The first set of SNP calls of four genomes of HapMap LCLs (3 samples from a CEU parents-child trio and 1 YRI sample) were released Dec., 2008 from the high coverage (>20×) pilot.
P-values and false discovery rates for these 18 miRNAs (17 CEU and 1 YRI) for genotype association are included in Additional file 6.
The population was indicated with numeric codes (CEU = 1, YRI = 2) in the group column of the phenodata, and the population codes (CEU and YRI) were entered in the description column in order to use them as sample labels in visualizations.
For example, if the CEU proportion in the final sample is 50% and under moderate population stratification (the prevalence of the disease was 1.25 fold higher in CEU than YRI), then the CEU cases should be 278, CEU controls should be 222, YRI cases should be 222, YRI controls should be 278.
Although the reported peak SNP, rs9379851, was not in strong LD against frequency-derived fmSNPs (r2 = 0.04, 0.21, 0.40 in YRI, CEU, and CHB/JPT populations, respectively), it was highly correlated with many other SNPs tagging the haplotype B4 within the 24 kb LD block (3%, 12%, 9% frequency in YRI, CEU, and CHB/JPT, respectively).
CPAs are calculated based on data from different populations, including 45 Han Chinese (CHB), 45 Japanese (JPT), 60 Africans (YRI), 60 Caucasians (CEU), 90 Asians (CHB+JPT), and 210 combined samples (CHB+JPT+YRI+CEU).
Of the 270 individuals examined in the project, we used 180 unrelated individuals (60 from YRI; 60 from CEU; 30 from CHB; 30 from JPT).
HapMap phase III CEU (1,403,896 SNPs and 180 individuals), YRI (1,484,416 SNPs and 180 individuals), and ASW (1,536,247 SNPs and 90 individuals) genotype data were obtained from the International HapMap Project http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2008-07_phaseIII/.
In larger dataset of HAPMAP (CEU n=226, YRI n=226), the estimated minor allele frequency of rs1801239 was 7.5% in CEU and 1.8% in YRI.
Except for haplotype phasing, our HapMap-related analyses included 45 CHB, 45 JPT, 59 CEU, and 60 YRI.
For the continental reference population, we used HapMap (build 23) genotypes including unrelated subjects only (i.e., 60 CEU, 59 YRI and 89 JPT+CHB).
