Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities

Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an ‘exome-first’ approach

(2015) Satoko Miyatake et al.   JOURNAL OF HUMAN GENETICS

Clinical management of hereditary colorectal cancer syndromes

(2015) Hans F. A. Vasen et al.   Nature Reviews Gastroenterology & Hepatology

Abstract IA16: Evaluating the implementation and utility of clinical tumor exome sequencing in the pediatric oncology clinic: Early results of the BASIC3 study

(2015) D. Williams Parsons et al.   CANCER RESEARCH

Clinical whole exome sequencing in child neurology practice

(2014) Siddharth Srivastava et al.   ANNALS OF NEUROLOGY

Ethical issues raised by whole genome sequencing

(2014) Wim Pinxten et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

(2014) Claudia Calabrese et al.   BIOINFORMATICS

ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data

(2014) Javad Nadaf et al.   BIOINFORMATICS

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

(2014) A. Alkodsi et al.   BRIEFINGS IN BIOINFORMATICS

Clinical whole-exome sequencing: are we there yet?

(2014) Paldeep Singh Atwal et al.   GENETICS IN MEDICINE

Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory

(2014) Samuel P. Strom et al.   GENETICS IN MEDICINE

De novo mutations in beta-catenin (CTNNB1) appear to be a frequent cause of intellectual disability: expanding the mutational and clinical spectrum

(2014) Alma Kuechler et al.   HUMAN GENETICS

An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data

(2014) Renjie Tan et al.   HUMAN MUTATION

The Challenge for the Next Generation of Medical Geneticists

(2014) Thierry Frebourg   HUMAN MUTATION

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Applications of next-generation whole exome sequencing

(2014) Katharine E. Harding et al.   JOURNAL OF NEUROLOGY

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

Resistance to Therapy in Acute Promyelocytic Leukemia

(2014) Jacqueline Lehmann-Che et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders

(2014) S. E. Soden et al.   Science Translational Medicine

Clinical exome sequencing in daily practice: 1,000 patients and beyond

(2014) Wendy A van Zelst-Stams et al.   Genome Medicine

Exome sequencing greatly expedites the progressive research of Mendelian diseases

(2014) Xuejun Zhang   Frontiers of Medicine

Implementing Genomic Medicine in Pathology

(2013) Eli S. Williams et al.   ADVANCES IN ANATOMIC PATHOLOGY

Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder

(2013) Christopher S. Poultney et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Whole-exome sequencing emerges as clinical diagnostic tool

(2013) Deborah Levenson   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Genomic Sequencing for Cancer Diagnosis and Therapy

(2013) Linghua Wang et al.   Annual Review of Medicine

Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome

(2013) Darrell L. Dinwiddie et al.   GENOMICS

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing

(2013) Joep de Ligt et al.   HUMAN MUTATION

The promise of whole-exome sequencing in medical genetics

(2013) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

Next generation molecular diagnosis of mitochondrial disorders

(2013) Lee-Jun C. Wong   MITOCHONDRION

CNVs conferring risk of autism or schizophrenia affect cognition in controls

(2013) Hreinn Stefansson et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Rare-disease genetics in the era of next-generation sequencing: discovery to translation

(2013) Kym M. Boycott et al.   NATURE REVIEWS GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Diagnostic interpretation of array data using public databases and internet sources

(2012) Nicole de Leeuw et al.   HUMAN MUTATION

A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease

(2012) C S Ku et al.   MOLECULAR PSYCHIATRY

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Exome sequencing identifies a novel TRPV4 mutation in a CMT2C family

(2012) G. Landoure et al.   NEUROLOGY

Molecular Genetic Testing for Mitochondrial Disease: From One Generation to the Next

(2012) Elizabeth McCormick et al.   Neurotherapeutics

Limitations of the Human Reference Genome for Personalized Genomics

(2012) Jeffrey A. Rosenfeld et al.   PLoS One

Challenges in Medical Applications of Whole Exome/Genome Sequencing Discoveries

(2012) Ali J. Marian   TRENDS IN CARDIOVASCULAR MEDICINE

All your base: a fast and accurate probabilistic approach to base calling

(2012) Tim Massingham et al.   GENOME BIOLOGY

Revisiting Mendelian disorders through exome sequencing

(2011) Chee-Seng Ku et al.   HUMAN GENETICS

An informatics project and online “Knowledge Centre” supporting modern genotype-to-phenotype research

(2011) Adam J. Webb et al.   HUMAN MUTATION

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

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

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

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

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

(2010) A. McKenna et al.   GENOME RESEARCH

Public data archives for genomic structural variation

(2010) Deanna M Church et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

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

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

Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome

(2010) Amélie Bonnefond et al.   PLoS One

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

(2009) Helen V. Firth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

(2008) Iuliana Ionita-Laza et al.   GENOMICS

Inherited Susceptibility to Common Cancers

(2008) William D. Foulkes   NEW ENGLAND JOURNAL OF MEDICINE