Structural variation in the 3D genome

M Spielmann, DG Lupiáñez, S Mundlos - Nature Reviews Genetics, 2018 - nature.com
Structural and quantitative chromosomal rearrangements, collectively referred to as
structural variation (SV), contribute to a large extent to the genetic diversity of the human …

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Z Chen, V Snetkova, G Bower, S Jacinto, B Clock… - Nature …, 2024 - nature.com
Remote enhancers are thought to interact with their target promoters via physical proximity,
yet the importance of this proximity for enhancer function remains unclear. Here we …

Hi-C identifies complex genomic rearrangements and TAD-shuffling in developmental diseases

US Melo, R Schöpflin, R Acuna-Hidalgo… - The American Journal of …, 2020 - cell.com
Genome-wide analysis methods, such as array comparative genomic hybridization (CGH)
and whole-genome sequencing (WGS), have greatly advanced the identification of structural …

Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short-and long-read genome sequencing

A Sanchis-Juan, J Stephens, CE French, N Gleadall… - Genome medicine, 2018 - Springer
Background Studies have shown that complex structural variants (cxSVs) contribute to
human genomic variation and can cause Mendelian disease. We aimed to identify cxSVs …

Chromatin features constrain structural variation across evolutionary timescales

G Fudenberg, KS Pollard - Proceedings of the National Academy of …, 2019 - pnas.org
The potential impact of structural variants includes not only the duplication or deletion of
coding sequences, but also the perturbation of noncoding DNA regulatory elements and …

Combining callers improves the detection of copy number variants from whole-genome sequencing

M Coutelier, M Holtgrewe, M Jäger… - European Journal of …, 2022 - nature.com
Abstract Copy Number Variants (CNVs) are deletions, duplications or insertions larger than
50 base pairs. They account for a large percentage of the normal genome variation and play …

The performance of genome sequencing as a first-tier test for neurodevelopmental disorders

BPGH van der Sanden, G Schobers… - European Journal of …, 2023 - nature.com
Genome sequencing (GS) can identify novel diagnoses for patients who remain
undiagnosed after routine diagnostic procedures. We tested whether GS is a better first-tier …

Expanded insights into mechanisms of gene expression and disease related disruptions

M Smith, PL Flodman - Frontiers in molecular biosciences, 2018 - frontiersin.org
Definitive molecular diagnoses in disorders apparently due to genetic or genomic defects
are still lacking in a significant number of investigated cases, despite use of studies …

Computational and experimental methods for classifying variants of unknown clinical significance

M Spielmann, M Kircher - Molecular Case Studies, 2022 - molecularcasestudies.cshlp.org
The increase in sequencing capacity, reduction in costs, and national and international
coordinated efforts have led to the widespread introduction of next-generation sequencing …

CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients

F Requena, HH Abdallah, A García… - Nucleic Acids …, 2021 - academic.oup.com
Abstract Copy Number Variants (CNVs) are an important cause of rare diseases. Array-
based Comparative Genomic Hybridization tests yield a∼ 12% diagnostic rate, with∼ 8% of …