Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes

Purpose Previous studies have highlighted the importance of an appropriate human epidermal growth factor receptor 2 (HER2) evaluation for the proper identification of patients eligible for treatment with anti-HER2 targeted therapies. Today, the relationship remains unclear between the level of HER2 amplification and the outcome of HER2-positive gastric cancer treated with first-line chemotherapy with trastuzumab. The aim of this study was to determine whether the level of HER2 gene amplification determined by the HER2/CEP17 ratio and HER2 gene copy number could significantly predict some benefit in overall survival and response to therapy in advanced gastric cancer treated with trastuzumab-based chemotherapy. Patients and Methods Ninety patients with metastatic gastric cancer treated with first-line trastuzumab-based chemotherapy were studied. The optimal cutoff values for HER2/CEP17 ratio and HER2 gene copy number (GCN) for discriminating positive results in terms of response and prolonged survival were determined using receiver operating characteristic curves analyses. Results In this study, a median HER2/CEP17 ratio of 6.11 (95% CI, 2.27 to 21.90) and a median HER2 gene copy number of 11.90 (95% CI, 3.30 to 43.80) were found. A mean HER2/CEP17 ratio of 4.7 was identified as the optimal cutoff value discriminating sensitive and refractory patients (P = .005). Similarly, the optimal cutoff for predicting survival longer than 12 months was 4.45 (P = .005), and for survival longer than 16 months was 5.15 (P = .004). For HER2 GCN, the optimal cutoff values were 9.4, 10.0, and 9.5, respectively (P = .02). Conclusion The level of HER2 gene amplification significantly predicts sensitivity to therapy and overall survival in advanced gastric cancer treated with trastuzumab-based chemotherapy.

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Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray Analysis of Genomic Representations

Genome Research ◽

10.1101/gr.138300 ◽

2000 ◽

Vol 10 (11) ◽

pp. 1726-1736 ◽

Cited By ~ 65

Author(s):

R. Lucito

Keyword(s):

Tumor Cells ◽

Microarray Analysis ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy

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Prognostic impact of gene copy number instability and tumor mutation burden in patients with resectable gastric cancer

Cancer Communications ◽

10.1002/cac2.12007 ◽

2020 ◽

Vol 40 (1) ◽

pp. 63-66

Author(s):

Lisheng Cai ◽

Linhai Li ◽

Dandan Ren ◽

Xue Song ◽

Beibei Mao ◽

...

Keyword(s):

Gastric Cancer ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Prognostic Impact ◽

Tumor Mutation Burden ◽

Mutation Burden ◽

Resectable Gastric Cancer

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The potential of soil microorganisms to mineralize atrazine as predicted by MCH-PCR followed by nested PCR

Canadian Journal of Microbiology ◽

10.1139/w00-004 ◽

2000 ◽

Vol 46 (5) ◽

pp. 425-432 ◽

Cited By ~ 14

Author(s):

Nir Shapir ◽

Sebastien Goux ◽

Raphi T Mandelbaum ◽

Luc Pussemier

Keyword(s):

Nested Pcr ◽

Copy Number ◽

Soil Microorganisms ◽

Target Genes ◽

Gene Copy Number ◽

Small Population ◽

Gene Copy ◽

Mineralization Rate ◽

Magnetic Capture ◽

High Concentrations

The potential of soil microorganisms to mineralize atrazine was studied in soil samples collected from fields with various histories of atrazine application. In contrast to many previous studies, which showed no atrazine mineralization activity, all the tested soils mineralized atrazine regardless of their atrazine application history. However, the delay before mineralization and the variation in the subsequent mineralization rate were in agreement with the initial copy number of the atrazine dechlorinaze gene, and the proliferation rate of the degraders. Soils from corn fields, which had up to 100 copies of the atzA gene per gram of soil, had a lag period of 4-5 days before atrazine mineralization started, and final mineralization percentages ranged from 40% to 54%. However, soils from fields that were never amended with atrazine had much longer lag periods (more than 17 days), which decreased after enrichment of the degrader population with high concentrations of atrazine for 15 days. Generally the mineralization rate and the atzA gene copy number increased after the enrichment period. The atrazine mineralization potential was measured by PCR of genes from the atrazine mineralization pathway. Magnetic capture hybridization was the most efficient of the two tested methods for purifying target DNA of PCR inhibitors, without reducing the copy number of the required fragment. Nested PCR proved to be the most effective method for predicting the exact potential of the soil to mineralize the pollutant even without enrichment of a small population with the target genes. This method can complement microcosm studies and eliminate futile efforts when the potential to mineralize the pollutant does not exist in the soil.Key words: MCH-PCR, mineralization, atrazine.

