Exome sequencing and whole genome sequencing for the detection of copy number variation

Next-Generation Sequencing of Duplication CNVs Reveals that Most Are Tandem and Some Create Fusion Genes at Breakpoints

(2015) Scott Newman et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

(2015) Min Wang et al.   BMC GENOMICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

The diagnostic pathway in complex paediatric neurology: A cost analysis

(2015) K.J.M. van Nimwegen et al.   EUROPEAN JOURNAL OF PAEDIATRIC NEUROLOGY

Mosaic structural variation in children with developmental disorders

(2015) Daniel A. King et al.   HUMAN MOLECULAR GENETICS

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

(2015) Caroline F Wright et al.   LANCET

Whole-genome sequencing of quartet families with autism spectrum disorder

(2015) Ryan K C Yuen et al.   NATURE MEDICINE

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination

(2015) Michał Startek et al.   NUCLEIC ACIDS RESEARCH

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

(2015) Søren Besenbacher et al.   Nature Communications

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss

(2015) Rajini R Haraksingh et al.   BMC GENOMICS

Evaluating the Consent Preferences of UK Research Volunteers for Genetic and Clinical Studies

(2015) Susan E. Kelly et al.   PLoS One

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data

(2014) Evangelos Bellos et al.   BIOINFORMATICS

Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination

(2014) Ian M Campbell et al.   BMC BIOLOGY

Increased Frequency of De Novo Copy Number Variants in Congenital Heart Disease by Integrative Analysis of Single Nucleotide Polymorphism Array and Exome Sequence Data

(2014) Joseph T. Glessner et al.   CIRCULATION RESEARCH

Copy number variation in schizophrenia in Sweden

(2014) J P Szatkiewicz et al.   MOLECULAR PSYCHIATRY

Large-scale discovery of novel genetic causes of developmental disorders

(2014) T. W. Fitzgerald et al.   NATURE

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Targeted next generation sequencing for molecular diagnosis of Usher syndrome

(2014) María J Aparisi et al.   Orphanet Journal of Rare Diseases

Evolutionarily Dynamic Alternative Splicing of GPR56 Regulates Regional Cerebral Cortical Patterning

(2014) B.-I. Bae et al.   SCIENCE

Copy number variants are a common cause of non-syndromic hearing loss

(2014) A Shearer et al.   Genome Medicine

Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease

(2014) Wigard P Kloosterman et al.   Molecular Cytogenetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Performance evaluation of Sanger sequencing for the diagnosis of primary hyperoxaluria and comparison with targeted next generation sequencing

(2014) Emma L. Williams et al.   Molecular Genetics & Genomic Medicine

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

(2013) Tobias Marschall et al.   BIOINFORMATICS

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Pathogenic or not? Assessing the clinical relevance of copy number variants

(2013) JY Hehir-Kwa et al.   CLINICAL GENETICS

CNVs of noncoding cis-regulatory elements in human disease

(2013) Malte Spielmann et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles

(2013) P. M. Boone et al.   GENOME RESEARCH

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

Clinical Significance of De Novo and Inherited Copy-Number Variation

(2013) Anneke T. Vulto-van Silfhout et al.   HUMAN MUTATION

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

(2013) Joep de Ligt et al.   HUMAN MUTATION

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Increasing the Yield in Targeted Next-Generation Sequencing by Implicating CNV Analysis, Non-Coding Exons and the Overall Variant Load: The Example of Retinal Dystrophies

(2013) Tobias Eisenberger et al.   PLoS One

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

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

(2012) Jacob J. Michaelson et al.   CELL

On the Structural Plasticity of the Human Genome: Chromosomal Inversions Revisited

(2012) Joao M. Alves et al.   CURRENT GENOMICS

Functional characterization of tissue-specific enhancers in the DLX5/6 locus

(2012) Ramon Y. Birnbaum et al.   HUMAN MOLECULAR GENETICS

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study

(2012) Anita Rauch et al.   LANCET

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

(2012)   NATURE

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

(2012) Joep de Ligt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human limb abnormalities caused by disruption of hedgehog signaling

(2012) Eve Anderson et al.   TRENDS IN GENETICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Detecting structural variations in the human genome using next generation sequencing

(2011) R. Xi et al.   Briefings in Functional Genomics

Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics

(2011) Nicolien M Hanemaaijer et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Retracted: Exploring the potential role of disease-causing mutation in a gene desert: Duplication of noncoding elements 5′ ofGRIA3is associated withGRIA3silencing and X-linked intellectual disability

(2011) Céline Bonnet et al.   HUMAN MUTATION

What can exome sequencing do for you?

(2011) J. Majewski et al.   JOURNAL OF MEDICAL GENETICS

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

ASOX9Duplication and Familial 46,XX Developmental Testicular Disorder

(2011) James J. Cox et al.   NEW ENGLAND JOURNAL OF MEDICINE

Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes

(2011) Santhosh Girirajan et al.   PLoS Genetics

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

(2010) David T. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Copy-Number Variations Involving the IHH Locus Are Associated with Syndactyly and Craniosynostosis

(2010) Eva Klopocki et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Massively parallel sequencing and rare disease

(2010) S. B. Ng et al.   HUMAN MOLECULAR GENETICS

Detection of clinically relevant exonic copy-number changes by array CGH

(2010) Philip M. Boone et al.   HUMAN MUTATION

Functional impact of global rare copy number variation in autism spectrum disorders

(2010) Dalila Pinto et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

(2010) Donald F Conrad et al.   NATURE GENETICS

A de novo paradigm for mental retardation

(2010) Lisenka E L M Vissers et al.   NATURE GENETICS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Inversion variants in the human genome: role in disease and genome architecture

(2010) Lars Feuk   Genome Medicine

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

Duplications Involving a Conserved Regulatory Element Downstream of BMP2 Are Associated with Brachydactyly Type A2

(2009) Katarina Dathe et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Duplication hotspots, rare genomic disorders, and common disease

(2009) Heather C Mefford et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Array analysis and karyotyping: Workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands

(2009) Ron Hochstenbach et al.   European Journal of Medical Genetics

Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects

(2009) Gurdeep S Sagoo et al.   GENETICS IN MEDICINE

Balanced translocations in mental retardation

(2009) Geert Vandeweyer et al.   HUMAN GENETICS

Genomic microarrays in mental retardation: from copy number variation to gene, from research to diagnosis

(2009) L. E. L. M. Vissers et al.   JOURNAL OF MEDICAL GENETICS

Enhancer deletions of the SHOX gene as a frequent cause of short stature: the essential role of a 250 kb downstream regulatory domain

(2009) J Chen et al.   JOURNAL OF MEDICAL GENETICS

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease

(2009) Steven A McCarroll et al.   NATURE GENETICS

Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis

(2009) Rafael de Cid et al.   NATURE GENETICS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

(2009) Barbara D'haene et al.   PLoS Genetics

Genomic microarrays in mental retardation: A practical workflow for diagnostic applications

(2008) David A. Koolen et al.   HUMAN MUTATION

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE