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   Articles with "structural variant" as a keyword



A Structural Variant Approach for Establishing a Detection Limit in Differential Hydrogen Exchange-Mass Spectrometry Measurements.

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recommendations! 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

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recommendations! 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

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recommendations! 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.

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recommendations! 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
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Genome sequencing identifies KMT2E-disrupting cryptic structural variant in a female with O'Donnell-Luria-Rodan syndrome.

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recommendations! 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

Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species

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recommendations! Published in 2024 at "Molecular Ecology"

DOI: 10.1111/mec.17631

Abstract: The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged in the management of threatened species. The functional consequences of SVs are more complex… read more here.

Keywords: fitness; load; lifetime fitness; single nucleotide ... See more keywords

SVhet: towards accurate detection of germline heterozygous deletions using short reads.

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recommendations! Published in 2025 at "BMC bioinformatics"

DOI: 10.1186/s12859-025-06342-7

Abstract: Accurate structural variant detection from short-read sequencing data remains challenged by false positives, particularly for heterozygous deletions where reduced allelic support and coverage-based detection methods are ambiguous. Existing SV genotyping and filtering approaches suffer from… read more here.

Keywords: detection; short reads; svhet towards; using short ... See more keywords

Comparison of structural variant callers for massive whole-genome sequence data

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recommendations! Published in 2024 at "BMC Genomics"

DOI: 10.1186/s12864-024-10239-9

Abstract: Background Detecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational resources and processing time. Here, we compared the performances of 11 SV callers: Delly, Manta, GridSS, Wham, Sniffles, Lumpy,… read more here.

Keywords: massive whole; whole genome; sequence; structural variant ... See more keywords

PSVRP: a pig structural variant reference panel for complex trait genomics and precision breeding

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recommendations! Published in 2025 at "BMC Genomics"

DOI: 10.1186/s12864-025-12273-7

Abstract: Pigs are not only a key source of animal protein worldwide, but also serve as important models in biological research. With the rapid development of short- and long-read sequencing technologies, genetic studies in pigs have… read more here.

Keywords: panel; pig structural; reference panel; variant reference ... See more keywords
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Transcriptome and Genome Analysis Uncovers a DMD Structural Variant

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recommendations! 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

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recommendations! 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