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Analysis of Array Data and Clinical Validation of Array-Based Assays

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Book cover Microarrays in Diagnostics and Biomarker Development

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Abstract

High-throughput array-based assays have been widely used for diagnostics and biomarker discovery. However, the development of these assays requires analysis of high-dimensional genomic data and clinical validation of the resulting models, which remain challenging. In this chapter, we describe all the steps of array-based data analysis from data quality control and normalization to higher-level analyses such as clustering, dimensionality reduction, and predictive modeling, with special emphasis on the pitfalls and dangers of such analyses. We then tackle the problems related to clinical validation of array-based biomarkers and predictive assays, which include reproducibility and portability of the initial discovery and its translation into clinics. As array-based data, and those generated by the next-generation sequencing technologies, become less expensive to produce and more widely available, the growing number of patients for whom we have genomic data will open new opportunities for development of robust and reliable genomic biomarkers—provided we apply the lessons we have learned from this last decade of array-based studies.

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Notes

  1. 1.

    http://www.transcriptome.ens.fr/AffyGCQC/.

  2. 2.

    http://statistics.byu.edu/johnson/ComBat/.

  3. 3.

    Although it may be helpful to think of the hazard as the instantaneous probability of an event at time t, this quantity is not a probability and may be greater than 1. This is due to the division by Δt. Although the hazard has no upper bound, it cannot be smaller than 0.

  4. 4.

    http://www.r-project.org/.

  5. 5.

    http://www.latex-project.org/.

  6. 6.

    http://www.broadinstitute.org/cancer/software/genepattern/.

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Authors and Affiliations

  1. Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA

    Benjamin Haibe-Kains & John Quackenbush

  2. Biostatistics, Harvard School of Public Health, Boston, MA, USA

    Benjamin Haibe-Kains & John Quackenbush

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  1. CNRS, clos du Landenet 2, La Cadière d’Azur, France

    Bertrand Jordan

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Haibe-Kains, B., Quackenbush, J. (2012). Analysis of Array Data and Clinical Validation of Array-Based Assays. In: Jordan, B. (eds) Microarrays in Diagnostics and Biomarker Development. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28203-4_11

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