This article is part of the supplement: Genetic Analysis Workshop 16

Open Access Open Badges Proceedings

Single versus multiple imputation for genotypic data

Brooke L Fridley*, Shannon K McDonnell, Kari G Rabe, Rui Tang, Joanna M Biernacka, Jason P Sinnwell, David N Rider and Ellen L Goode

Author affiliations

Department of Health Sciences Research, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA

For all author emails, please log on.

Citation and License

BMC Proceedings 2009, 3(Suppl 7):S7  doi:

Published: 15 December 2009


Due to the growing need to combine data across multiple studies and to impute untyped markers based on a reference sample, several analytical tools for imputation and analysis of missing genotypes have been developed. Current imputation methods rely on single imputation, which ignores the variation in estimation due to imputation. An alternative to single imputation is multiple imputation. In this paper, we assess the variation in imputation by completing both single and multiple imputations of genotypic data using MACH, a commonly used hidden Markov model imputation method. Using data from the North American Rheumatoid Arthritis Consortium genome-wide study, the use of single and multiple imputation was assessed in four regions of chromosome 1 with varying levels of linkage disequilibrium and association signals. Two scenarios for missing genotypic data were assessed: imputation of untyped markers and combination of genotypic data from two studies. This limited study involving four regions indicates that, contrary to expectations, multiple imputations may not be necessary.