scholarly journals DNA Copy Number Analysis in Gastrointestinal Stromal Tumors Using Gene Expression Microarrays

2008 ◽  
Vol 6 ◽  
pp. CIN.S387 ◽  
Author(s):  
Cristina R. Antonescu ◽  
Kai Wu ◽  
Guoliang Leon Xing ◽  
Manqiu Cao ◽  
Yaron Turpaz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Copy Number ◽  
Gastrointestinal Stromal Tumors ◽  
Rna Expression ◽  
Copy Number Analysis ◽  
Stromal Tumors ◽  
Gene Expression Microarrays ◽  
Expression Microarrays ◽  
Copy Number Changes

We report a method, Expression-Microarray Copy Number Analysis (ECNA) for the detection of copy number changes using Affymetrix Human Genome U133 Plus 2.0 arrays, starting with as little as 5 ng input genomic DNA. An analytical approach was developed using DNA isolated from cell lines containing various X-chromosome numbers, and validated with DNA from cell lines with defined deletions and amplifications in other chromosomal locations. We applied this method to examine the copy number changes in DNA from 5 frozen gastrointestinal stromal tumors (GIST). We detected known copy number aberrations consistent with previously published results using conventional or BAC-array CGH, as well as novel changes in GIST tumors. These changes were concordant with results from Affymetrix 100K human SNP mapping arrays. Gene expression data for these GIST samples had previously been generated on U133A arrays, allowing us to explore correlations between chromosomal copy number and RNA expression levels. One of the novel aberrations identified in the GIST samples, a previously unreported gain on 1q21.1 containing the PEX11B gene, was confirmed in this study by FISH and was also shown to have significant differences in expression pattern when compared to a control sample. In summary, we have demonstrated the use of gene expression microarrays for the detection of genomic copy number aberrations in tumor samples. This method may be used to study copy number changes in other species for which RNA expression arrays are available, e.g. other mammals, plants, etc., and for which SNPs have not yet been mapped.

Identification of oncogenic events in gastrointestinal stromal tumors (GISTs) by combined gene expression and copy number analysis.

2010 ◽  
Vol 28 (15_suppl) ◽  
pp. 10039-10039
Author(s):  
M. Nannini ◽  
M. A. Pantaleo ◽  
A. Astolfi ◽  
A. Maleddu ◽  
M. C. Heinrich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Gastrointestinal Stromal Tumors ◽  
Copy Number Analysis ◽  
Stromal Tumors

Prognostic impacts of DNA copy number changes in gastrointestinal stromal tumors

2004 ◽  
Vol 200 (4) ◽  
pp. 317
Author(s):  
S. Lukas ◽  
B. Gunawan ◽  
C. Enders ◽  
H.-J. Schulten ◽  
A. Von Heydebreck ◽  
...  
Keyword(s):  
Copy Number ◽  
Gastrointestinal Stromal Tumors ◽  
Dna Copy Number ◽  
Stromal Tumors ◽  
Copy Number Changes

Gene expression profiling and copy number analysis to identify predictive molecular markers in breast cancer: Successful use of formalin fixed paraffin embedded tissue (FFPE)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 574-574
Author(s):  
M. Y. Iddawela ◽  
Y. Wang ◽  
R. Russell ◽  
G. Cowley ◽  
M. El-Sheemy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Treatment Response ◽  
Expression Profiling ◽  
Copy Number ◽  
Predictive Markers ◽  
Copy Number Analysis ◽  
Significant Differential Expression ◽  
Response To Chemotherapy ◽  
Copy Number Changes

