When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer

Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism

(2022) Martin Franke et al.   AMERICAN JOURNAL OF HUMAN GENETICS

LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions

(2022) Helle Lybæk et al.   Autism Research

Somatic structural variant formation is guided by and influences genome architecture

(2022) Nikos Sidiropoulos et al.   GENOME RESEARCH

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

(2022) Miguel Martinez-Ara et al.   MOLECULAR CELL

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

(2022) Alessa R. Ringel et al.   CELL

Subtype-specific 3D genome alteration in acute myeloid leukaemia

(2022) Jie Xu et al.   NATURE

Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes

(2022) Robert Schöpflin et al.   Nature Communications

Structural variants drive context-dependent oncogene activation in cancer

(2022) Zhichao Xu et al.   NATURE

Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells

(2022) Karin Purshouse et al.   eLife

Position effects at the FGF8 locus are associated with femoral hypoplasia

(2021) Magdalena Socha et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

(2021) Xiaotao Wang et al.   NATURE METHODS

ecDNA hubs drive cooperative intermolecular oncogene expression

(2021) King L. Hung et al.   NATURE

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases

(2020) Uirá Souto Melo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization

(2020) Daniel M Ibrahim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

(2020) Suzanne E. de Bruijn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome

(2019) Bjørt K Kragesteen et al.   JOURNAL OF MEDICAL GENETICS

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

(2019) Magdalena Laugsch et al.   Cell Stem Cell

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

TADs as the Caller Calls Them

(2019) Elzo de Wit   JOURNAL OF MOLECULAR BIOLOGY

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer

(2018) David Y. Takeda et al.   CELL

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

(2018) Yu Amanda Guo et al.   Nature Communications

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

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

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

Mechanisms underlying structural variant formation in genomic disorders

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

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

(2015) Darío G. Lupiáñez et al.   CELL

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Recurrent Hemizygous Deletions in Cancers May Optimize Proliferative Potential

(2012) N. L. Solimini et al.   SCIENCE