Results 11 to 20 of about 374,677 (247)
Inferring structural variant cancer cell fraction [PDF]
Nature Communications, 2020 Abstract We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number.
Marek Cmero +264 more
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Structure-Based Understanding of ABCA3 Variants [PDF]
International Journal of Molecular Sciences, 2021 ABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants is mandatory for genetic counseling and patient care.
Onnée, Marion +3 more
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Structural variant evolution after telomere crisis [PDF]
Nature Communications, 2020 AbstractTelomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of previous experimental telomere crisis studies. We examine the spectrum of SVs instigated by natural telomere crisis.
Sally M. Dewhurst +8 more
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VarSite: Disease variants and protein structure [PDF]
Protein Science, 2019 AbstractVarSite is a web server mapping known disease‐associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank. The analyses are primarily image‐based and provide both an overview for each human protein, as well as a report for any specific variant of interest.
Roman A. Laskowski +4 more
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Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma
Frontiers in Pharmacology, 2021 High-risk neuroblastoma (NB) remains a significant therapeutic challenge facing current pediatric oncology patients. Structural variants such as gene fusions have shown an initial promise in enhancing mechanistic understanding of NB and improving ...
Zhichao Liu +6 more
doaj +1 more source
Structural variant identification and characterization
Chromosome Research, 2020 Structural variant (SV) differences between human genomes can cause germline and mosaic disease as well as inter-individual variation. De-regulation of accurate DNA repair and genomic surveillance mechanisms results in a large number of SVs in cancer. Analysis of the DNA sequences at SV breakpoints can help identify pathways of mutagenesis and regions ...
Parithi Balachandran, Christine R. Beck
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Structural variants in 3000 rice genomes [PDF]
Genome Research, 2019 Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million ...
Roven Rommel Fuentes +11 more
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Genomic Alteration Burden in Advanced Prostate Cancer and Therapeutic Implications
Frontiers in Oncology, 2019 The increasing number of patients with sequenced prostate cancer genomes enables us to study not only individual oncogenic mutations, but also capture the global burden of genomic alterations.
Matthew J. Ryan +7 more
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Molecular Genetics & Genomic Medicine, 2021 Background Currently available structural variant (SV) detection methods do not span the complete spectrum of disease‐causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to ...
Heidi Cope +12 more
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TRPV1 splice variants: structure and function [PDF]
Frontiers in Bioscience, 2010 The capsaicin receptor (TRPV1) is a non-selective cation channel predominantly expressed in specialized sensory neurons that detect painful stimuli. Although its many functional roles continue to be revealed, it has been confirmed to play a critical role in the perception of peripheral inflammatory hyperalgesia and pain.
Mark A, Schumacher, Helge, Eilers
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