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Gene copy number gain of EGFR is a poor prognostic biomarker in gastric cancer: evaluation of 855 patients with bright-field dual in situ hybridization (DISH) method

Gastric Cancer ◽

10.1007/s10120-014-0449-9 ◽

2014 ◽

Vol 19 (1) ◽

pp. 63-73 ◽

Cited By ~ 15

Author(s):

Eiji Higaki ◽

Takeshi Kuwata ◽

Akiko Kawano Nagatsuma ◽

Yasunori Nishida ◽

Takahiro Kinoshita ◽

...

Keyword(s):

Gastric Cancer ◽

In Situ Hybridization ◽

Copy Number ◽

Prognostic Biomarker ◽

Gene Copy Number ◽

Copy Number Gain ◽

Gene Copy ◽

Bright Field ◽

Gene Copy Number Gain

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Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2018-1306 ◽

2019 ◽

Vol 57 (8) ◽

pp. 1142-1152 ◽

Cited By ~ 1

Author(s):

Hua-Jun He ◽

Biswajit Das ◽

Megan H. Cleveland ◽

Li Chen ◽

Corinne E. Camalier ◽

...

Keyword(s):

Reference Material ◽

Copy Number ◽

Target Genes ◽

Human Cancer ◽

Gene Copy Number ◽

Digital Pcr ◽

Cancer Diagnostics ◽

Gene Copy ◽

Human Cancer Cell Lines ◽

Copy Numbers

Abstract Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.

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CDKL2 Is Associated with HER2 Status and Overall Survival in Gastric Cancer: Comparative Analysis of CDKL2 Protein Expression and Gene Copy Number

BioMed Research International ◽

10.1155/2020/1712723 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Qiong Shao ◽

Fang Wang ◽

Yuxia Xu ◽

Xu Zhang ◽

Wenting Tang ◽

...

Keyword(s):

Gastric Cancer ◽

Overall Survival ◽

Protein Expression ◽

Copy Number ◽

Epithelial Mesenchymal Transition ◽

Mrna Level ◽

Gene Copy Number ◽

Gene Copy ◽

Her2 Status ◽

Mesenchymal Transition

Background. Cyclin-dependent kinase-like 2 (CDKL2) is a member of the CDKL family and recognized as a novel regulator of epithelial-mesenchymal transition of breast cancer cells, but its role has not been explored in gastric cancer (GC). This study was to characterize the CDKL2 protein expression and gene copy number in relation to human epidermal growth factor receptor 2 (HER2) status, clinicopathological features, and overall survival (OS) in GC. Methods. This study detected the CDKL2 protein expression and gene copy number by immunochemistry (IHC) and fluorescent in situ hybridization (FISH), respectively, in 334 GC samples. HER2 status was determined according to established criteria. Associations of the CDKL2 protein expression and gene copy number with OS in GC were evaluated, and the association between CDKL2 mRNA expression and OS in GC was also analyzed using TCGA data. Results. The detection results suggested that 34.1% cases showed high CDKL2 protein expression; 11.4% cases had ≥5 copies of CDKL2 gene or a ratio of CDKL2 to chromosome of ≥2. The CDKL2 protein expression was markedly correlated with its gene copy number. High protein expression and high gene copy number were both significantly associated with positive HER2 status, and they both could predicted a shorter OS, although not as independent markers suggested by the multivariate Cox proportional hazard regression analysis. The TCGA data indicated that higher CDKL2 mRNA level also predicted a shorter OS in GC. Conclusions. The combined detection of the CDKL2 protein level and gene copy number could be of important value in predicting HER2 status and prognosis of patients with GC.

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