scholarly journals Identification and meta‑analysis of copy number variation‑driven circadian clock genes for colorectal cancer

2019 ◽  
Author(s):  
Wenliang Yuan ◽  
Li Liu ◽  
Cai Wei ◽  
Xiaobo Li ◽  
Dan Sun ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number Variation ◽  
Circadian Clock ◽  
Copy Number ◽  
Clock Genes ◽  
Meta Analysis ◽  
Number Variation ◽  
Circadian Clock Genes

The mutational landscape of circulating cell-free DNA to identify neoadjuvant chemotherapy response in colorectal cancer patients.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15096-e15096
Author(s):  
Yanlong Liu ◽  
Xiaoli Wei ◽  
Xinying Shi ◽  
Ying Yang ◽  
Lili Fu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Neoadjuvant Chemotherapy ◽  
Copy Number Variation ◽  
Cancer Patients ◽  
Candidate Genes ◽  
Copy Number ◽  
Free Dna ◽  
Number Variation ◽  
Colorectal Cancer Patients ◽  
Response To Neoadjuvant Chemotherapy

e15096 Background: The neoadjuvant chemotherapy plays an important role in the current treatment of colorectal cancer (CRC), even though parts of patients could not be benefit from it. This study was aimed to explore the specific mutational profile of plasma cell free DNA (cfDNA) in CRC patients with or without response to neoadjuvant chemotherapy. Methods: 16 eligible CRC patients were enrolled in this study from Harbin Medical University Cancer Hospital. These patients were divided into two groups: with response ( R, n = 8) and without response (NR, n = 8) to neoadjuvant chemotherapy. All patients received neoadjuvant chemotherapy and their baseline blood samples were collected. The cfDNA fragments were extracted for enrichment of a panel covering exon regions of 1,086 genes. Gene alterations were analyzed to investigate the relationship between genetic characterizations of cfDNA and response to neoadjuvant chemotherapy. Results: Principal component (PCA) analysis for copy number variation(CNV) of cfDNA differed significantly in two groups. In the R group, there were higher frequency CNV loss in ABL-1, ERBB3, SMO, IGF1R, AURKA, PDGFRA, IDH1, BRAF, PIK3CB, NRAS, NF1, MITF, PTCH1 genes, and CNV gain in MTRR, HSP90AA1, VHL, CREBBP, CHEK2, DDR2, MUTYH, NCOA1, XPC, FANCA genes. Regarding to the area under the ROC curve, CNV of these genes had a high value of 0.967, which implied that CNV of the candidate genes have predictive value for identifying response to neoadjuvant chemotherapy in CRC patients. Furthermore, the Copy Number Instability (CNI) value of R group was significantly higher than NR group(p = 0.0014). Conclusions: The candidate genes’ copy number variation and CNI value of baseline plasma cfDNA can identify the colorectal cancer patients with response or without response to neoadjuvant chemotherapy in this small cohort. The molecular profile of cfDNA in plasma may be a potential biomarker for predicting the response to neoadjuvant chemotherapy in colorectal cancer patients. These findings warrant further expanded prospective cohorts to validate.

scholarly journals The effect of copy number variation in the phase II detoxification genesUGT2B17andUGT2B28on colorectal cancer risk

Cancer ◽  
2013 ◽  
Vol 119 (13) ◽  
pp. 2477-2485 ◽  
Author(s):  
Andrea Y. Angstadt ◽  
Arthur Berg ◽  
Junjia Zhu ◽  
Paige Miller ◽  
Terryl J. Hartman ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Risk ◽  
Copy Number Variation ◽  
Phase Ii ◽  
Copy Number ◽  
Colorectal Cancer Risk ◽  
Number Variation

Analysis of TGCA data reveals genetic and epigenetic changes and biological function of MUC family genes in colorectal cancer