574 Background: FFPE is a valuable and widely available resource for translational research which to date has been under-used due to technical limitations. Improvement in technology has enabled genome-wide analysis of FFPE samples. We have assessed gene expression and copy number changes in the same cohort of breast cancers to identify markers or pathways important in prediction of treatment response. Methods: FFPE tissues from patients treated with neoadjuvant adriamycin/cyclophosphamide followed by taxanes in a clinical study were used. Gene expression profiling was assessed using the cDNA mediated annealing selection and ligation assay using the cancer panel which assess 502 genes (DASL assay, Illumina). Data was analysed using BeadStudio software. Copy number changes were assessed using the Molecular inversion probe assay with the 50K SNP panel (Affymetrix, California) and analysed using Nexus software (Biodiscovery). Results: Gene expression profiling was carried out on 44 samples. 12/44 (27%) patients had a pathological complete response (pCR) following chemotherapy. Significant differential expression of genes between pCR and non-pCR cancers were shown. TNFRSF5, CTSD, BCL3, ARNT, BIRC3, TGFBR1, MLLT6, and EVI2A were over-expressed and COL18A1, FGF12, IGFBP1 and NOTCH4 which were down-regulated in cancers that have a pCR (p ≤ 0.01). Copy number changes were assessed in 33 samples and comparison of copy number changes in pCR vs. non-pCR showed gains in regions 6q22, 21q21, 4p14, 4q21, 4p14, and loss at 11q11 (p ≤ 0.01). Three regions containing microRNA coding sequences, mir130a (11q11) mir142 (17q23) and mir21 (17q23) showed significant loss among pCR tumours (p < 0.05). Conclusions: This feasibility study shows that FFPE can be used for gene expression and copy number analysis which is a useful tool for the discovery of predictive markers for treatment response in neoadjuvant treatment trials. The role of TNFRSF5, microRNA 21/130a/142, and 11q11 loss should be further investigated as predictive markers of response to chemotherapy. [Table: see text]

Copy number variants associated with epilepsy from gene expression microarrays

2015 ◽  
Vol 22 (12) ◽  
pp. 1907-1910 ◽  
Author(s):  
Dong Wang ◽  
Xia Li ◽  
Shanshan Jia ◽  
Yan Wang ◽  
Zhijing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Copy Number Variants ◽  
Gene Expression Microarrays ◽  
Expression Microarrays

Gene expression profiling and gene copy-number changes in malignant mesothelioma cell lines

2007 ◽  
Vol 46 (10) ◽  
pp. 895-908 ◽  
Author(s):  
Claudia Zanazzi ◽  
Remko Hersmus ◽  
Imke M. Veltman ◽  
Ad J.M. Gillis ◽  
Ellen van Drunen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Cell Lines ◽  
Malignant Mesothelioma ◽  
Expression Profiling ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Mesothelioma Cell ◽  
Copy Number Changes

Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

The Prostate ◽  
2005 ◽  
Vol 63 (2) ◽  
pp. 187-197 ◽  
Author(s):  
Hongjuan Zhao ◽  
Young Kim ◽  
Pei Wang ◽  
Jacques Lapointe ◽  
Rob Tibshirani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Copy Number ◽  
Prostate Cancer Cell ◽  
Prostate Cancer Cell Lines ◽  
Genome Wide ◽  
Copy Number Changes

Transcriptional profiling of iPSC-derived neurons with reciprocal monogenic CNV in 3p26.3 region

2020 ◽  
pp. 10-11
Author(s):  
М.Е. Лопаткина ◽  
В.С. Фишман ◽  
М.М. Гридина ◽  
Н.А. Скрябин ◽  
Т.В. Никитина ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
System Development ◽  
Transcriptional Profiling ◽  
Global Gene Expression ◽  
Nervous System Development ◽  
Number Variation ◽  
The Central Nervous System ◽  
Cntn6 Gene ◽  
Copy Number Changes

Проведен анализ генной экспрессии в нейронах, дифференцированных из индуцированных плюрипотентных стволовых клеток пациентов с идиопатическими интеллектуальными нарушениями и реципрокными хромосомными мутациями в регионе 3p26.3, затрагивающими единственный ген CNTN6. Для нейронов с различным типом хромосомных аберраций была показана глобальная дисрегуляция генной экспрессии. В нейронах с вариациями числа копий гена CNTN6 была снижена экспрессия генов, продукты которых вовлечены в процессы развития центральной нервной системы. The gene expression analysis of iPSC-derived neurons, obtained from patients with idiopathic intellectual disability and reciprocal microdeletion and microduplication in 3p26.3 region affecting the single CNTN6 gene was performed. The global gene expression dysregulation was demonstrated for cells with CNTN6 copy number variation. Gene expression in neurons with CNTN6 copy number changes was downregulated for genes, whose products are involved in the central nervous system development.

Sign in / Sign up

Export Citation Format

Share Document