scholarly journals Patterns of copy number alterations in primary breast tumors of South African patients and their impact on functional cellular pathways

2018 ◽  
Author(s):  
Kamil Lupicki ◽  
Selene Elifio-Esposito ◽  
Aline Fonseca ◽  
Saulo Weber ◽  
Bruna Sugita ◽  
...  
Keyword(s):  
South African ◽  
Copy Number ◽  
Breast Tumors ◽  
Copy Number Alterations ◽  
Cellular Pathways ◽  
African Patients

High-resolution genomic and expression analyses of copy number alterations in breast tumors

2008 ◽  
Vol 47 (6) ◽  
pp. 530-542 ◽  
Author(s):  
Peter M. Haverty ◽  
Jane Fridlyand ◽  
Li Li ◽  
Gad Getz ◽  
Rameen Beroukhim ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Breast Tumors ◽  
Copy Number Alterations

Copy Number Analysis of the DLX4 and ERBB2 Genes in South African Breast Cancer Patients

2015 ◽  
Vol 146 (3) ◽  
pp. 195-203 ◽  
Author(s):  
Bridget C. Langa ◽  
Márcia M.C. Oliveira ◽  
Silma R.F. Pereira ◽  
Kamil Lupicki ◽  
Catalin Marian ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
South African ◽  
Copy Number ◽  
Linear Regression Analysis ◽  
African Women ◽  
Racial Groups ◽  
Western Cape ◽  
Copy Number Alterations ◽  
Breast Cancer Patients

Breast cancer is one of the main causes of cancer death among South African women. Although several risk factors can be attributed to the observed high mortality rate, the biology of the tumors is not extensively investigated. Copy number gain of the DLX4 homeobox gene has been observed in breast cancer in association with poor prognosis and specific racial groups. Therefore, we aimed to assess the copy number and prognostic role of DLX4 in breast cancer from South African patients. Due to the co-location of ERBB2 and DLX4 in the 17q21 region, its copy number was also evaluated. Our results in the analysis of 66 cases demonstrated copy number gains of DLX4 and ERBB2 in 24.1 and 29.7% of the cases, respectively. Linear regression analysis showed no dependency between the copy number alterations in these genes. Although not significant, patients with DLX4 and ERBB2 gains presented a higher frequency of advanced-grade tumors. In addition, copy number alterations of these genes were not significantly differently observed in the 3 main racial groups of the Western Cape population: Colored, White, and Black. These findings indicate that gains of DLX4 and ERBB2 occur in South African breast cancer patients irrespectively of their race and factors known to influence prognosis.

scholarly journals Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

2013 ◽  
Vol 14 (11) ◽  
pp. R126 ◽  
Author(s):  
Miriam Aure ◽  
Suvi-Katri Leivonen ◽  
Thomas Fleischer ◽  
Qian Zhu ◽  
Jens Overgaard ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mirna Expression ◽  
Copy Number ◽  
Breast Tumors ◽  
Combined Effects ◽  
Copy Number Alterations

scholarly journals Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 379 ◽  
Author(s):  
LO Baumbusch ◽  
J Aarøe ◽  
FE Johansen ◽  
J Hicks ◽  
H Sun ◽  
...  
Keyword(s):  
Copy Number ◽  
Breast Tumors ◽  
Copy Number Alterations ◽  
Human Breast

scholarly journals 731 Gene Copy Number Alterations in Male Breast Tumors

2012 ◽  
Vol 48 ◽  
pp. S173-S174
Author(s):  
P. Rizzolo ◽  
A.S. Navazio ◽  
M. Falchetti ◽  
V. Silvestri ◽  
V. Graziano ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Copy Number ◽  
Breast Tumors ◽  
Male Breast ◽  
Gene Copy ◽  
Copy Number Alterations

Sex-dependent differences in DNA copy number alterations in hepatocellular carcinoma

2012 ◽  
Vol 32 (1) ◽  
pp. 5-9 ◽  
Author(s):  
Bing-ji WEN ◽  
Wen-ming CONG ◽  
Ai-zhong WANG ◽  
Song-qin HE ◽  
Hong-mei JIANG ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Dna Copy Number Alterations

scholarly journals EPCO-29. EPIGENOMICS OF THE GLIOMA LONGITUDINAL ANALYSIS (GLASS) CONSORTIUM

