Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

A survey of algorithms for the detection of genomic structural variants from long-read sequencing data

MU Ahsan, Q Liu, JE Perdomo, L Fang, K Wang - Nature Methods, 2023 - nature.com
As long-read sequencing technologies are becoming increasingly popular, a number of
methods have been developed for the discovery and analysis of structural variants (SVs) …

Sequencing and characterizing short tandem repeats in the human genome

HA Tanudisastro, IW Deveson, H Dashnow… - Nature Reviews …, 2024 - nature.com
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human
genome that are composed of repeated copies of a 1–6-bp motif. Over 1 million variable …

The GGC repeat expansion in NOTCH2NLC is associated with oculopharyngodistal myopathy type 3

J Yu, J Deng, X Guo, J Shan, X Luan, L Cao, J Zhao… - Brain, 2021 - academic.oup.com
Oculopharyngodistal myopathy (OPDM) is an adult-onset neuromuscular disease
characterized by progressive ocular, facial, pharyngeal and distal limb muscle involvement …

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

P Giesselmann, B Brändl, E Raimondeau… - Nature …, 2019 - nature.com
Expansions of short tandem repeats are genetic variants that have been implicated in
several neuropsychiatric and other disorders, but their assessment remains challenging with …

Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences

T Gall-Duncan, N Sato, RKC Yuen… - Genome …, 2022 - genome.cshlp.org
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a
disease-causing mutation in humans, are now known to cause> 60 phenotypes, not just …

Expansion of GGC repeat in GIPC1 is associated with oculopharyngodistal myopathy

J Deng, J Yu, P Li, X Luan, L Cao, J Zhao, M Yu… - The American Journal of …, 2020 - cell.com
Oculopharyngodistal myopathy (OPDM) is an adult-onset inherited neuromuscular disorder
characterized by progressive ptosis, external ophthalmoplegia, and weakness of the …

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

S Mitsuhashi, MC Frith, T Mizuguchi, S Miyatake… - Genome biology, 2019 - Springer
Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to
detect pathogenic repeat expansions genome-wide. Here, we report robust detection of …

Long-read sequencing identified repeat expansions in the 5′ UTR of the NOTCH2NLC gene from Chinese patients with neuronal intranuclear inclusion disease

J Deng, M Gu, Y Miao, S Yao, M Zhu, P Fang… - Journal of medical …, 2019 - jmg.bmj.com
Background Neuronal intranuclear inclusion disease (NIID) is a heterogenous
neurodegenerative disorder named after its pathological features. It has long been …

NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing

CY Tham, R Tirado-Magallanes, Y Goh, MJ Fullwood… - Genome biology, 2020 - Springer
The recent advent of third-generation sequencing technologies brings promise for better
characterization of genomic structural variants by virtue of having longer reads. However …