Structural variation in the 3D genome

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Paediatric genomics: diagnosing rare disease in children

(2018) Caroline F. Wright et al.   NATURE REVIEWS GENETICS

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Noncoding copy-number variations are associated with congenital limb malformation

(2017) Ricarda Flöttmann et al.   GENETICS IN MEDICINE

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Bladder Cancer: 4 Big questions

(2017) Chris Berdik   NATURE

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

(2017) Anja J Will et al.   NATURE GENETICS

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Frequency and Complexity of De Novo Structural Mutation in Autism

(2016) William M. Brandler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis

(2016) Zehra Ordulu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

(2016) Guillaume Andrey et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Parent-of-origin-specific signatures of de novo mutations

(2016) Jakob M Goldmann et al.   NATURE GENETICS

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Characteristics of de novo structural changes in the human genome

(2015) Wigard P. Kloosterman et al.   GENOME RESEARCH

A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

(2015) Elisa Giorgio et al.   HUMAN MOLECULAR GENETICS

Microdeletions on 6p22.3 are associated with mesomelic dysplasia Savarirayan type

(2015) Ricarda Flöttmann et al.   JOURNAL OF MEDICAL GENETICS

UK gears up to decode 100 000 genomes from NHS patients

(2015) Nayanah Siva   LANCET

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Microduplications encompassing the Sonic hedgehog limb enhancer ZRS are associated with Haas-type polysyndactyly and Laurin-Sandrow syndrome

(2014) S. Lohan et al.   CLINICAL GENETICS

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Next generation sequencing of chromosomal rearrangements in patients with split-hand/split-foot malformation provides evidence forDYNC1I1exonic enhancers ofDLX5/6expression in humans

(2014) Hana Lango Allen et al.   JOURNAL OF MEDICAL GENETICS

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

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

(2014) Laurent C Francioli et al.   NATURE GENETICS

Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families

(2014) Naeimeh Tayebi et al.   Orphanet Journal of Rare Diseases

Disruption of Autoregulatory Feedback by a Mutation in a Remote, Ultraconserved PAX6 Enhancer Causes Aniridia

(2013) Shipra Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Structural variations, the regulatory landscape of the genome and their alteration in human disease

(2013) Malte Spielmann et al.   BIOESSAYS

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Platelet defects in congenital variant of Rett syndrome patients with FOXG1 mutations or reduced expression due to a position effect at 14q12

(2013) Christophe Goubau et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

Homeotic Arm-to-Leg Transformation Associated with Genomic Rearrangements at the PITX1 Locus

(2012) Malte Spielmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Contribution of Global Rare Copy-Number Variants to the Risk of Sporadic Congenital Heart Disease

(2012) Rachel Soemedi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

De novo microdeletion of 5q14.3 excludingMEF2Cin a patient with infantile spasms, microcephaly, and agenesis of the corpus callosum

(2012) Keiko Shimojima et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

(2012) Michael E. Talkowski et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

(2012) Laura A. Lettice et al.   DEVELOPMENTAL CELL

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

Diagnostic interpretation of array data using public databases and internet sources

(2012) Nicole de Leeuw et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Mutations in KANSL1 cause the 17q21.31 microdeletion syndrome phenotype

(2012) Marcella Zollino et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Oncogene-mediated alterations in chromatin conformation

(2012) D. S. Rickman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of 2q23.1 Microdeletion Syndrome Implicates MBD5 as a Single Causal Locus of Intellectual Disability, Epilepsy, and Autism Spectrum Disorder

(2011) Michael E. Talkowski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Enhancer-adoption as a mechanism of human developmental disease

(2011) Laura A. Lettice et al.   HUMAN MUTATION

Disruption of a long distance regulatory region upstream of SOX9 in isolated disorders of sex development

(2011) S. Benko et al.   JOURNAL OF MEDICAL GENETICS

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

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

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

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

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia

(2009) Ingo Kurth et al.   NATURE GENETICS

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Structural Variation of Chromosomes in Autism Spectrum Disorder

(2008) Christian R. Marshall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Strong association of de novo copy number mutations with sporadic schizophrenia

(2008) Bin Xu et al.   NATURE GENETICS

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

(2008) T. Walsh et al.   SCIENCE