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    A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data

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    Author
    Barbosa-Morais, NL; Dunning, MJ; Samarajiwa, SA; Darot, JFJ; Ritchie, ME; Lynch, AG; Tavare, S
    Date
    2010-01-01
    Source Title
    Nucleic Acids Research
    Publisher
    OXFORD UNIV PRESS
    University of Melbourne Author/s
    Ritchie, Matthew
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Barbosa-Morais, N. L., Dunning, M. J., Samarajiwa, S. A., Darot, J. F. J., Ritchie, M. E., Lynch, A. G. & Tavare, S. (2010). A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. NUCLEIC ACIDS RESEARCH, 38 (3), https://doi.org/10.1093/nar/gkp942.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256883
    DOI
    10.1093/nar/gkp942
    Abstract
    Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also applicable to other platforms, with its output available through a Web interface and incorporated into Bioconductor packages. We have identified several problems with the design of individual probes and we show the benefits of probe re-annotation on the analysis of BeadArray gene expression data sets. We discuss the importance of aspects such as probe coverage of individual transcripts, alternative messenger RNA splicing, single-nucleotide polymorphisms, repeat sequences, RNA degradation biases and probes targeting genomic regions with no known transcription. We conclude that many of the Illumina probes have unreliable original annotation and that our re-annotation allows analyses to focus on the good quality probes, which form the majority, and also to expand the scope of biological information that can be extracted.

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