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path_3032_sm_supportinginforsuppl.doc108KSupporting Information: Supplementary methods: details of power calculation, immunohistochemistry, chromogenic/fluorescence in situ hybridization, MassARRAY Sequenom Oncocarta, Sanger sequencing and microarray comparative genomic hybridization (aCGH)
path_3032_sm_supportinginforFS1.tif522KSupporting Information: Figure S1. Work flow for classification of papillary carcinomas and exclusion of in situ papillary carcinomas and neuroendocrine carcinomas.
path_3032_sm_supportinginforFS2.tif3110KSupporting Information: Figure S2. Amplifications of CCND1 and at 7q11.23 in two encapsulated low-grade papillary carcinomas.
path_3032_sm_supportinginforFS3.tif1144KSupporting Information: Figure S3. Subgroup analysis of the prevalence of gene copy number aberrations found in papillary carcinomas and in grade- and ER-matched IDC-NSTs according to histological grade.
path_3032_sm_supportinginforFS4.tif1972KSupporting Information: Figure S4. Unsupervised hierarchical clustering analysis of low-grade and grade I papillary carcinomas and grade- and ER-matched IDC-NSTs.
path_3032_sm_supportinginforFS5.tif1378KSupporting Information: Figure S5. Hierarchical clustering analysis of encapsulated, solid and invasive papillary carcinomas.
path_3032_sm_supportinginforTS1.pdf86KSupporting Information: Table S1. Summary of the antibodies, clones, dilutions, antigen retrieval methods, scoring systems and cut-offs used for immunohistochemical analysis.
path_3032_sm_supportinginforTS2.pdf15KSupporting Information: Table S2. Primers used for Sanger sequencing.
path_3032_sm_supportinginforTS3.doc44KSupporting Information: Table S3. Histopathological features of 63 papillary carcinomas of the breast.
path_3032_sm_supportinginforTS4.pdf139KSupporting Information: Table S4. Copy number gains and losses found in > 10% of papillary carcinomas of the breast**.
path_3032_sm_supportinginforTS5.pdf58KSupporting Information: Table S5. Recurrent (in two or more cases) amplifications found in 49 papillary carcinomas of the breast**.
path_3032_sm_supportinginforTS6.pdf39KSupporting Information: Table S6. Summary of genomic regions differentially gained or lost between papillary carcinomas and grade- and ER- matched IDC-NSTs (multi-Fisher's exact test p < 0.05)**.
path_3032_sm_supportinginforTS7.pdf8KSupporting Information: Table S7. Oncocarta panel mutation profiling of 49 papillary carcinomas of the breast and results of mutation validation by Sanger sequencing.
path_3032_sm_supportinginforTS8.pdf12KSupporting Information: Table S8. Histopathological and immunohistochemical features of 39 encapsulated, nine solid and 12 invasive papillary carcinomas of the breast.
path_3032_sm_supportinginforTS9.pdf13KSupporting Information: Table S9. Summary of genomic regions differentially gained or lost between encapsulated, solid and invasive papillary carcinomas of the breast**.
path_3032_sm_supportinginforTS10.doc42KSupporting Information: Table S10. Differences in the proportions of specific immunophenotypic and genomic features between papillary carcinomas and grade- and ER-matched IDC-NSTs at 80% power and a two-sided α of 1%.

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