Multiplex Diagnosis of Oncogenic Fusion and MET Exon Skipping by Molecular Counting Using Formalin-Fixed Paraffin Embedded Lung Adenocarcinoma Tissues

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Multiplex Diagnosis of Oncogenic Fusion and MET Exon Skipping by Molecular Counting Using Formalin-Fixed Paraffin Embedded Lung Adenocarcinoma Tissues Kuniko Sunami, MD, Koh Furuta, MD, PhD, Koji Tsuta, MD, PhD, Shinji Sasada, MD, PhD, Takehiro Izumo, MD, PhD, Takashi Nakaoku, MD, Yoko Shimada, MFSc, Motonobu Saito, MD, PhD, Hiroshi Nokihara, MD, PhD, Shun-ichi Watanabe, MD, PhD, Yuichiro Ohe, MD, PhD, Takashi Kohno, PhD Journal of Thoracic Oncology Volume 11, Issue 2, Pages 203-212 (February 2016) DOI: 10.1016/j.jtho.2015.10.005 Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Figure 1 (A) Selection of study subjects. From 608 consecutive patients who underwent surgical resection of lung adenocarcinoma, we selected 41 who harbored oncogenic gene fusions or exon skipping. Patients were classified into two cohorts. Cases in which RNA isolated from snap-frozen tumor samples had been analyzed by whole transcriptome RNA sequencing were included in the test cohort (n = 22), whereas those in which RNA isolated from snap-frozen tumors samples had been analyzed by reverse transcription polymerase chain reaction were included in the validation cohort (n = 19). (B) Sample characteristics and molecular counting assay results. RNA was extracted from fresh frozen and/or formalin-fixed and paraffin-embedded tissues. Status was determined by counting the signals generated by fusion probes (F) or those generated by fusion and imbalance probes (FI). (Black box) Diagnosis based on counts generated by the fusion probe only. (Gray box) Diagnosis based on counts generated by the FI probes. (C) Strategy for diagnosing gene fusions and MET exon skipping. (Left) Twenty-six cases of gene fusion and one case of MET exon 14 skipping were diagnosed on the basis of counts generated by the fusion probes alone. (Right) Nine cases of gene fusion were diagnosed on the basis of counts generated by both FI probes. Journal of Thoracic Oncology 2016 11, 203-212DOI: (10.1016/j.jtho.2015.10.005) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Figure 2 Results for the validation cohort. The results for fresh frozen samples (A) and formalin-fixed and paraffin-embedded samples (B) are shown. (Upper) The reporter counts for the fusion probes are expressed as log2 (fusion probe counts/threshold counts). Values are shown when the counting results were greater than the threshold. (Lower) The results of 3′ overexpression are expressed as log2 ratios (3′/5′ probe count ratio divided by the 3′/5′ probe count threshold). Journal of Thoracic Oncology 2016 11, 203-212DOI: (10.1016/j.jtho.2015.10.005) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Figure 2 Results for the validation cohort. The results for fresh frozen samples (A) and formalin-fixed and paraffin-embedded samples (B) are shown. (Upper) The reporter counts for the fusion probes are expressed as log2 (fusion probe counts/threshold counts). Values are shown when the counting results were greater than the threshold. (Lower) The results of 3′ overexpression are expressed as log2 ratios (3′/5′ probe count ratio divided by the 3′/5′ probe count threshold). Journal of Thoracic Oncology 2016 11, 203-212DOI: (10.1016/j.jtho.2015.10.005) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Figure 3 Results for the nonsurgical samples. The results from the biopsy samples (A) and lavage samples (B) are shown. The reporter counts of the fusion probes are expressed as log2 ratios (fusion probe counts/threshold counts). Values are shown when the counting results were greater than the threshold. Journal of Thoracic Oncology 2016 11, 203-212DOI: (10.1016/j.jtho.2015.10.005) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions