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Movassagh M, Alomran N, Mudvari P, Dede M, Dede C, Kowsari K, Restrepo P, Cauley E, Bahl S, Li M, Waterhouse W, Tsaneva-Atanasova K, Edwards N, Horvath A. RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data. Nucleic Acids Res 2016; 44:e161. [PMID: 27576531 PMCID: PMC5159535 DOI: 10.1093/nar/gkw757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022] Open
Abstract
We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting). We applied RNA2DNAlign on 360 matching normal and tumor exomes and transcriptomes from 90 breast cancer patients from TCGA. Under high-confidence settings, RNA2DNAlign identified 2038 distinct SNV sites associated with one of the aforementioned asymetries, the majority of which have not been linked to functionality before. The performance assessment shows very high specificity and sensitivity, due to the corroboration of signals across multiple matching datasets. RNA2DNAlign is freely available from http://github.com/HorvathLab/NGS as a self-contained binary package for 64-bit Linux systems.
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Affiliation(s)
- Mercedeh Movassagh
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.,University of Massachusetts Medical School, Graduate School of Biomedical Sciences, Program in Bioinformatics and Integrative Biology, Worcester, MA 01605, USA
| | - Nawaf Alomran
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - Prakriti Mudvari
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA
| | - Merve Dede
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA
| | - Cem Dede
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA
| | - Kamran Kowsari
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.,Department of Computer Science, School of Engineering and applied Science, The George Washington University, Washington, DC 20037, USA
| | - Paula Restrepo
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA
| | - Edmund Cauley
- Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA
| | - Sonali Bahl
- Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA
| | - Muzi Li
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - Wesley Waterhouse
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics, College of Engineering, Mathematics and Physical Sciences & EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, EX4 4QJ, UK
| | - Nathan Edwards
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - Anelia Horvath
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA .,Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA
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