An 8-Gene Signature for Classifying Major Subtypes of Non-Small-Cell Lung Cancer

Abstract

Motivation: The precise diagnosis of the major subtypes, lung adenocarcinoma and lung squamous cell carcinoma, of non-small-cell lung cancer is of practical importance as some treatments are subtype-specific. However, in some cases diagnosis via the commonly-used method, that is staining the specimen using immunohistochemical markers, may be challenging. Hence, having a computational method that complements the diagnosis is desirable. In this paper, we propose a gene signature for this purpose. Results: We developed an expression-based method that systematically suggests a huge set of candidate gene signatures and finds the best candidate. By applying this method to a training set, the optimal gene signature was found by considering close to 765 billion candidate signatures. The 8-gene signature found for classifying the 2 aforementioned subtypes comprises TP63, CALML3, KRT5, PKP1, TESC, SPINK1, C9orf152, and KRT7. The signature achieved a high overall prediction accuracy of 0.936 when tested using 34 independent gene expression datasets obtained using different technologies and comprising 2556 adenocarcinoma and 1630 squamous cell carcinoma samples. Additionally, the signature performed well in clinically challenging cases, that is poorly differentiated tumors and specimens obtained from biopsies. In comparison with 2 previously reported signatures, our signature performed better in terms of overall accuracy and especially accuracy of classifying lung squamous cell carcinoma. Conclusions: Our signature is easy to use and accurate regardless of the technology used to obtain the gene expression profiles. It performs well even in clinically challenging cases and thus can assist pathologists in diagnosis of the ambiguous cases.