Most SNP assays for the fatSNP studies were genotyped in the Cardiff laboratory using the Sequenom iPlexGold system. Additional SNPs were genotyped in Cardiff using TaqMan (on demand) probes (Applied Biosystems; rs17584522) or Amplifluor AssayArchitect (Millipore; rs12476147) using an Analyst™ AD fluorometer (Molecular Devices). Additionally, rs17584522 was genotyped by the Dublin group with TaqMan (on demand) probes using a 7900HT Sequence Detection System (Applied Biosystems). For SNPs for which we could not design a reliable assay using either method, we genotyped the HapMap CEU sample using SNaPshot chemistry (Applied Biosystems) and a 3100 capillary sequencer (AppliedBiosystems). For rs5836928, a 3bp insertion deletion, we genotyped the HapMap CEU sample using fluorescently tagged primers with genotypes discriminated by size using a 3100 capillary sequencer (AppliedBiosystems).
