scholarly journals dbVar structural variant cluster set for data analysis and variant comparison

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 673 ◽  
Author(s):  
Lon Phan ◽  
Jeffrey Hsu ◽  
Le Quang Minh Tri ◽  
Michaela Willi ◽  
Tamer Mansour ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Chromosomal Rearrangements ◽  
Copy Number Variations ◽  
Structural Variant ◽  
Variant Type ◽  
External Data ◽  
Cluster Set ◽  
Genomic Location ◽  
Complex Chromosomal Rearrangements ◽  
Genomic Regions

dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR  that are presumably identical, but were ascertained by different platforms and samples,  to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary – including fuzzy locations where the start and/or end points are not precisely known – analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.

scholarly journals dbVar structural variant cluster set for data analysis and variant comparison

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 673 ◽  
Author(s):  
Lon Phan ◽  
Jeffrey Hsu ◽  
Le Quang Minh Tri ◽  
Michaela Willi ◽  
Tamer Mansour ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Chromosomal Rearrangements ◽  
Copy Number Variations ◽  
Structural Variant ◽  
Variant Type ◽  
External Data ◽  
Cluster Set ◽  
Genomic Location ◽  
Complex Chromosomal Rearrangements ◽  
Genomic Regions

dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR  that are presumably identical, but were ascertained by different platforms and samples,  to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary – including fuzzy locations where the start and/or end points are not precisely known – analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.

scholarly journals Nuclear Envelope Integrity in Health and Disease: Consequences on Genome Instability and Inflammation

2021 ◽  
Vol 22 (14) ◽  
pp. 7281
Author(s):  
Benoit R. Gauthier ◽  
Valentine Comaills
Keyword(s):  
Nuclear Envelope ◽  
Clinical Symptoms ◽  
Genome Instability ◽  
Chromosomal Rearrangements ◽  
Wide Range ◽  
Complex Chromosomal Rearrangements ◽  
Health And Disease ◽  
Dna Release ◽  
Sting Pathway ◽  
Eukaryote Genome

The dynamic nature of the nuclear envelope (NE) is often underestimated. The NE protects, regulates, and organizes the eukaryote genome and adapts to epigenetic changes and to its environment. The NE morphology is characterized by a wide range of diversity and abnormality such as invagination and blebbing, and it is a diagnostic factor for pathologies such as cancer. Recently, the micronuclei, a small nucleus that contains a full chromosome or a fragment thereof, has gained much attention. The NE of micronuclei is prone to collapse, leading to DNA release into the cytoplasm with consequences ranging from the activation of the cGAS/STING pathway, an innate immune response, to the creation of chromosomal instability. The discovery of those mechanisms has revolutionized the understanding of some inflammation-related diseases and the origin of complex chromosomal rearrangements, as observed during the initiation of tumorigenesis. Herein, we will highlight the complexity of the NE biology and discuss the clinical symptoms observed in NE-related diseases. The interplay between innate immunity, genomic instability, and nuclear envelope leakage could be a major focus in future years to explain a wide range of diseases and could lead to new classes of therapeutics.

scholarly journals Metabolic Effects of Recurrent Genetic Aberrations in Multiple Myeloma

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 396
Author(s):  
Timon A. Bloedjes ◽  
Guus de Wilde ◽  
Jeroen E. J. Guikema
Keyword(s):  
Multiple Myeloma ◽  
Cell Metabolism ◽  
Chromosomal Rearrangements ◽  
Chromosomal Translocations ◽  
Metabolic Effects ◽  
Aberrant Expression ◽  
Metabolic Functions ◽  
Complex Chromosomal Rearrangements ◽  
Cancer Cell Metabolism ◽  
The Many

Oncogene activation and malignant transformation exerts energetic, biosynthetic and redox demands on cancer cells due to increased proliferation, cell growth and tumor microenvironment adaptation. As such, altered metabolism is a hallmark of cancer, which is characterized by the reprogramming of multiple metabolic pathways. Multiple myeloma (MM) is a genetically heterogeneous disease that arises from terminally differentiated B cells. MM is characterized by reciprocal chromosomal translocations that often involve the immunoglobulin loci and a restricted set of partner loci, and complex chromosomal rearrangements that are associated with disease progression. Recurrent chromosomal aberrations in MM result in the aberrant expression of MYC, cyclin D1, FGFR3/MMSET and MAF/MAFB. In recent years, the intricate mechanisms that drive cancer cell metabolism and the many metabolic functions of the aforementioned MM-associated oncogenes have been investigated. Here, we discuss the metabolic consequences of recurrent chromosomal translocations in MM and provide a framework for the identification of metabolic changes that characterize MM cells.

Complex chromosomal rearrangements in an unusual variant of hairy cell leukemia

1992 ◽  
Vol 62 (2) ◽  
pp. 186-190 ◽  
Author(s):  
Elisabeth Nacheva ◽  
Patricia Fischer ◽  
Sheila O'Connor ◽  
David Bloxham ◽  
Catherine Hoggarth ◽  
...  
Keyword(s):  
Hairy Cell Leukemia ◽  
Chromosomal Rearrangements ◽  
Hairy Cell ◽  
Cell Leukemia ◽  
Complex Chromosomal Rearrangements ◽  
Unusual Variant

scholarly journals Generation of a whole chromosome painting probe from monochromosomal hybrid cells by the alu-polymerase chain reaction

2007 ◽  
Vol 59 (2) ◽  
pp. 89-95 ◽  
Author(s):  
Danijela Drakulic ◽  
Gordana Nikcevic ◽  
Vesna Djordjevic ◽  
Milena Stevanovic
Keyword(s):  
Chromosome Painting ◽  
Fluorescent In Situ Hybridization ◽  
Chromosomal Rearrangements ◽  
Painting Probe ◽  
Complex Chromosomal Rearrangements ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Complex Chromosome ◽  
Whole Chromosome Painting

Fluorescent in situ hybridization (FISH) has become a widespread technique applicable in basic science and diagnostics. Chromosome painting represents a special application of FISH that has found increasing use in identification of complex chromosome rearrangements. Here we present a version of the Alu-PCR method modified to generate a whole chromosome painting probe (WCP) for human chromosome 19 using monochromosomal cell hybrids. In setting up conditions for this method, we established a cheap and fast approach to generation of WCPs for other human chromosomes that could be particularly useful for unambiguous identification of complex chromosomal rearrangements associated with cancer. .

scholarly journals RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome

2018 ◽  
Author(s):  
Weizhong Chen ◽  
Zhangming Yan ◽  
Simin Li ◽  
Norman Huang ◽  
Xuerui Huang ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Genomic Sequence ◽  
Single Cells ◽  
Regulation Of Gene Expression ◽  
Nuclear Genome ◽  
Fold Increase ◽  
Nuclear Speckles ◽  
Nuclear Speckle ◽  
Interaction Sites ◽  
Genomic Regions

AbstractNuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA,nuclearspeckleassociated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.

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