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RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer

View ORCID ProfileYang-Yang Feng, Avinash Ramu, Kelsy C. Cotto, Zachary L. Skidmore, Jason Kunisaki, Donald F. Conrad, Yiing Lin, William C. Chapman, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
doi: https://doi.org/10.1101/436634
Yang-Yang Feng
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Avinash Ramu
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Kelsy C. Cotto
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Zachary L. Skidmore
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Jason Kunisaki
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Donald F. Conrad
2Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Yiing Lin
3Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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William C. Chapman
3Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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Ravindra Uppaluri
4Department of Head and Neck Surgical Oncology, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, MA, USA.
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Ramaswamy Govindan
2Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
4Department of Head and Neck Surgical Oncology, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, MA, USA.
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Obi L. Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
4Department of Head and Neck Surgical Oncology, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, MA, USA.
5Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Malachi Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
4Department of Head and Neck Surgical Oncology, Dana-Farber Cancer Institute and Brigham & Women’s Hospital, Boston, MA, USA.
5Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Abstract

Abstract The interpretation of variants in cancer is frequently focused on direct protein coding alterations. However, this analysis strategy excludes somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences. Here we present RegTools (www.regtools.org), a free, open-source software package designed to integrate analysis of somatic variant calls from genomic data with splice junctions extracted from transcriptomic data in order to efficiently identify variants that may cause aberrant splicing in tumors.

Contributions Y.-Y.F. was involved in all aspects of this study, including designing methodology, developing and testing the tool software, analyzing and interpreting data, and writing the manuscript, with input from A.R., K.C.C, Z.L.S., J.K., D.F.C., O.L.G., and M.G. A.R. designed the tool and led software development efforts. Y.L., W.C.C., R.U., and R.G. provided unpublished tumor datasets and provided critical feedback on the manuscript. O.G. and M.G. supervised the study. All authors read and approved the final manuscript

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  • Competing Interests The authors declare no competing interests.

Copyright 
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 November 25, 2018.
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RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer
Yang-Yang Feng, Avinash Ramu, Kelsy C. Cotto, Zachary L. Skidmore, Jason Kunisaki, Donald F. Conrad, Yiing Lin, William C. Chapman, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
bioRxiv 436634; doi: https://doi.org/10.1101/436634
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RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer
Yang-Yang Feng, Avinash Ramu, Kelsy C. Cotto, Zachary L. Skidmore, Jason Kunisaki, Donald F. Conrad, Yiing Lin, William C. Chapman, Ravindra Uppaluri, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith
bioRxiv 436634; doi: https://doi.org/10.1101/436634

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