scholarly journals Classification of lung adenocarcinoma and squamous cell carcinoma samples based on their gene expression profile in the sbv IMPROVER Diagnostic Signature Challenge

2013 ◽  
Vol 1 (4) ◽  
pp. 268-277 ◽  
Author(s):  
Rotem Ben-Hamo ◽  
Stephanie Boue ◽  
Florian Martin ◽  
Marja Talikka ◽  
Sol Efroni
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Lung Adenocarcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell ◽  
Diagnostic Signature

scholarly journals Weighted gene expression profiles identify diagnostic and prognostic genes for lung adenocarcinoma and squamous cell carcinoma

2019 ◽  
Vol 48 (3) ◽  
pp. 030006051989383 ◽  
Author(s):  
Xing Wu ◽  
Linlin Wang ◽  
Fan Feng ◽  
Suyan Tian
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Squamous Cell Carcinoma ◽  
Lung Adenocarcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Prognostic Signature ◽  
Diagnostic Signature

Objective To construct a diagnostic signature to distinguish lung adenocarcinoma from lung squamous cell carcinoma and a prognostic signature to predict the risk of death for patients with nonsmall-cell lung cancer, with satisfactory predictive performances, good stabilities, small sizes and meaningful biological implications. Methods Pathway-based feature selection methods utilize pathway information as a priori to provide insightful clues on potential biomarkers from the biological perspective, and such incorporation may be realized by adding weights to test statistics or gene expression values. In this study, weighted gene expression profiles were generated using the GeneRank method and then the LASSO method was used to identify discriminative and prognostic genes. Results The five-gene diagnostic signature including keratin 5 ( KRT5), mucin 1 ( MUC1), triggering receptor expressed on myeloid cells 1 ( TREM1), complement C3 ( C3) and transmembrane serine protease 2 ( TMPRSS2) achieved a predictive error of 12.8% and a Generalized Brier Score of 0.108, while the five-gene prognostic signature including alcohol dehydrogenase 1C (class I), gamma polypeptide ( ADH1C), alpha-2-glycoprotein 1, zinc-binding ( AZGP1), clusterin ( CLU), cyclin dependent kinase 1 ( CDK1) and paternally expressed 10 ( PEG10) obtained a log-rank P-value of 0.03 and a C-index of 0.622 on the test set. Conclusions Besides good predictive capacity, model parsimony and stability, the identified diagnostic and prognostic genes were highly relevant to lung cancer. A large-sized prospective study to explore the utilization of these genes in a clinical setting is warranted.

Gene Expression Profile in Oral Squamous Cell Carcinoma: A Pilot Study

2005 ◽  
Vol 63 (6) ◽  
pp. 786-792 ◽  
Author(s):  
José Manuel Somoza-Martín ◽  
Abel García-García ◽  
Francisco Barros-Angueira ◽  
Eva Otero-Rey ◽  
María Torres-Español ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Pilot Study ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell

Fibroblast gene expression profile reflects the stage of tumour progression in oral squamous cell carcinoma

2011 ◽  
Vol 223 (4) ◽  
pp. 459-469 ◽  
Author(s):  
Kue Peng Lim ◽  
Nicola Cirillo ◽  
Yazan Hassona ◽  
Wenbin Wei ◽  
Johanna K Thurlow ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell ◽  
Tumour Progression

scholarly journals Analytical validity of DecisionDx-SCC, a gene expression profile test to identify risk of metastasis in cutaneous squamous cell carcinoma (SCC) patients

2021 ◽  
Author(s):  
Sherri Borman ◽  
Jeff Wilkinson ◽  
Lauren Meldi-Sholl ◽  
Clare Johnson ◽  
Kelsey Carter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
High Risk ◽  
Cell Carcinoma ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Squamous Cell ◽  
Cutaneous Squamous Cell Carcinoma ◽  
Risk Class ◽  
Class 1

Abstract Background To improve identification of patients with cutaneous squamous cell carcinoma (SCC) at high risk for metastatic disease, the DecisionDx-SCC assay, a prognostic 40-gene expression profile (40-GEP) test, was developed and validated. The 40-GEP assay utilizes RT-PCR gene expression analysis on primary tumor biopsy tissue to evaluate the expression of 34 signature gene targets and 6 normalization genes. The test provides classifications of low risk (Class 1), moderate risk (Class 2A), and high risk (Class 2B) of metastasis within 3 years of diagnosis. The primary objective of this study was to validate the analytical performance of the 40 gene expression signature. Methods The repeatability and reproducibility of the 40-GEP test was evaluated by performance of inter-assay, intra-assay, and inter-operator precision experiments along with monitoring the reliability of sample and reagent stability for class call concordance. The technical performance of clinical orders from September 2020 through July 2021 for the 40-GEP test was assessed. Results Patient hematoxylin and eosin (H&E) stained slides were reviewed by a board-certified pathologist to assess minimum acceptable tumor content. Class specific controls (Class 1 and Class 2B) were evaluated with Levey Jennings analysis and demonstrated consistent and reproducible results. Inter-assay, inter-operator and intra-assay concordance were all ≥90%, with short-term and long-term RNA stability also meeting minimum concordance requirements. Of the 2,446 orders received, 93.4% remained eligible for testing, with 96.8% of all tested samples that completed the assay demonstrating actionable class call results. Conclusion DecisionDx-SCC demonstrates a high degree of analytical precision, yielding high concordance rates across multiple performance experiments, along with exhibiting robust technical reliability on clinical samples.

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