A Structural Variant Approach for Establishing a Detection Limit in Differential Hydrogen Exchange-Mass Spectrometry Measurements.
Sign Up to like & getrecommendations! Published in 2019 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.9b01326
Abstract: Hydrogen exchange-mass spectrometry (HX-MS) is widely promoted for its ability to detect subtle perturbations in protein structure, but such perturbations will result in small differences in HX. However, the detection limit of HX-MS has not… read more here.
Keywords: detection; structural variant; hydrogen exchange; detection limit ... See more keywords
A comprehensive benchmarking of WGS-based deletion structural variant callers
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac221
Abstract: Advances in whole-genome sequencing (WGS) promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from WGS data presents a substantial number of challenges and a plethora of SV detection methods have… read more here.
Keywords: deletion; variant; detection; wgs ... See more keywords
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac042
Abstract: Abstract Summary StructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the… read more here.
Keywords: caller agnostic; ecosystem; bioconductor; structural variant ... See more keywords
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.
Sign Up to like & getrecommendations! Published in 2019 at "Genome research"
DOI: 10.1101/gr.244939.118
Abstract: We sequenced the genome of the Yoruban reference individual NA19240 on the long read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, and a… read more here.
Keywords: nanopore promethion; long read; structural variants; structural variant ... See more keywords
Genome sequencing identifies KMT2E-disrupting cryptic structural variant in a female with O'Donnell-Luria-Rodan syndrome.
Sign Up to like & getrecommendations! Published in 2023 at "Clinical genetics"
DOI: 10.1111/cge.14355
Abstract: We describe a patient from the 100,000 Genomes Project with a complex de novo structural variant within KMT2E leading to O'Donnell-Luria-Rodan syndrome. This case expands the mutational spectrum for this syndrome and highlights the importance… read more here.
Keywords: genome sequencing; luria rodan; rodan syndrome; donnell luria ... See more keywords
Transcriptome and Genome Analysis Uncovers a DMD Structural Variant
Sign Up to like & getrecommendations! Published in 2023 at "Neurology: Genetics"
DOI: 10.1212/nxg.0000000000200064
Abstract: Objective Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the dystrophin gene (DMD). Hypermethylated CGG expansions within DIP2B 5′ UTR are associated with an intellectual development disorder. Here, we demonstrate the diagnostic utility… read more here.
Keywords: dip2b; expansion; analysis; dmd ... See more keywords
Different structural variant prediction tools yield considerably different results in Caenorhabditis elegans
Sign Up to like & getrecommendations! Published in 2022 at "PLOS ONE"
DOI: 10.1371/journal.pone.0278424
Abstract: The accurate characterization of structural variation is crucial for our understanding of how large chromosomal alterations affect phenotypic differences and contribute to genome evolution. Whole-genome sequencing is a popular approach for identifying structural variants, but… read more here.
Keywords: different structural; caenorhabditis elegans; variant; variant prediction ... See more keywords
Prioritisation of structural variant calls in cancer genomes
Sign Up to like & getrecommendations! Published in 2017 at "PeerJ"
DOI: 10.7717/peerj.3166
Abstract: Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe… read more here.
Keywords: prioritisation structural; calls cancer; variant calls; structural variant ... See more keywords