sj-pdf-1-aor-10.1177_00034894211037416 – Supplemental material for Phosphaturic Mesenchymal Tumors of the Sinonasal Area and Skull Base: Experience at a Single Institution

Supplemental material, sj-pdf-1-aor-10.1177_00034894211037416 for Phosphaturic Mesenchymal Tumors of the Sinonasal Area and Skull Base: Experience at a Single Institution by Davis P. Argersinger, Catherine T. Haring, John E. Hanks, Kevin J. Kovatch, S. Ahmed Ali, Jonathan B. McHugh, Melissa A. Pynnonen and Erin L. McKean in Annals of Otology, Rhinology & Laryngology</p

Supplemental Table 4 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Number of viral-cellular amplicons generated and sequenced from responsive and recurrent tumors.</p

Supplemental Figure 2 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Differential mRNA expression of genes with copy number alterations. The relative mRNA expression of amplified genes was assessed across the all publically available next generation sequencing data where matched genome or exome-sequencing and transcriptome sequencing were available using the Oncomine database. Three plots were generated for each gene with copy number alterations, the respective gene is indicated on top of the plot. RNA expression was not evaluable for TCGA-CN-A49A, which harbored a SMOC1 amplification. DNA copy number calculated from exome or whole genome sequencing data is shown along the x-axis and absolute fragments per kilobase million are shown along the y-axis (Values are presented as Log base 2). Samples within the plots have either do not have genomic alterations or have mutations, gene fusions or copy number alterations as indicated in the inset legend. Blue dashed line indicates the limit for calling genomic deletions and the pink line for genomic amplifications. The black line indicates best fit for correlation between DNA copy number and gene expression.</p

Supplemental Table 6 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Supplemental Table 6. Summary of genomic aberrations to identified genes with integrated HPV. The Oncomine database was used to assess genomic aberrations in all publicly available HNSCC next generation sequencing data sets including (1, 2) 1.Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Trevino L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011;333(6046):1154-7. doi: 10.1126/science.1206923. PubMed PMID: 21798897; PMCID: PMC3162986. 2.Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortes ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio RC, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareno C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR. The mutational landscape of head and neck squamous cell carcinoma. Science. 2011;333(6046):1157-60. doi: 10.1126/science.1208130. PubMed PMID: 21798893; PMCID: PMC3415217.</p

Supplemental Figure 1 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Supplemental Figure 1. Representative DIPS PCR and transcript analysis electrophoretic gel images. M=100 bp ladder. Panel A. Representative Responsive Tumor DIPS PCR Gels. Panel B. Representative Recurrent Tumor DIPS PCR Gels. Panel C. Gel Electrophoresis of Tumor Integration Transcript Analysis. Bold text= Viral/cellular fusion transcript, Italicized text=Transcript spans integration site</p

Supplemental Table 1 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

RT-PCR assay primer sequences and corresponding amplicon sizes.</p

Supplemental Table 3 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

DIPS primer sequences and predicted episome-only amplicon sizes.</p

Supplemental Table 2 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

TaqMan quantitative RT-PCR assay primer and probe sequences.</p

Supplemental Table 5 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Summary of Integration Transcription Analysis in HPV16-Positive Tumors. (F), (R) = Forward or Reverse viral orientation in relation to the cellular gene. Bold text= Viral/cellular fusion transcript, Italicized text=Transcript spans integration site, Grey shade= No transcript produced, a = Nonsense sequence, no alignment, b= Sequence was correct and spliced in frame, c= Sequence mapped to unexpected or rearranged sequences.</p