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii75-ii75
Author(s):  
Thais Sabedot ◽  
Michael Wells ◽  
Indrani Datta ◽  
Tathiane Malta ◽  
Ana Valeria Castro ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Longitudinal Analysis ◽  
Copy Number ◽  
Large Scale ◽  
Molecular Classification ◽  
Tumor Burden ◽  
Copy Number Alterations ◽  
Unsupervised Analysis ◽  
Diffuse Gliomas ◽  
New Biomarkers

Abstract Adult diffuse gliomas are central nervous system (CNS) tumors that arise from the malignant transformation of glial cells. Nearly all gliomas will recur despite standard treatment however, current histopathological grading fails to predict which of them will relapse and/or progress. The Glioma Longitudinal AnalySiS (GLASS) consortium is a large-scale collaboration that aims to investigate the molecular profiling of matched primary and recurrent glioma samples from multiple institutions in order to better understand the dynamic evolution of these tumors. At this time, the cohort comprises 946 samples across 11 institutions and among those, 864 have DNA methylation data available. The current molecular classification based on 7 subtypes published by TCGA in 2016 was applied to the dataset. Among the IDH wildtype tumors, 33% (16/49) of the patients showed a change of subtype upon recurrence, whereas most of them (9/16) were Classic-like at the primary stage but changed to either Mesenchymal-like or PA-like at the recurrent level. Among the IDH mutant tumors, 15% (22/142) showed a change of subtype at recurrent stage, in which 16 out of 22 progressed from G-CIMP-high to G-CIMP-low. Although some tumors progressed to a different subtype upon recurrence, an unsupervised analysis showed that the samples tend to cluster by patient instead of by subtype. By estimating the copy number alterations of these tumors using DNA methylation, the overall copy number profile of the recurrent samples remains similar to their primary counterpart. From this initial analysis using epigenomic data, we were able to characterize some aspects of glioma evolution and how the DNA methylation is associated with the progression of these tumors to different subtypes. These findings corroborate the importance of epigenetics in gliomas and can potentially lead to the identification of new biomarkers that can reflect tumor burden and predict its development.

scholarly journals From Benign Inflammatory Dermatosis to Cutaneous Lymphoma. DNA Copy Number Imbalances in Mycosis Fungoides versus Large Plaque Parapsoriasis

Medicina ◽  
2021 ◽  
Vol 57 (5) ◽  
pp. 502
Author(s):  
Georgiana Gug ◽  
Caius Solovan
Keyword(s):  
Mycosis Fungoides ◽  
Copy Number ◽  
Snp Array ◽  
Chromosome 1 ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Large Plaque ◽  
Inflammatory Dermatosis ◽  
Fresh Frozen ◽  
Dna Copy Number Alterations

Background and Objectives: Mycosis fungoides (MF) and large plaque parapsoriasis (LPP) evolution provide intriguing data and are the cause of numerous debates. The diagnosis of MF and LPP is associated with confusion and imprecise definition. Copy number alterations (CNAs) may play an essential role in the genesis of cancer out of genes expression dysregulation. Objectives: Due to the heterogeneity of MF and LPP and the scarcity of the cases, there are an exceedingly small number of studies that have identified molecular changes in these pathologies. We aim to identify and compare DNA copy number alterations and gene expression changes between MF and LPP to highlight the similarities and the differences between these pathologies. Materials and Methods: The patients were prospectively selected from University Clinic of Dermatology and Venereology Timișoara, Romania. From fresh frozen skin biopsies, we extracted DNA using single nucleotide polymorphism (SNP) data. The use of SNP array for copy number profiling is a promising approach for genome-wide analysis. Results: After reviewing each group, we observed that the histograms generated for chromosome 1–22 were remarkably similar and had a lot of CNAs in common, but also significant differences were seen. Conclusions: This study took a step forward in finding out the differences and similarities between MF and LPP, for a more specific and implicitly correct approach of the case. The similarity between these two pathologies in terms of CNAs is striking, emphasizing once again the difficulty of approaching and differentiating them.

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