Validation of the lung subtyping panel in multiple fresh-frozen and formalin-fixed, paraffin-embedded lung tumor gene expression data sets

Hawazin Faruki*, Gregory M. Mayhew, Cheng Fan, Matthew D. Wilkerson, Scott Parker, Lauren Kam-Morgan, Marcia Eisenberg, Bruce Horten, D. Neil Hayes, Charles M. Perou, Myla Lai-Goldman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Context. - A histologic classification of lung cancer subtypes is essential in guiding therapeutic management. Objective. - To complement morphology-based classification of lung tumors, a previously developed lung subtyping panel (LSP) of 57 genes was tested using multiple public fresh-frozen gene-expression data sets and a prospectively collected set of formalin-fixed, paraffin-embedded lung tumor samples. Design. - The LSP gene-expression signature was evaluated in multiple lung cancer gene-expression data sets totaling 2177 patients collected from 4 platforms: Illumina RNAseq (San Diego, California), Agilent (Santa Clara, California) and Affymetrix (Santa Clara) microarrays, and quantitative reverse transcription-polymerase chain reaction. Gene centroids were calculated for each of 3 genomic-defined subtypes: adenocarcinoma, squamous cell carcinoma, and neuroendocrine, the latter of which encompassed both small cell carcinoma and carcinoid. Classification by LSP into 3 subtypes was evaluated in both fresh-frozen and formalin-fixed, paraffin-embedded tumor samples, and agreement with the original morphology-based diagnosis was determined. Results. - The LSP-based classifications demonstrated overall agreement with the original clinical diagnosis ranging from 78% (251 of 322) to 91% (492 of 538 and 869 of 951) in the fresh-frozen public data sets and 84% (65 of 77) in the formalin-fixed, paraffin-embedded data set. The LSP performance was independent of tissue-preservation method and gene-expression platform. Secondary, blinded pathology review of formalin-fixed, paraffin-embedded samples demonstrated concordance of 82% (63 of 77) with the original morphology diagnosis. Conclusions. - The LSP gene-expression signature is a reproducible and objective method for classifying lung tumors and demonstrates good concordance with morphology-based classification across multiple data sets. The LSP panel can supplement morphologic assessment of lung cancers, particularly when classification by standard methods is challenging.

Original languageEnglish
Pages (from-to)536-542
Number of pages7
JournalArchives of Pathology and Laboratory Medicine
Issue number6
StatePublished - Jun 2016
Externally publishedYes


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