Dataset Information

The association between DNA copy number aberrations at chromosome 5q22 and gastric cancer.

ABSTRACT:

Background

Gastric cancer is common cancer. Discovering novel genetic biomarkers might help to identify high-risk individuals. Copy number variation (CNV) has recently been shown to influence risk for several cancers. The aim of the present study was sought to test the association between copy number at a variant region and GC.

Methods

A total of 110 gastric cancer patients and 325 healthy volunteers were enrolled in this study. We searched for a CNV and found a CNV (Variation 7468) containing part of the APC gene, the SRP19 gene and the REEP5 gene. We chose four probes targeting at APC-intron8, APC-exon9, SRP19 and REEP5 to interrogate this CNV. Specific Taqman probes labeled by different reporter fluorophores were used in a real-time PCR platform to obtain copy number. Both the original non-integer data and transformed integer data on copy number were used for analyses.

Results

Gastric caner patients had a lower non-integer copy number than controls for the APC-exon9 probe (Adjusted p?=?0.026) and SRP19 probe (Adjusted p?=?0.002). The analysis of integer copy number yielded a similar pattern although less significant (Adjusted p?=?0.07 for APC-exon9 probe and Adjusted p?=?0.02 for SRP19 probe).

Conclusions

Losses of a CNV at 5q22, especially in the DNA region surrounding APC-exon 9, may be associated with a higher risk of gastric cancer.

SUBMITTER: Tsai PC

PROVIDER: S-EPMC4161348 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

The association between DNA copy number aberrations at chromosome 5q22 and gastric cancer.

Tsai Pei-Chien PC Huang Szu-Wei SW Tsai Hsiang-Lin HL Ma Cheng-Jen CJ Hou Ming-Feng MF Yang I-Ping IP Wang Yung-Song YS Juo Suh-Hang Hank SH Wang Jaw-Yuan JY

PloS one 20140911 9

<h4>Background</h4>Gastric cancer is common cancer. Discovering novel genetic biomarkers might help to identify high-risk individuals. Copy number variation (CNV) has recently been shown to influence risk for several cancers. The aim of the present study was sought to test the association between copy number at a variant region and GC.<h4>Methods</h4>A total of 110 gastric cancer patients and 325 healthy volunteers were enrolled in this study. We searched for a CNV and found a CNV (Variation 746 ...[more]

PMID: 25210923

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Project description:Breast cancer recurrence (BCR) is a common treatment outcome despite curative-intent primary treatment of non-metastatic breast cancer. Currently used prognostic and predictive factors utilize tumor-based markers, and are not optimal determinants of risk of BCR. Germline-based copy number aberrations (CNAs) have not been evaluated as determinants of predisposition to experience BCR. In this study, we accessed germline DNA from 369 female breast cancer subjects who received curative-intent primary treatment following diagnosis. Of these, 155 experienced BCR and 214 did not, after a median duration of follow up after breast cancer diagnosis of 6.35 years (range?=?0.60-21.78) and 8.60 years (range?=?3.08-13.57), respectively. Whole genome CNA genotyping was performed on the Affymetrix SNP array 6.0 platform. CNAs were identified using the SNP-Fast Adaptive States Segmentation Technique 2 algorithm implemented in Nexus Copy Number 6.0. Six samples were removed due to poor quality scores, leaving 363 samples for further analysis. We identified 18,561 CNAs with ?1 kb as a predefined cut-off for observed aberrations. Univariate survival analyses (log-rank tests) identified seven CNAs (two copy number gains and five copy neutral-loss of heterozygosities, CN-LOHs) showing significant differences (P<2.01×10(-5)) in recurrence-free survival (RFS) probabilities with and without CNAs.We also observed three additional but distinct CN-LOHs showing significant differences in RFS probabilities (P<2.86×10(-5)) when analyses were restricted to stratified cases (luminal A, n?=?208) only. After adjusting for tumor stage and grade in multivariate analyses (Cox proportional hazards models), all the CNAs remained strongly associated with the phenotype of BCR. Of these, we confirmed three CNAs at 17q11.2, 11q13.1 and 6q24.1 in representative samples using independent genotyping platforms. Our results suggest further investigations on the potential use of germline DNA variations as prognostic markers in cancer-associated phenotypes.

Dataset Information

The association between DNA copy number aberrations at chromosome 5q22 and gastric cancer.

Background

Methods

Results

Conclusions

Publications

The association between DNA copy number aberrations at chromosome 5q22 and gastric cancer.

Similar Datasets

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