scholarly journals Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer

2013 ◽  
Vol 52 (5) ◽  
pp. 450-466 ◽  
Author(s):  
Lenora W. M. Loo ◽  
Maarit Tiirikainen ◽  
Iona Cheng ◽  
Annette Lum-Jones ◽  
Ann Seifried ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Copy Number ◽  
Cpg Island ◽  
Integrated Analysis ◽  
Copy Number Alterations ◽  
Cpg Island Methylator Phenotype ◽  
Genome Wide ◽  
Methylator Phenotype

scholarly journals Integrated Analysis of Genome-Wide Copy Number Alterations and Gene Expression Profiling of Lung Cancer in Xuanwei, China

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0169098 ◽  
Author(s):  
Yanliang Zhang ◽  
Qiuyue Xue ◽  
Guoqing Pan ◽  
Qing H. Meng ◽  
Xiaoyu Tuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Copy Number ◽  
Integrated Analysis ◽  
Copy Number Alterations ◽  
Genome Wide

scholarly journals Diet and lifestyle factor associations with CpG island methylator phenotype and BRAF mutations in colon cancer

2006 ◽  
Vol 120 (3) ◽  
pp. 656-663 ◽  
Author(s):  
Martha L. Slattery ◽  
Karen Curtin ◽  
Carol Sweeney ◽  
Theodore R. Levin ◽  
John Potter ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cpg Island ◽  
Lifestyle Factor ◽  
Cpg Island Methylator Phenotype ◽  
Braf Mutations ◽  
Methylator Phenotype ◽  
Diet And Lifestyle

scholarly journals Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e17490 ◽  
Author(s):  
Zhifu Sun ◽  
Yan W. Asmann ◽  
Krishna R. Kalari ◽  
Brian Bot ◽  
Jeanette E. Eckel-Passow ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Deep Sequencing ◽  
Copy Number ◽  
Breast Cancer Cells ◽  
Cpg Island ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Integrated Analysis ◽  
Cpg Island Methylation

scholarly journals MSH6 G39E polymorphism and CpG island methylator phenotype in colon cancer

2009 ◽  
Vol 48 (11) ◽  
pp. 989-994 ◽  
Author(s):  
Karen Curtin ◽  
Wade S. Samowitz ◽  
Roger K. Wolff ◽  
Bette J. Caan ◽  
Cornelia M. Ulrich ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cpg Island ◽  
Cpg Island Methylator Phenotype ◽  
Methylator Phenotype

scholarly journals Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities

2009 ◽  
Vol 25 (24) ◽  
pp. 3228-3235 ◽  
Author(s):  
Martin Schäfer ◽  
Holger Schwender ◽  
Sylvia Merk ◽  
Claudia Haferlach ◽  
Katja Ickstadt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Integrated Analysis ◽  
Copy Number Alterations

scholarly journals The Role of the CpG Island Methylator Phenotype on Survival Outcome in Colon Cancer

Gut and Liver ◽  
2015 ◽  
Vol 9 (2) ◽  
pp. 202-207 ◽  
Author(s):  
Ki Joo Kang ◽  
Byung-Hoon Min ◽  
Kyung Ju Ryu ◽  
Kyoung-Mee Kim ◽  
Dong Kyung Chang ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cpg Island ◽  
Survival Outcome ◽  
Cpg Island Methylator Phenotype ◽  
Methylator Phenotype

scholarly journals P.051 5-hydroxymethylcytosine profiling identifies differential targeting in IDH1 mutant versus IDH1 wild-type high-grade gliomas

2018 ◽  
Vol 45 (s2) ◽  
pp. S29-S29
Author(s):  
W Glowacka ◽  
H Jain ◽  
M Okura ◽  
A Maimaitiming ◽  
R Nejad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Cpg Island ◽  
High Grade ◽  
Spearman Correlation ◽  
Wild Type ◽  
Cpg Island Methylator Phenotype ◽  
B Values ◽  
Active Demethylation ◽  
Methylator Phenotype

Background: Gliomas demonstrate epigenetic dysregulation highlighted by the Glioma CpG-Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. IDH1 mutation perturbs the balance between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by inhibiting TET-mediated active demethylation. The role 5hmC plays in IDH1 mutant tumors remains poorly understood. Methods: We profiled 5hmC in high grade IDH1 mutant (n = 12) and wild-type (n = 9) tumors on the Illumina MethylationEPIC Beadchip. We examined regions with high 5hmC abundance (top 1% probes), and differentially hydroxymethylated regions (DHMR). 5hmC profiles were correlated with gene expression. Results: Mean 5hmC b-values were 4.6%% and 3.8% for IDH1 mutant and wild-type tumors, respectively. Top 1% and DHMR probes demonstrated increased 5hmC among IDH1 mutants. 5hmC enriched for enhancer and super-enhancers. Among G-CIMP target genes, 22/50 were hydroxymethylated in our IDH1 mutant cohort, suggesting that 5hmC contributes to their overall methylation. Gene expression was associated with gene body 5hmC. 48 genes differentially expressed between IDH1 cohorts showed a positive Spearman correlation between 5hmC and gene expression, in particular for genes upregulated in IDH1 mutants. Conclusions: Locus-specific gain of 5hmC, targeting regulatory regions and associated with over-expressed genes, suggests a significant role for 5hmC in IDH1 mutant HGG.

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