2019 ◽  
Vol 15 (35) ◽  
pp. 4031-4043 ◽  
Author(s):  
Zhipeng Jiang ◽  
Huashe Wang ◽  
Liang Li ◽  
Zehui Hou ◽  
Wei Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Regulatory Networks ◽  
The Cancer Genome Atlas ◽  
Epigenetic Changes ◽  
Copy Number Variation Analysis ◽  
Number Variation ◽  
Cancer Genome Atlas ◽  
Drug Influence

Aim: Few studies focused on functions and regulatory networks of MUC family members in colorectal cancer based on comprehensive analysis of online database. Materials & methods: Copy number variation, methylation, pathway analysis and drug influence on MUC expression were analyzed based on The Cancer Genome Atlas and GTEx database. Results: Copy number variation analysis showed MUC heterozygous amplification and heterozygous deletion predominate. Methylation of MUC17, MUC12 and MUC4 were found related to gene expression. Function of MUC family genes mainly affects pathways such as apoptosis, cell cycle, DNA damage and EMT pathways. PLX4720, dabrafenib, gefitinib, afatinib and austocystin D can alter the expression of MUC gene. Conclusion: The genetic and epigenetic changes of MUC are related to the level of MUC expression in colorectal cancer.

scholarly journals A Novel Method to Detect Early Colorectal Cancer Based on Chromosome Copy Number Variation in Plasma

2018 ◽  
Vol 45 (4) ◽  
pp. 1444-1454 ◽  
Author(s):  
Jun-Feng Xu ◽  
Qian Kang ◽  
Xing-Yong Ma ◽  
Yuan-Ming Pan ◽  
Lang Yang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Diagnostic Methods ◽  
Support Vector ◽  
Svm Classifier ◽  
Health Examination ◽  
Plasma Samples ◽  
Z Score ◽  
Number Variation

Background/Aims: Colonoscopy screening has been accepted broadly to evaluate the risk and incidence of colorectal cancer (CRC) during health examination in outpatients. However, the intrusiveness, complexity and discomfort of colonoscopy may limit its application and the compliance of patients. Thus, more reliable and convenient diagnostic methods are necessary for CRC screening. Genome instability, especially copy-number variation (CNV), is a hallmark of cancer and has been proved to have potential in clinical application. Methods: We determined the diagnostic potential of chromosomal CNV at the arm level by whole-genome sequencing of CRC plasma samples (n = 32) and healthy controls (n = 38). Arm level CNV was determined and the consistence of arm-level CNV between plasma and tissue was further analyzed. Two methods including regular z score and trained Support Vector Machine (SVM) classifier were applied for detection of colorectal cancer. Results: In plasma samples of CRC patients, the most frequent deletions were detected on chromosomes 6, 8p, 14q and 1p, and the most frequent amplifications occurred on chromosome 19, 5, 2, 9p and 20p. These arm-level alterations detected in plasma were also observed in tumor tissues. We showed that the specificity of regular z score analysis for the detection of colorectal cancer was 86.8% (33/38), whereas its sensitivity was only 56.3% (18/32). Applying a trained SVM classifier (n = 40 in trained group) as the standard to detect colorectal cancer relevance ratio in the test samples (n = 30), a sensitivity of 91.7% (11/12) and a specificity 88.9% (16/18) were finally reached. Furthermore, all five early CRC patients in stages I and II were successfully detected. Conclusion: Trained SVM classifier based on arm-level CNVs can be used as a promising method to screen early-stage CRC.

scholarly journals Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e92553 ◽  
Author(s):  
Nur Zarina Ali Hassan ◽  
Norfilza Mohd Mokhtar ◽  
Teow Kok Sin ◽  
Isa Mohamed Rose ◽  
Ismail Sagap ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number Variation ◽  
Expression Profiling ◽  
Copy Number ◽  
Integrated Analysis ◽  
Genome Wide ◽  
Number Variation ◽  
Cancer Tissues ◽  
Genome Wide Expression
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