Focal copy number
WebSep 1, 2024 · Oncogene amplification, a major driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA) - enabling gene amplification, rapid tumor evolution, and the rewiring of … WebNov 12, 2013 · By examining regions of focal copy-number change that lack protein-coding targets, we identified an intergenic lncRNA on chromosome 1, OVAL, that shows narrow focal genomic amplification in a subset of tumors. While weakly expressed in most tumors, focal amplification coincided with strong OVAL transcriptional activation.
Focal copy number
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WebNov 1, 2014 · Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack. Focal aberrations are present in most cancer types. Due to their small …
WebApr 16, 2024 · We have developed CNAtra framework to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from a single whole-genome sequencing (WGS) sample. CNAtra first utilizes a multimodal-based distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. WebJul 2, 2024 · Guichard, C. et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet. 44 , 694–698 (2012).
WebSep 1, 2024 · Focal copy number amplifications (fCNAs), which drive cancer pathogenicity, arise by a number of mechanisms and can be challenging to call. Here the authors present AmpliconReconstructor for ... WebJan 4, 2013 · Here we provide additional evidence for the importance of focal DNA copy number gains and losses, which are predominantly observed in MYCN amplified tumors. …
WebApr 16, 2024 · Next, we identified focal alterations in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. Using …
WebJul 10, 2024 · (A): Example of copy number plot from a CDK12‐LOF prostate tumor harboring multiple CDK12 truncating mutations. The red arrow indicates short chromosomal segments at copy number 3 (CN + 1), indicative of focal tandem duplications. x‐axis indicates copy number, y‐axis indicates genomic position ordered by chromosome … can an ear infection cause bad taste in mouthWebAug 7, 2024 · A large number of focal copy number alterations (FCNAs) were detected, including homozygous deletions (HDs) targeting WWOX and GATA4. Progression of OVDM1 from early to late passages was accompanied by preservation of the near-diploid status, acquisition of only few additional large chromosomal rearrangements and more … can an ear infection cause eye painWebJul 28, 2024 · Somatic copy number alterations (SCNAs) are a pervasive trait of human cancers that contributes to tumorigenesis by affecting the dosage of multiple genes at the same time. ... Subsequently, a pan-cancer analysis intersected somatic focal (≤ 5 Mb) deletions identified by TCGA in 10,221 tumor specimens spanning 30 cancer types with … can an ear infection cause coughWebFeb 9, 2024 · “Copy number calls are used to identify focal deletions, deep deletions, and gene amplifications. All these calculations start with segment level relative copy number from the CCLE dataset. A gene is considered to be focally deleted if any of its exons have a copy number of less than 0.2. can an ear infection cause body achesWebGenomic copy number aberrations and corresponding transcriptional deregulation in the cancer genome have been suggested to have regulatory roles in cancer development and progression. fishersobm.comWebApr 21, 2024 · Focal copy-number amplifications occur subclonally and are spatially and temporally separated from common resistance mutations such as EGFRC797S. can an ear infection cause brain fogWebNov 12, 2013 · By examining regions of focal copy-number change that lack protein-coding targets, we identified an intergenic lncRNA on chromosome 1, OVAL, that shows narrow focal genomic amplification in a subset of tumors. While weakly expressed in most tumors, focal amplification coincided with strong OVAL transcriptional activation. fisher soccer