Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

Revertant Somatic Mosaicism by Mitotic Recombination in Dyskeratosis Congenita

(2012) Marjolijn C.J. Jongmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome Sequencing Identifies Autosomal-Dominant SRP72 Mutations Associated with Familial Aplasia and Myelodysplasia

(2012) Michael Kirwan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

De Novo Pathogenic SCN8A Mutation Identified by Whole-Genome Sequencing of a Family Quartet Affected by Infantile Epileptic Encephalopathy and SUDEP

(2012) Krishna R. Veeramah et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cantú Syndrome Is Caused by Mutations in ABCC9

(2012) Bregje W.M. van Bon et al.   AMERICAN JOURNAL OF HUMAN GENETICS

VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

(2012) Jamie K. Teer et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

Evaluating Pathogenicity of Rare Variants From Dilated Cardiomyopathy in the Exome Era

(2012) Nadine Norton et al.   Circulation-Cardiovascular Genetics

In search of triallelism in Bardet–Biedl syndrome

(2012) Leen Abu-Safieh et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Somatic mosaicism in two unrelated patients with X-linked chronic granulomatous disease characterized by the presence of a small population of normal cells

(2012) Masafumi Yamada et al.   GENE

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

The Human Variome Project Beijing meeting

(2012) Timothy D Smith et al.   JOURNAL OF MEDICAL GENETICS

Clinical application of exome sequencing in undiagnosed genetic conditions

(2012) Anna C Need et al.   JOURNAL OF MEDICAL GENETICS

Bring clinical standards to human-genetics research

(2012) Gholson J. Lyon   NATURE

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities

(2012) Lynn M. Boyden et al.   NATURE

Developing predictive molecular maps of human disease through community-based modeling

(2012) Jonathan M J Derry et al.   NATURE GENETICS

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

Detectable clonal mosaicism from birth to old age and its relationship to cancer

(2012) Cathy C Laurie et al.   NATURE GENETICS

From patients to partners: participant-centric initiatives in biomedical research

(2012) Jane Kaye et al.   NATURE REVIEWS GENETICS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Escaping the EHR Trap — The Future of Health IT

(2012) Kenneth D. Mandl et al.   NEW ENGLAND JOURNAL OF MEDICINE

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

(2012) Miao-Xin Li et al.   NUCLEIC ACIDS RESEARCH

Nanopores: A journey towards DNA sequencing

(2012) Meni Wanunu   Physics of Life Reviews

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy

(2012) F. Cartault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Solving the Puzzle: Case Examples of Array Comparative Genomic Hybridization as a Tool to End the Diagnostic Odyssey

(2012) Amelia R. Mroch et al.   Current Problems in Pediatric and Adolescent Health Care

Improving bioinformatic pipelines for exome variant calling

(2012) Hanlee P Ji   Genome Medicine

Modifier Genes and the Plasticity of Genetic Networks in Mice

(2012) Bruce A. Hamilton et al.   PLoS Genetics

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

Finding Disease Variants in Mendelian Disorders By Using Sequence Data: Methods and Applications

(2011) Iuliana Ionita-Laza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency

(2011) Alan F. Rope et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide Studies of Copy Number Variation and Exome Sequencing Identify Rare Variants in BAG3 as a Cause of Dilated Cardiomyopathy

(2011) Nadine Norton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome sequencing: Dual role as a discovery and diagnostic tool

(2011) Chee-Seng Ku et al.   ANNALS OF NEUROLOGY

Copy-Number Variations, Noncoding Sequences, and Human Phenotypes

(2011) Eva Klopocki et al.   Annual Review of Genomics and Human Genetics

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

(2011) Yan W. Asmann et al.   BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Clan Genomics and the Complex Architecture of Human Disease

(2011) James R. Lupski et al.   CELL

The advent of personal genome sequencing

(2011) Radoje Drmanac   GENETICS IN MEDICINE

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

EX-HOM (EXome HOMozygosity): A Proof of Principle

(2011) Tommaso Pippucci et al.   HUMAN HEREDITY

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

(2011) Stephanie Hicks et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Exome and genome analysis as a tool for disease identification and treatment: The 2011 human genome variation society scientific meeting

(2011) William S. Oetting   HUMAN MUTATION

Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience

(2011) Jyotishman Pathak et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Exome sequencing: a transformative technology

(2011) Andrew B Singleton   LANCET NEUROLOGY

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Accelerated clinical discovery using self-reported patient data collected online and a patient-matching algorithm

(2011) Paul Wicks et al.   NATURE BIOTECHNOLOGY

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

A Mosaic Activating Mutation inAKT1Associated with the Proteus Syndrome

(2011) Marjorie J. Lindhurst et al.   NEW ENGLAND JOURNAL OF MEDICINE

SpliceDisease database: linking RNA splicing and disease

(2011) J. Wang et al.   NUCLEIC ACIDS RESEARCH

Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells

(2011) N. G. Coufal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Next-generation human genetics

(2011) Jay Shendure   GENOME BIOLOGY

Exome sequencing: the expert view

(2011) Leslie G Biesecker et al.   GENOME BIOLOGY

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

Genome variation discovery with high-throughput sequencing data

(2010) A. V. Dalca et al.   BRIEFINGS IN BIOINFORMATICS

Whole-exome sequencing: a powerful technique for identifying novel genes of complex disorders

(2010) SS Sanders   CLINICAL GENETICS

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

(2010) Mark J Pallen et al.   CURRENT OPINION IN MICROBIOLOGY

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

(2010) Sarah E. Flanagan et al.   Genetic Testing and Molecular Biomarkers

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

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3)

(2010) Victor Enciso-Mora et al.   NATURE GENETICS

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

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

(2010) Amélie Bonnefond et al.   PLoS One

Molecular prenatal diagnosis: the impact of modern technologies

(2010) F. Lucy Raymond et al.   PRENATAL DIAGNOSIS

Mitotic Recombination in Patients with Ichthyosis Causes Reversion of Dominant Mutations in KRT10

(2010) K. A. Choate et al.   SCIENCE

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

The power of social networking in medicine

(2009) Catherine A Brownstein et al.   NATURE BIOTECHNOLOGY

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Multiple loci on 8q24 associated with prostate cancer susceptibility

(2009) Ali Amin Al Olama et al.   NATURE GENETICS

Next-generation gap

(2009) John D McPherson   NATURE METHODS

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

(2009) Prateek Kumar et al.   Nature Protocols

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Genomic Landscape of a Three-Generation Pedigree Segregating Affective Disorder

(2009) Shuzhang Yang et al.   PLoS One

Exome Sequencing of a Multigenerational Human Pedigree

(2009) Dale Hedges et al.   PLoS One

Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae

(2009) E. E. Kenny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease

(2008) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Somatic mosaicism for copy number variation in differentiated human tissues

(2008) Arkadiusz Piotrowski et al.   HUMAN MUTATION

A wiki for the life sciences where authorship matters

(2008) Robert Hoffmann   NATURE GENETICS

Sequence variant on 8q24 confers susceptibility to urinary bladder cancer

(2008) Lambertus A Kiemeney et al.   NATURE GENETICS

A Gene Wiki for Community Annotation of Gene Function

(2008) Jon W Huss et al.   PLOS BIOLOGY

Genetic Variation in an Individual Human Exome

(2008) Pauline C. Ng et al.   PLoS Genetics