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path4209-sup-0001-FigureS1.tifTIFF image1184KCapture enrichment increases target coverage. RNA sequencing libraries were prepared from lung cancer samples and were subjected to capture enrichment with biotinylated RNA probes that target the human kinome. The percentage of reads mapped to the genes of interest was assessed in both the captured and uncaptured libraries. Libraries were generated from frozen material (FF) and from formalin-fixed tissue (FFPE). A. Read counts were plotted for each gene before or after capture. The total read count was normalized to 10 million reads. Genes included in the capture set are plotted in pink, all other genes are plotted in black. B. The average level of enrichment was calculated across 17 pairs. Values are plotted separately for FF and FFPE samples.
path4209-sup-0002-FigureS2.tifTIFF image2303KFGFR3 is highly expressed in a subset of SCCs. A. Three tissue microarrays were assembled to assess FGFR3 expression across a panel of NSCLCs. Representative samples are shown to demonstrate negative (at left) or positive (at right) staining. B. Of SCC samples, 10/136 were positive, whereas none of the 144 adenocarcinomas were positive. Two additional FGFR3–TACC3 fusion events were detected in samples that were positive by immunohistochemistry.
path4209-sup-0003-TableS1.pdfPDF document1048KNSCLC patient information. Clinical details are provided for the 95 primary NSCLC samples used in this study. The table includes clinical stage, smoking status (former, current or never), gender (M = male, F = female), and age of diagnosis (years).
path4209-sup-0004-TableS2.docWord document57KFusion transcript validation. High priority candidates were selected from the de novo assembly fusion detection method. Candidate fusions with more than 10 spanning pairs (read pairs with one read on either side of the fusion boundary) are listed, unless the fusion was also identified in an unrelated normal sample. The distance between the two genes is listed for intrachromosomal events (Gap, measured in kilo bases). Candidate fusions that were also detected with TopHat-Fusion are marked (Y = yes). Each fusion transcript was assessed to determine if the transcript would produce an in-frame fusion (Y = yes, N = no). PCR primers were designed to amplify candidate fusions from cDNA from the patients. Successful PCR of the fusion is noted in the table (PCR, Y = yes, NT = not tested) and we confirmed the fusion event by capillary sequencing of the PCR products (Seq, Y = yes). Structural variants involving RPS6KB1 have been described previously [30].
path4209-sup-0005-DatasetS1.txtplain text document31551KGene expression levels for kinome-captured NSCLC samples. SD1: ENSEMBL transcript counts for each lung sample.
path4209-sup-0006-DatasetS2.csvExcel spreadsheet907KSNV detection for kinome-captured NSCLC samples. SD2: Variant calls for all lung samples, provided in VCF format.
path4209-sup-0007-DatasetS3.csvExcel spreadsheet7KFusion prediction de novo assembly. SD3: All fusions predicted using de novo assembly.

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