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Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power

Author

Listed:
  • Matthews Abigail G

    (Rockefeller University)

  • Haynes Chad

    (Rockefeller University)

  • Liu Chang

    (Rockefeller University)

  • Ott Jurg

    (Rockefeller University and Beijing Institute of Genomics, Chinese Academy of Sciences)

Abstract

Genome-wide association studies are now widely used tools to identify genes and/or regions which may contribute to the development of various diseases. With case-control data a 2x3 contingency table can be constructed for each SNP to perform genotype-based tests of association. An increasingly common technique to increase the power to detect an association is to collapse each 2x3 table into a table assuming either a dominant or recessive mode of inheritance (2x2 table). We consider three different methods of determining which genetic model to choose and show that each of these methods of collapsing genotypes increases the type I error rate (i.e., the rate of false positives). However, one of these methods does lead to an increase in power compared with the usual genotype- and allele-based tests for most genetic models.

Suggested Citation

  • Matthews Abigail G & Haynes Chad & Liu Chang & Ott Jurg, 2008. "Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-17, July.
    • Handle: RePEc:bpj:sagmbi:v:7:y:2008:i:1:n:23
    DOI: 10.2202/1544-6115.1325
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