplasms

(2013) E Tenedini et al.   LEUKEMIA

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

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors

(2013) Juliann Chmielecki et al.   NATURE GENETICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

First FDA Authorization for Next-Generation Sequencer

(2013) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Investigating the Antiproliferative Activity of High Affinity DNA Aptamer on Cancer Cells

(2013) Harleen Kaur et al.   PLoS One

Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer

(2013) L. Magnani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing

(2013) Anelia Horvath et al.   Scientific Reports

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

(2013) Lauren M. Bragg et al.   PLoS Computational Biology

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

Using gene-environment interaction analyses to clarify the role of well-done meat and heterocyclic amine exposure in the etiology of colorectal polyps

(2012) Zhenming Fu et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

(2012) Jason M Rizzo et al.   BMC MOLECULAR BIOLOGY

MicroRNA-152 targets DNA methyltransferase 1 in NiS-transformed cells via a feedback mechanism

(2012) Weidong Ji et al.   CARCINOGENESIS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

(2012) Jacob J. Michaelson et al.   CELL

Mutagenicity and DNA adduct formation by aristolochic acid in the spleen of Big Blue® rats

(2012) L. Patrice McDaniel et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

MicroRNA-22 is induced by vitamin D and contributes to its antiproliferative, antimigratory and gene regulatory effects in colon cancer cells

(2012) Silvia Alvarez-Díaz et al.   HUMAN MOLECULAR GENETICS

Deep Sequencing in Cancer Research

(2012) K. Yoshida et al.   JAPANESE JOURNAL OF CLINICAL ONCOLOGY

RETFusions Define a Unique Molecular and Clinicopathologic Subtype of Non–Small-Cell Lung Cancer

(2012) Rui Wang et al.   JOURNAL OF CLINICAL ONCOLOGY

Dietary, lifestyle and clinicopathological factors associated with APC mutations and promoter methylation in colorectal cancers from the EPIC-Norfolk study

(2012) Laura J Gay et al.   JOURNAL OF PATHOLOGY

A Genome-Wide Methylation Study of Severe Vitamin D Deficiency in African American Adolescents

(2012) Haidong Zhu et al.   JOURNAL OF PEDIATRICS

Medullary thyroid carcinoma (MTC) and RET proto-oncogene: Mutation spectrum in the familial cases and a meta-analysis of studies on the sporadic form

(2012) Gisella Figlioli et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia

(2012) Catherine C. Smith et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Oxford Nanopore announcement sets sequencing sector abuzz

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens

(2012) Ahmad Besaratinia et al.   NUCLEIC ACIDS RESEARCH

Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma

(2012) D. Singh et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

Inherited Effects of Low-Dose Exposure to Methylmercury in Neural Stem Cells

(2012) Raj Bose et al.   TOXICOLOGICAL SCIENCES

Trace metals alter DNA repair and histone modification pathways concurrently in mouse embryonic stem cells

(2012) Sanket R. Gadhia et al.   TOXICOLOGY LETTERS

Molecular Profiling of Colon Tumors: The Search for Clinically Relevant Biomarkers of Progression, Prognosis, Therapeutics, and Predisposition

(2011) Manny D. Bacolod et al.   ANNALS OF SURGICAL ONCOLOGY

Unraveling the Genetics of Cancer: Genome Sequencing and Beyond

(2011) Kit Man Wong et al.   Annual Review of Genomics and Human Genetics

KRAS mutations detected by the amplification refractory mutation system–Scorpion assays strongly correlate with therapeutic effect of cetuximab

(2011) H Bando et al.   BRITISH JOURNAL OF CANCER

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

(2011) Zhenqiang Su et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Increased Detection Sensitivity for KRAS Mutations Enhances the Prediction of Anti-EGFR Monoclonal Antibody Resistance in Metastatic Colorectal Cancer

(2011) F. Molinari et al.   CLINICAL CANCER RESEARCH

Inhalable Metal-Rich Air Particles and Histone H3K4 Dimethylation and H3K9 Acetylation in a Cross-sectional Study of Steel Workers

(2011) Laura Cantone et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Aristolochic acid-induced carcinogenesis examined by ACB-PCR quantification of H-Ras and K-Ras mutant fraction

(2011) Y. Wang et al.   MUTAGENESIS

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer

(2011) Dan R Robinson et al.   NATURE MEDICINE

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Bioinformatic and Genetic Association Analysis of MicroRNA Target Sites in One-Carbon Metabolism Genes

(2011) Nicole Stone et al.   PLoS One

Very Few RNA and DNA Sequence Differences in the Human Transcriptome

(2011) Daniel R. Schrider et al.   PLoS One

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Amplification of the Driving Oncogene, KRAS or BRAF, Underpins Acquired Resistance to MEK1/2 Inhibitors in Colorectal Cancer Cells

(2011) A. S. Little et al.   Science Signaling

Next generation sequencing in epigenetics: Insights and challenges

(2011) Emma Meaburn et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

(2010) John C Castle et al.   BMC GENOMICS

Gemcitabine Sensitivity Can Be Induced in Pancreatic Cancer Cells through Modulation of miR-200 and miR-21 Expression by Curcumin or Its Analogue CDF

