scholarly journals Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study

2011 ◽  
Vol 32 (2) ◽  
pp. 240-248 ◽  
Author(s):  
Gaëlle Marenne ◽  
Benjamín Rodríguez-Santiago ◽  
Montserrat García Closas ◽  
Luis Pérez-Jurado ◽  
Nathaniel Rothman ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Snp Array ◽  
Number Variation ◽  
Methodological Approaches

scholarly journals Transcriptomics & copy number variation of radiotoxicity points to altered mitochondrial and DNA repair mechanisms

2020 ◽  
Author(s):  
Gita A Pathak ◽  
Renato Polimanti ◽  
Talisa K Silzer ◽  
Frank R Wendt ◽  
Ranajit Chakraborty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Copy Number Variation ◽  
Whole Blood ◽  
Copy Number ◽  
Radiation Treatment ◽  
Snp Array ◽  
Prostate Tissue ◽  
Repair Mechanisms ◽  
Number Variation

Abstract Proctitis is an inflammation of the rectum and may be induced by radiation treatment for cancer. We investigated proctitis as a radiotoxic endpoint in prostate cancer patients who received radiotherapy (n=222). We analyzed the copy number variation and SNP-derived transcriptomic profiles of whole-blood and prostate tissue associated with proctitis. The SNP and copy number data were genotyped on Affymetrix® Genome-wide Human SNP Array 6.0. Following QC measures, the genotypes were used to obtain gene expression by leveraging GTEx, a reference dataset for gene expression association based on genotype and RNA-seq information for prostate (n= 132) and whole-blood tissue (n=369). In prostate tissue, 62 genes were significantly associated with proctitis, and 98 genes in whole-blood tissue. Six genes - CABLES2, ATP6AP1L, IFIT5, ATRIP, TELO2 , and PARD6G were common to both tissues. The copy number analysis identified seven regions associated with proctitis, one of which ( ALG1L2) was also associated with proctitis based on transcriptomic profiles in the whole-blood tissue. The genes identified via transcriptomics and copy number variation association were further investigated for enriched pathways and gene ontology. Some of the enriched processes were DNA repair, mitochondrial apoptosis regulation, cell-to-cell signaling interaction processes for renal and urological system, and organismal injury.

scholarly journals Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer

2021 ◽  
Vol 22 (8) ◽  
pp. 664-681
Author(s):  
Wenwen Zhong ◽  
Dejuan Wang ◽  
Bing Yao ◽  
Xiaoxia Chen ◽  
Zhongyang Wang ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Integrative Analysis ◽  
Number Variation ◽  
Non Coding Rnas

scholarly journals SNP array mapping of chromosome 20p deletions: Genotypes, phenotypes, and copy number variation

2009 ◽  
Vol 30 (3) ◽  
pp. 371-378 ◽  
Author(s):  
Binita M. Kamath ◽  
Brian D. Thiel ◽  
Xiaowu Gai ◽  
Laura K. Conlin ◽  
Pedro S. Munoz ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Snp Array ◽  
Number Variation

scholarly journals Clinical impact of copy number variation changes in bladder cancer samples

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Victoria Spasova ◽  
Boris Mladenov ◽  
Simeon Rangelov ◽  
Zora Hammoudeh ◽  
Desislava Nesheva ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Clinical Impact ◽  
Number Variation

scholarly journals Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Jeanette E Eckel-Passow ◽  
Elizabeth J Atkinson ◽  
Sooraj Maharjan ◽  
Sharon LR Kardia ◽  
Mariza de Andrade
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Snp Array ◽  
Array Platform ◽  
Genomic Copy Number ◽  
Software Comparison ◽  
Genomic Copy ◽  
Number Variation ◽  
Genomic Copy Number Variation
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