PLOS ONE Moelans & Holst et al. 2013 Optical Dataset S1

<strong>Moelans CB, Holst F, Hellwinkel O, Simon R, van Diest PJ (2013) ESR1Amplification in Breast Cancer by Optimized RNase FISH: Frequent but Low-Level and Heterogeneous. PLoS ONE 8(12): e84189. doi:10.1371/journal.pone.0084189</strong> <strong>Optical Dataset S1 (with RNase) of S1+2</strong> OD S2: http://dx.doi.org/10.6084/m9.figshare.864525 Description for Optical Dataset S1 and S2: Optical dataset illustrating FISH signal appearance containing full size <em>ESR1</em> FISH photos (not all of them representative) of a total of 35 breast cancer cases (Case#1-35) including 24 tumors with increased <em>ESR1</em> copy numbers by FISH (15 ESR1 amplified and 9 <em>ESR1</em> gained, Case#01-#24) and 11 tumors without <em>ESR1</em> copy number increase (Case#25-#35), selected out of a consecutive subset of 90 formalin fixed, paraffin embedded grade 3 breast cancers from the archives of the Department of Pathology in Hamburg that had been previously used in an <em>ESR1</em> FISH mapping study [1]. For all 24 cases with <em>ESR1</em> copy number increase different pictures (Fig.01-19) with (+RNase A: optical dataset S2; “OD2”) and without RNase A treatment (optical dataset S1; “OD1”) are available. FISH data are optical patterns visualized by imaging technology and translated by subjective interpretation into numerical information. Therefore, to support the confirmability especially in regard to reproducible interpretation of the optical FISH “raw data”, we thoroughly photo documented the analyzed cases. The pictures document by three color photographs the <em>ESR1</em> FISH appearance of nuclei with <em>ESR1</em> copy number increase and nuclei without <em>ESR1</em> copy number increase on 4µm full section FFPE tissue slides, showing <em>ESR1</em> signals (green), CEN6 signals (orange) and nuclei chromatin (blue) in 100´ or 63´ magnification. Pictures are subscribed “CNI” for observed gene “copy number increase” and “NO” for “normal” or “no copy number increase”. Gene loci with additional allelic copies (CNI) are marked exemplarily in some cases (white arrows and edges). Especially if nuclei with “CNI” occur in a pattern of mosaic heterogeneity intermingled with nuclei without “CNI” and appear sporadic distributed. Due to intensity variations and the three dimensional distribution of signals not all present gene copies can be shown. To illustrate the distribution of signals within the z-axis, some pictures are taken with two different z-layers (Z-Stack A-D). To illustrate the difference of cases/areas showing <em>ESR1</em> copy number increase (CNI) to cases/areas without <em>ESR1</em> copy number increase, pictures of the 11 cases and other sample areas with clearly normal copy number or “no copy number increase” (“NO”) are shown in addition. 1. Holst F, Stahl PR, Ruiz C, Hellwinkel O, Jehan Z, et al. (2007) Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Nat Genet 39: 655-660.