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Using SNPs to Characterize Genetic Effects in Clinical Trials

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Proceedings of the Fourth Seattle Symposium in Biostatistics: Clinical Trials

Part of the book series: Lecture Notes in Statistics ((LNSP,volume 1205))

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Abstract

Characterizing the genetic basis of responses in clinical trials has been made substantially easier and more powerful through the use of single nucleotide polymorphism data. A million of more of these markers can now be scored cheaply with commercial SNP-chips and ten million or more additional SNPs can be inferred by imputation. These rich datasets offer a deep look at the human genome and they are likely to tag many of the response causal genes. It has already become common for SNP types to be included in drug box labels.The ease and low cost of obtaining SNP profiles in clinical trials comes with the price of noisy data: it is common to have to reject data at 10% of the assayed SNPs. However, those SNPs that pass rigorous data cleaning protocols not only offer the chance of identifying the genes that affect response variables but also may reveal information about the genetic architectures of the trial participants and the populations to which they belong, as well as the relationships among the participants. Among novel applications of SNP profiles is the ability to determine HLA type without expensive sequencing.

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Acknowledgements

This work was supported in part by NIH grants GM 075091, HG 004464 and HG 005157.

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Authors and Affiliations

  1. Department of Biostatistics, University of Washington, 357232, Seattle, WA, 98915-7232, USA

    B. S. Weir

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  1. B. S. Weir
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Correspondence to B. S. Weir .

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Editors and Affiliations

  1. University of Washington, Department of Biostatistics, Seattle, 98195-7232, Washington, USA

    Thomas R. Fleming

  2. University of Washington, Department of Biostatistics, Seattle, 98195-7232, Washington, USA

    Bruce S. Weir

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Weir, B.S. (2013). Using SNPs to Characterize Genetic Effects in Clinical Trials. In: Fleming, T., Weir, B. (eds) Proceedings of the Fourth Seattle Symposium in Biostatistics: Clinical Trials. Lecture Notes in Statistics(), vol 1205. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5245-4_6

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