Copy number changes of clinically actionable genes in melanoma, non-small cell lung cancer and colorectal cancer-A survey across 822 routine diagnostic cases

2016 ◽  
Vol 55 (11) ◽  
pp. 821-833 ◽  
Author(s):  
Nicole Pfarr ◽  
Roland Penzel ◽  
Frederick Klauschen ◽  
Daniel Heim ◽  
Regine Brandt ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Small Cell ◽  
Small Cell Lung ◽  
Copy Number Changes

551 DNA copy number changes in non-small cell lung cancer (NSCLC)

Lung Cancer ◽  
1997 ◽  
Vol 18 ◽  
pp. 141
Author(s):  
A.-M. Björkqvist ◽  
S. Nordling ◽  
K. Mattson ◽  
S. Knuutila
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Small Cell ◽  
Small Cell Lung ◽  
Dna Copy Number ◽  
Copy Number Changes

scholarly journals Circulating tumor cell copy-number heterogeneity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Marianne Oulhen ◽  
Patrycja Pawlikowska ◽  
Tala Tayoun ◽  
Marianna Garonzi ◽  
Genny Buson ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Epithelial To Mesenchymal Transition ◽  
Kinase Inhibitors ◽  
Small Cell ◽  
Small Cell Lung ◽  
Mesenchymal Transition ◽  
Anaplastic Lymphoma

AbstractGatekeeper mutations are identified in only 50% of the cases at resistance to Anaplastic Lymphoma Kinase (ALK)-tyrosine kinase inhibitors (TKIs). Circulating tumor cells (CTCs) are relevant tools to identify additional resistance mechanisms and can be sequenced at the single-cell level. Here, we provide in-depth investigation of copy number alteration (CNA) heterogeneity in phenotypically characterized CTCs at resistance to ALK-TKIs in ALK-positive non-small cell lung cancer. Single CTC isolation and phenotyping were performed by DEPArray or fluorescence-activated cell sorting following enrichment and immunofluorescence staining (ALK/cytokeratins/CD45/Hoechst). CNA heterogeneity was evaluated in six ALK-rearranged patients harboring ≥ 10 CTCs/20 mL blood at resistance to 1st and 3rd ALK-TKIs and one presented gatekeeper mutations. Out of 82 CTCs isolated by FACS, 30 (37%) were ALK+/cytokeratins-, 46 (56%) ALK-/cytokeratins+ and 4 (5%) ALK+/cytokeratins+. Sequencing of 43 CTCs showed highly altered CNA profiles and high levels of chromosomal instability (CIN). Half of CTCs displayed a ploidy >2n and 32% experienced whole-genome doubling. Hierarchical clustering showed significant intra-patient and wide inter-patient CTC diversity. Classification of 121 oncogenic drivers revealed the predominant activation of cell cycle and DNA repair pathways and of RTK/RAS and PI3K to a lower frequency. CTCs showed wide CNA heterogeneity and elevated CIN at resistance to ALK-TKIs. The emergence of epithelial ALK-negative CTCs may drive resistance through activation of bypass signaling pathways, while ALK-rearranged CTCs showed epithelial-to-mesenchymal transition characteristics potentially contributing to ALK-TKI resistance. Comprehensive analysis of CTCs could be of great help to clinicians for precision medicine and resistance to ALK-targeted therapies.

scholarly journals Classification of Non-Small Cell Lung Cancer Based on Copy Number Alterations

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88300 ◽  
Author(s):  
Bi-Qing Li ◽  
Jin You ◽  
Tao Huang ◽  
Yu-Dong Cai
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Small Cell ◽  
Copy Number Alterations ◽  
Small Cell Lung

scholarly journals Mutation analysis and copy number alterations of KIF23 in non-small-cell lung cancer exhibiting KIF23 over-expression

2017 ◽  
Vol Volume 10 ◽  
pp. 4969-4979 ◽  
Author(s):  
Ann-Louise Vikberg ◽  
Tõnu Vooder ◽  
Kaie Lokk ◽  
Tarmo Annilo ◽  
Irina Golovleva
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Mutation Analysis ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Small Cell ◽  
Copy Number Alterations ◽  
Small Cell Lung ◽  
Over Expression

scholarly journals Prognostic Value of Germline Copy Number Variants and Environmental Exposures in Non-small Cell Lung Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Shizhen Chen ◽  
Liming Lu ◽  
Jianfeng Xian ◽  
Changhong Shi ◽  
Jinbin Chen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Chinese Population ◽  
Validation Cohort ◽  
Small Cell ◽  
Polygenic Risk Score ◽  
Small Cell Lung ◽  
Training Cohort

Germline copy number variant (gCNV) has been studied as a genetic determinant for prognosis of several types of cancer, but little is known about how it affects non-small cell lung cancer (NSCLC) prognosis. We aimed to develop a prognostic nomogram for NSCLC based on gCNVs. Promising gCNVs that are associated with overall survival (OS) of NSCLC were sorted by analyzing the TCGA data and were validated in a small Chinese population. Then the successfully verified gCNVs were determined in a training cohort (n = 570) to develop a prognostic nomogram, and in a validation cohort (n = 465) to validate the nomogram. Thirty-five OS-related gCNVs were sorted and were reduced to 15 predictors by the Lasso regression analysis. Of them, only CNVR395.1 and CNVR2239.1 were confirmed to be associated with OS of NSCLC in the Chinese population. High polygenic risk score (PRS), which was calculated by the hazard effects of CNVR395.1 and CNVR2239.1, exerted a significantly higher death rate in the training cohort (HR = 1.41, 95%CI: 1.16–1.74) and validation cohort (HR = 1.42, 95%CI: 1.13–1.77) than low PRS. The nomogram incorporating PRS and surrounding factors, achieved admissible concordance indexes of 0.678 (95%CI: 0.664–0.693) and 0.686 (95%CI: 0.670–0.702) in predicting OS in the training and validation cohorts, respectively, and had well-fitted calibration curves. Moreover, an interaction between PRS and asbestos exposure was observed on affecting OS (Pinteraction = 0.042). Our analysis developed a nomogram that achieved an admissible prediction of NSCLC survival, which would be beneficial to the personalized intervention of NSCLC.

scholarly journals Increased MET Gene Copy Number but Not mRNA Level Predicts Postoperative Recurrence in Patients with Non–Small Cell Lung Cancer

2014 ◽  
Vol 7 (5) ◽  
pp. 605-612 ◽  
Author(s):  
Oksana Kowalczuk ◽  
Miroslaw Kozlowski ◽  
Wiesława Niklinska ◽  
Joanna Kisluk ◽  
Barbara Joanna Niklinska ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Mrna Level ◽  
Gene Copy Number ◽  
Postoperative Recurrence ◽  
Small Cell ◽  
Gene Copy ◽  
Small Cell Lung
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