This approach can improve imputation accuracy in Scenario A, as we show in the Results section, but another major motivation of this work is to extend IMPUTE [6] to handle “next-generation” association datasets. By this, we refer to studies in the near future that will have access to additional reference data that could inform imputation. Next-generation reference panels will present new challenges for imputation, including larger sample sizes; unphased and incomplete genotypes; and multiple reference panels containing different SNP sets. Our method aims to use the principles outlined above to address these challenges and improve imputation accuracy in next-generation studies.
