In this review, we will first attempt to provide the reader with an intuition for how genotype imputation approaches work and for their theoretical underpinnings. We will start with the relatively intuitive setting of imputing missing genotypes for a set of individuals using information on their close relatives. We will then proceed to examine how genotype imputation works when applied to more distantly related individuals. Next, we will survey results of studies that have used genotype imputation to study complex disease susceptibility. We will attempt to provide the reader with critical information to assess the merits of genotype imputation based analyses and to provide guidance to analysts attempting to implement these approaches. Finally, we will survey potential uses of imputation based analyses in the context of whole genome resequencing studies that we believe will soon become commonplace.
