Table 3.
Genotyping methods used by the CHARGE cohorts
| Study | AGES | ARIC | CHS | FHS | RS |
|---|---|---|---|---|---|
| Array type | Illumina 370CNV | Affymetrix 6.0 | Illumina 370CNV | