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    Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.

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    Author
    Tong, L; Wu, P-Y; Phan, JH; Hassazadeh, HR; SEQC Consortium; Tong, W; Wang, MD
    Date
    2020-10-21
    Source Title
    Scientific Reports
    Publisher
    Springer Science and Business Media LLC
    University of Melbourne Author/s
    Shi, Wei; Liao, Yang
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Tong, L., Wu, P. -Y., Phan, J. H., Hassazadeh, H. R., SEQC Consortium, Tong, W. & Wang, M. D. (2020). Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.. Sci Rep, 10 (1), pp.17925-. https://doi.org/10.1038/s41598-020-74567-y.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/252951
    DOI
    10.1038/s41598-020-74567-y
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7578822
    Abstract
    To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline's performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.

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