Parallel FISH and Immunohistochemical Studies of ALK Status in 3244 Non–Small-Cell Lung Cancers Reveal Major Discordances Florian Cabillic, PharMD, PhD,

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Parallel FISH and Immunohistochemical Studies of ALK Status in 3244 Non–Small-Cell Lung Cancers Reveal Major Discordances Florian Cabillic, PharMD, PhD, Audrey Gros, PharMD, PhD, Frédéric Dugay, PharMD, Hugues Begueret, MD, PhD, Laura Mesturoux, MD, Dan Cristian Chiforeanu, MD, Leila Dufrenot, MD, Vincent Jauffret, Dominique Dachary, MD, Romain Corre, MD, Alexandra Lespagnol, PhD, Gwendoline Soler, MD, PhD, Julien Dagher, Véronique Catros, PharMD, PhD, Michèle Le Calve, PharMD, Jean- Philippe Merlio, MD, PhD, Marc-Antoine Belaud-Rotureau, PharMD, PhD Journal of Thoracic Oncology Volume 9, Issue 3, Pages 295-306 (March 2014) DOI: 10.1097/JTO.0000000000000072 Copyright © 2014 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 1 Illustration of discordant cases of ALK gene rearrangement and ALK protein overexpression. HE staining (A–E), IHC staining (F–J), and FISH patterns (K–O) of 4-μm–fixed, paraffin-embedded tissue sections of non–small-cell lung cancer. FISH analysis was performed with separating probes flanking the breakpoint of the ALK gene. IHC analysis was performed with an anti-ALK mouse monoclonal antibody (clone 5A4; Abcam). A, F, and K, A case exhibiting positive (2/3+) IHC staining (F) and a negative FISH result with adjacent orange/green or yellow fusion signals (K). B, G, and L, A case exhibiting negative IHC staining (G) and a rearranged-ALK gene with a BA pattern (L). C, H, and M, A case exhibiting negative IHC staining (H) and a rearranged-ALK gene with an IRS pattern (M). D, I, and N, A case exhibiting heterogeneity of ALK immunostaining with either low (1+) staining of most tumor cells or moderate staining (2+) of large polylobulated cells (I) and high polysomy with the presence of greater than six fusion signals (N). E, J, and O, A case exhibiting positive (2/3+) IHC staining (J) and high polysomy with the presence of greater than six fusion signals (O). IHC, immunohistochemistry; HE, hematoxylin-eosin; FISH, fluorescent in situ hybridization; BA, break-apart; IRS, isolated red signal; ALK, anaplastic lymphoma kinase. Journal of Thoracic Oncology 2014 9, 295-306DOI: (10.1097/JTO.0000000000000072) Copyright © 2014 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 3 Comparative FISH and IHC analyses. A, Histograms of the repartition of the IHC results (positive or negative) in the 116 FISH-positive cases and the repartition of the FISH results (positive, negative, and noncontributive) in the 114 IHC-positive cases. B, Histograms of the repartition of the IHC score (0, 1+, 2/3+) in the 116 FISH-positive cases. C, Histograms of the IHC results in the 116 FISH-positive cases. Rennes: 46 FISH-positive cases; Bordeaux: 70 FISH-positive cases. The values on the bars are the percentage of IHC-positive and IHC-negative results. FISH, fluorescent in situ hybridization; IHC, immunohistochemistry. Journal of Thoracic Oncology 2014 9, 295-306DOI: (10.1097/JTO.0000000000000072) Copyright © 2014 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 2 Percentage of positive nuclei in non–small-cell lung cancer harboring ALK rearrangements. Box-and-whisker plot of the percentage of positive nuclei in the FISH-positive samples. ALK locus rearrangement was considered positive if 15% or more nuclei exhibited BA or IRS patterns. The distribution is shown for all FISH-positive cases (n = 116), BA-positive cases (n = 77), and IRS-positive cases (n = 39). The line in the box represents the median, and the borders of the box represent the lower and upper quartiles of the data, respectively. The ends of the whiskers represent the minimum and maximum of all data. The threshold of 15% is depicted on the graph. FISH, fluorescent in situ hybridization; IRS, isolated red signal; BA, break-apart; ALK, anaplastic lymphoma kinase. Journal of Thoracic Oncology 2014 9, 295-306DOI: (10.1097/JTO.0000000000000072) Copyright © 2014 International Association for the Study of Lung Cancer Terms and Conditions