Phased genotype calls on 379 European samples from 1000 Genomes were used as the reference set (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521) for imputation. The NTR samples were split into two unrelated sets. SNPs with call rate <95%, or HWE P<1E-09 were excluded. Imputation was performed using MACH. For each NTR set, MAF bins of [0.005, 0.1), [0.01,0.03), [0.03, 0.05), and [0.05,0.5] were defined, and within each bin an r2 threshold defined such that the average r2=0.8. The r2 thresholds were 0.55, 0.4, 0.3, and 0.3, respectively. The final SNP numbers were 8.4 million for each of the twin sets, with the intersection of 8.3 million used here.
