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Complex structural variant visualization with SVTopo [PDF]

BMC Genomics
Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health.
Jonathan R. Belyeu, William J. Rowell, Juniper A. Lake, James Matthew Holt, Zev Kronenberg, Christopher T. Saunders, Michael A. Eberle   +6 more
doaj   +5 more sources

Computer-Aided Choosing of an Optimal Structural Variant of a Robot for Extracting Castings from Die Casting Machines

Actuators, 2023
In the present article, the solution for choosing the optimal structural variant of an industrial robot for extracting castings from die casting machines is considered.
Ivo Malakov, Velizar Zaharinov, Stiliyan Nikolov, Reneta Dimitrova   +3 more
doaj   +3 more sources

HapKled: a haplotype-aware structural variant calling approach for Oxford nanopore sequencing data

Frontiers in Genetics
Introduction: Structural Variants (SVs) are a type of variation that can significantly influence phenotypes and cause diseases. Thus, the accurate detection of SVs is a vital part of modern genetic analysis.
Zhendong Zhang, Yue Liu, Xin Li, Yadong Liu, Yadong Liu, Yadong Wang, Yadong Wang, Tao Jiang, Tao Jiang   +8 more
doaj   +3 more sources

Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders

Frontiers in Neurology, 2023
IntroductionNeuromuscular disorders (NMDs) have a heterogeneous etiology. A genetic diagnosis is key to personalized healthcare and access to targeted treatment for the affected individuals.MethodsIn this study, 861 patients with NMDs were analyzed with ...
Marlene Ek, Marlene Ek, Daniel Nilsson, Daniel Nilsson, Daniel Nilsson, Martin Engvall, Martin Engvall, Helena Malmgren, Helena Malmgren, Håkan Thonberg, Håkan Thonberg, Maria Pettersson, Maria Pettersson, Britt-Marie Anderlid, Britt-Marie Anderlid, Anna Hammarsjö, Anna Hammarsjö, Hafdis T. Helgadottir, Hafdis T. Helgadottir, Snjolaug Arnardottir, Karin Naess, Karin Naess, Inger Nennesmo, Martin Paucar, Martin Paucar, Helgi Thor Hjartarson, Rayomand Press, Göran Solders, Göran Solders, Thomas Sejersen, Thomas Sejersen, Anna Lindstrand, Anna Lindstrand, Malin Kvarnung, Malin Kvarnung   +34 more
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Whole genome sequencing for metastatic mutational burden in extraskeletal myxoid chondrosarcoma

Frontiers in Molecular Medicine, 2023
Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer that makes up less than 3% of all soft tissue sarcomas. It most often arises in the soft tissues of the proximal limbs and has a higher incidence in males. Though EMC has a good prognosis,
Trudy Zou, Rahil Sethi, Jiefei Wang, Gungor Budak, Uma Chandran, Ivy John, Rebecca Watters, Kurt Weiss   +7 more
doaj   +1 more source

A multi-platform reference for somatic structural variation detection

Cell Genomics, 2022
Summary: Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and ...
Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart de Bruijn, Daniel L. Cameron, Jana Ebler, Joachim Kutzera, Stef van Lieshout, Tobias Marschall, Marcel Nelen, Peter Priestley, Ivo Renkens, Margaretha G.M. Roemer, Markus J. van Roosmalen, Aaron M. Wenger, Bauke Ylstra, Remond J.A. Fijneman, Wigard P. Kloosterman, Edwin Cuppen   +17 more
doaj   +1 more source

Resolving complex structural variants via nanopore sequencing

Frontiers in Genetics, 2023
The recent development of high-throughput sequencing platforms provided impressive insights into the field of human genetics and contributed to considering structural variants (SVs) as the hallmark of genome instability, leading to the establishment of ...
Simone Romagnoli, Niccolò Bartalucci, Alessandro Maria Vannucchi   +2 more
doaj   +1 more source

Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution

Biology, 2023
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify.
Valentine Comaills, Maikel Castellano-Pozo   +1 more
doaj   +1 more source

Identification of region of difference and H37Rv-related deletion in Mycobacterium tuberculosis complex by structural variant detection and genome assembly

Frontiers in Microbiology, 2022
Mycobacterium tuberculosis complex (MTBC), the main cause of TB in humans and animals, is an extreme example of genetic homogeneity, whereas it is still nevertheless separated into various lineages by numerous typing methods, which differ in phenotype ...
Zhuochong Liu, Zhonghua Jiang, Wei Wu, Xinyi Xu, Yudong Ma, Xiaomei Guo, Senlin Zhang, Qun Sun   +7 more
doaj   +1 more source

Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies

Frontiers in Genetics, 2020
In the last few years, the role of non-coding regulatory elements and their involvement in human disease have received great attention. Among the non-coding regulatory sequences, enhancers are particularly important for the proper establishment of cell ...
Víctor Sánchez-Gaya, Maria Mariner-Faulí, Alvaro Rada-Iglesias, Alvaro Rada-Iglesias, Alvaro Rada-Iglesias   +4 more
doaj   +1 more source