These authors contributed equally to this work.
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing
Article first published online: 7 JUN 2013
© 2013 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
The Journal of Pathology
Volume 230, Issue 3, pages 270–276, July 2013
How to Cite
Majewski, I. J., Mittempergher, L., Davidson, N. M., Bosma, A., Willems, S. M., Horlings, H. M., de Rink, I., Greger, L., Hooijer, G. K., Peters, D., Nederlof, P. M., Hofland, I., de Jong, J., Wesseling, J., Kluin, R. J., Brugman, W., Kerkhoven, R., Nieboer, F., Roepman, P., Broeks, A., Muley, T. R., Jassem, J., Niklinski, J., van Zandwijk, N., Brazma, A., Oshlack, A., van den Heuvel, M. and Bernards, R. (2013), Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing. J. Pathol., 230: 270–276. doi: 10.1002/path.4209
Conflict of interest statement: RB, FN, and PR are employees of Agendia, a company that develops molecular diagnostic assays. This research was funded by independent research grants. The authors declare no conflicts of interest that impact on this study.
- Issue published online: 7 JUN 2013
- Article first published online: 7 JUN 2013
- Accepted manuscript online: 9 MAY 2013 10:40AM EST
- Manuscript Accepted: 6 MAY 2013
- Manuscript Received: 2 MAY 2013
- Manuscript Revised: 2 MAY 2013
|path4209-sup-0001-FigureS1.tif||TIFF image||1184K||Capture 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.tif||TIFF image||2303K||FGFR3 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.pdf||PDF document||1048K||NSCLC 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.doc||Word document||57K||Fusion 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 .|
|path4209-sup-0005-DatasetS1.txt||plain text document||31551K||Gene expression levels for kinome-captured NSCLC samples. SD1: ENSEMBL transcript counts for each lung sample.|
|path4209-sup-0006-DatasetS2.csv||Excel spreadsheet||907K||SNV detection for kinome-captured NSCLC samples. SD2: Variant calls for all lung samples, provided in VCF format.|
|path4209-sup-0007-DatasetS3.csv||Excel spreadsheet||7K||Fusion prediction de novo assembly. SD3: All fusions predicted using de novo assembly.|
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