copy number alteration
Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data
... Motivation: The role of personalised medicine and target treatment in the clinical management of cancer patients has become increasingly important in recent years. This has made the task of precise histological ...
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Characterisation of glyoxalase 1 mutant mouse and glyoxalase 1 copy number alteration
... the copy number alteration of GLO1 in clinical samples From the previous objectives and experimental outcomes, dicarbonyl stress- induced copy number increase of Glo1 appeared to be a ...
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Distribution differences in prognostic copy number alteration profiles in IDH-wild-type glioblastoma cause survival discrepancies across cohorts
... of copy number alterations (CNAs) using two population-based IDH -wild-type GBM cohorts: an original Japanese cohort and a dataset from The Cancer Genome Atlas ...
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SynthEx: a synthetic normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
... discrete copy number calls differed sig- nificantly from the discrete SNP gene-level copy num- ber by Wilcoxon tests are highlighted ...gene-level copy num- ber calls using SynthEx shared a ...
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Transcriptional analysis of bla NDM-1 and copy number alteration under carbapenem stress
... medium containing imipenem and could be conjuga- tively transferred from all 17 clinical E. coli isolates into recipient E. coli strain B. The transformation experiment revealed that the size of the transferable plasmids ...
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Genomic Landscape and Endocrine-Resistant Subgroup in Estrogen Receptor-Positive, Progesterone Receptor-Negative, and HER2-Negative Breast Cancer
... Somatic copy number alteration (SCNA) status of PR among the ER+PR-HER2-, ER+PR+HER2- and TNBC ...PR copy number loss in each group is displayed ...PR copy number status ...
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Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors
... genome-wide copy number alteration profiles (cumulative frequencies) between the two groups are illustrated and chromosomes displaying similar patterns of gain and loss in HPV+ and HPV- HNSCC samples ...
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Combined image and genomic analysis of high grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier
... through copy number alteration ...CNA, copy number alteration; IF, immunofluorescence; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; hetero, heterogeneous; ...
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Evaluation and consequences of heterogeneity in the circulating tumor cell compartment
... CNA, copy number alteration; CRC, colorectal cancer; CRPC, castration resistant prostate cancer; CTC, circulating tumor cell; DGE, digital gene extraction; EMT, epithelial‑to‑mesenchymal transition; ...
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Predicting chemoinsensitivity in breast cancer with ’omics/digital pathology data fusion
... expression, copy number alteration and digital pathology image data in 119 estrogen receptor (ER)-negative and 345 ER-positive breast tumours, we aim to predict two important clinical outcomes: death ...
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Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations
... CpG islands. The size of the points indicates the relative sample size and 95% confidence intervals are shown.. intersecting regions of copy number alteration are lower for the 657 C/C b[r] ...
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Comprehensive copy number profiles of breast cancer cell model genomes
... segmental copy losses and gains ...of copy number alterations (CNAs) in various breast cancer cell lines ...DNA copy changes of amplicons containing ERRB2 on 17q ...between copy ...
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iSOM-GSN: An Integrative Approach for Transforming Multi-omic Data into Gene Similarity Networks via Self-organizing Maps
... and copy number alteration, yielding accuracies in the 94-98% range for tumor stages of breast cancer and calculated Gleason scores of prostate cancer with just 14 input genes for both ...
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High MET gene copy number predicted poor prognosis in primary intestinal diffuse large B-cell lymphoma
... 3. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir ...
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PubMedCentral-PMC5599133.pdf
... somatic copy number alteration group in UCEC, a subgroup of UCS tumors appeared to have consistently more endometrioid features, including fewer overall somatic copy number alterations ...
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Complexity and algorithms for copy-number evolution problems
... In this paper we studied two problems in the evolu- tion of copy-number profiles. For the CN3 problem, we gave a pseudo-polynomial DP algorithm and an ILP formulation, and compared their efficiency on simu- ...
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Functional consequences of copy number variants in miscarriage
... their copy number change and included: PARK2, NDUFAF2, TIMP2, LIPC, CTNNA3, EGFL6, GPM6B, OFD1, RAB9A, TRAPPC2, CHSY3, PRMT3, POU6F2, and C7orf10 (Table ...
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Ty1 Copy Number Dynamics in Saccharomyces
... Figure 1.—Ty1 copy number dynam- ics. Ty1-4253 is located between RAD7 and CDC8 on chromosome X (Moore et al. 2004). Ty1-4253 was tagged with his3-AI, represented by the star, to determine the rate of ...
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COPY NUMBER CONTROL OF Tn5 TRANSPOSITION
... SupB-suppressed ISSOL proteins are synthesized at about 20% the rate of IS5OR proteins (R. REZNIKOFF, unpublished results). This level of synthesis corre- lates well with [r] ...
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Copy Number Profiling of Brazilian Astrocytomas.
... ABSTRACT Copy number alterations (CNA) are one of the driving mechanisms of glioma tumorigenesis, and are currently used as important biomarkers in the routine ...the number of genomic alterations ...
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