(2010) Shadan Ali et al.   CANCER RESEARCH

Exposure to Metal-Rich Particulate Matter Modifies the Expression of Candidate MicroRNAs in Peripheral Blood Leukocytes

(2010) Valentina Bollati et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

(2010) D. Pflueger et al.   GENOME RESEARCH

Big science: The cancer genome challenge

(2010) Heidi Ledford   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells

(2010) T. Angrisano et al.   NUCLEIC ACIDS RESEARCH

Bisphenol A exposure leads to specific microRNA alterations in placental cells

(2010) Michele Avissar-Whiting et al.   REPRODUCTIVE TOXICOLOGY

MicroRNA-dependent regulation of PTEN after arsenic trioxide treatment in bladder cancer cell line T24

(2010) Yan Cao et al.   TUMOR BIOLOGY

In Utero Exposure to Diethylstilbestrol (DES) or Bisphenol-A (BPA) Increases EZH2 Expression in the Mammary Gland: An Epigenetic Mechanism Linking Endocrine Disruptors to Breast Cancer

(2010) Leo F. Doherty et al.   Hormones & Cancer

Systems biology of human benzene exposure

(2009) Luoping Zhang et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Inflammation and colorectal cancer

(2009) Sarah Kraus et al.   CURRENT OPINION IN PHARMACOLOGY

Recommendations from the EGAPP Working Group: can UGT1A1 genotyping reduce morbidity and mortality in patients with metastatic colorectal cancer treated with irinotecan?

(2009)   GENETICS IN MEDICINE

Can UGT1A1 genotyping reduce morbidity and mortality in patients with metastatic colorectal cancer treated with irinotecan? An evidence-based review

(2009) Glenn E Palomaki et al.   GENETICS IN MEDICINE

Mutational spectra of human cancer

(2009) Gerd P. Pfeifer et al.   HUMAN GENETICS

American Society of Clinical Oncology Provisional Clinical Opinion: Testing forKRASGene Mutations in Patients With Metastatic Colorectal Carcinoma to Predict Response to Anti–Epidermal Growth Factor Receptor Monoclonal Antibody Therapy

(2009) Carmen J. Allegra et al.   JOURNAL OF CLINICAL ONCOLOGY

Decreased levels of UMP kinase as a mechanism of fluoropyrimidine resistance

(2009) R. Humeniuk et al.   MOLECULAR CANCER THERAPEUTICS

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Causes and consequences of microRNA dysregulation in cancer

(2009) Carlo M. Croce   NATURE REVIEWS GENETICS

Familial adenomatous polyposis

(2009) Elizabeth Half et al.   Orphanet Journal of Rare Diseases

Multi-Determinants Analysis of Molecular Alterations for Predicting Clinical Benefit to EGFR-Targeted Monoclonal Antibodies in Colorectal Cancer

(2009) Andrea Sartore-Bianchi et al.   PLoS One

Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

(2009) D. Stoddart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

(2009) F. Schembri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet and epigenetics in colon cancer

(2009) Minna Nyström et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Epigenetic Cross-Talk between DNA Methylation and Histone Modifications in Human Cancers

(2009) Yutaka Kondo   YONSEI MEDICAL JOURNAL

Prognostic significance of thymidylate synthase, dihydropyrimidine dehydrogenase and thymidine phosphorylase protein expression in colorectal cancer patients treated with or without 5-fluorouracil-based chemotherapy

(2008) R. Soong et al.   ANNALS OF ONCOLOGY

Nickel compounds induce phosphorylation of histone H3 at serine 10 by activating JNK-MAPK pathway

(2008) Q. Ke et al.   CARCINOGENESIS

Epigenetic silencing of O6 -methylguanine DNA methyltransferase gene in NiS-transformed cells

(2008) Weidong Ji et al.   CARCINOGENESIS

Arsenite alters global histone H3 methylation

(2008) X. Zhou et al.   CARCINOGENESIS

Selenite reactivates silenced genes by modifying DNA methylation and histones in prostate cancer cells

(2008) Nong Xiang et al.   CARCINOGENESIS

Wild-TypeKRASIs Required for Panitumumab Efficacy in Patients With Metastatic Colorectal Cancer

(2008) Rafael G. Amado et al.   JOURNAL OF CLINICAL ONCOLOGY

A review of human carcinogens—Part A: pharmaceuticals

(2008) Yann Grosse et al.   LANCET ONCOLOGY

UGT1A1 and UGT1A9 functional variants, meat intake, and colon cancer, among Caucasians and African-Americans

(2008) Hugo Girard et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

(2008) J. Korlach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A methyl‐deficient diet modifies histone methylation and altersIgf2andH19repression in the prostate

(2008) Joseph R. Dobosy et al.   PROSTATE

Generation of phosphorylated histone H2AX by benzene metabolites

(2008) Mio Ishihama et al.   TOXICOLOGY IN VITRO

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS