Introduction

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.

Publications

  1. RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data.
    Cite this
    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, 2016-12-01 - Nucleic acids research

Credits

  1. Mercedeh Movassagh
    Developer

    University of Massachusetts Medical School, Graduate School of Biomedical Sciences, United States of America

  2. Nawaf Alomran
    Developer

    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, United States of America

  3. Prakriti Mudvari
    Developer

    McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, United States of America

  4. Merve Dede
    Developer

    McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, United States of America

  5. Cem Dede
    Developer

    McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, United States of America

  6. Kamran Kowsari
    Developer

    Department of Computer Science, School of Engineering and applied Science, United States of America

  7. Paula Restrepo
    Developer

    McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, United States of America

  8. Edmund Cauley
    Developer

    Department of Pharmacology and Physiology, The George Washington University, United States of America

  9. Sonali Bahl
    Developer

    Department of Pharmacology and Physiology, The George Washington University, United States of America

  10. Muzi Li
    Developer

    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, United States of America

  11. Wesley Waterhouse
    Developer

    McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine, United States of America

  12. Krasimira Tsaneva-Atanasova
    Developer

    Department of Mathematics, College of Engineering

  13. Nathan Edwards
    Developer

    Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, United States of America

  14. Anelia Horvath
    Investigator

    Department of Pharmacology and Physiology, The George Washington University, United States of America

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Summary
AccessionBT006525
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByAnelia Horvath