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Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

Kjong-Van Lehmann, André Kahles, Cyriac Kandoth, William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Rätsch
doi: https://doi.org/10.1101/010256
Kjong-Van Lehmann
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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André Kahles
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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Cyriac Kandoth
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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William Lee
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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Nikolaus Schultz
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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Oliver Stegle
2European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, United Kingdom
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Gunnar Rätsch
1Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A
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Abstract

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing patterns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 19, 2014.
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Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma
Kjong-Van Lehmann, André Kahles, Cyriac Kandoth, William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Rätsch
bioRxiv 010256; doi: https://doi.org/10.1101/010256
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Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma
Kjong-Van Lehmann, André Kahles, Cyriac Kandoth, William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Rätsch
bioRxiv 010256; doi: https://doi.org/10.1101/010256

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