We used 108 estimated CEU haplotypes from the April 2009 release of the 1000 Genomes Pilot 1 data to carry out our fine-mapping experiments at the 15q25 locus (see the URL list for a link to the data source). We used these haplotypes to carry out imputation in the interval 76.4–77.0Mb on chr15 in 12 of the cohorts (GSK-Bipolar, GSK-Unipolar, GSK-COPD, KORA, POPGEN, Lausanne, GSKLolipop, GSK-GEMS, Medstar, SHIP, WTCCC-CAD and WTCCC-HT) using the program IMPUTE12. This release contains 2189 SNPs in this interval compared to 437 SNPs in release 22 of the HapMap data. Meta-analysis of the imputed data was then carried out in the same way as described above. An important technical detail when carrying out imputation using the 1000 Genomes haplotype data is how to align it with the genotype data from genome-wide studies. The program IMPUTE aligns SNPs between the haplotype and genotype data based on base-pair position (and not using SNP identifiers such as rs IDs) so as long as the same co-ordinate system is used for both the haplotype and genotype data the alignment is automatic.
