In the independent replication sample of obesity trios, we genotyped the two identified CNVR-tagging SNPs. For detailed analysis of the CNVR 11q11, this was additionally genotyped by qPCR in the family-based replication sample. For the CNVR-tagging SNPs, we applied the classical transmission disequilibrium test (TDT) (47). Replication analysis of the qPCR-typed CNVR 11q11 was performed by application of the CNV-FBAT on the derived copy number calls. Odds ratios (ORs) were calculated by applying the haplotype relative risk method (48), which uses the transmitted parental alleles as a case sample and the untransmitted parental alleles as a control sample.
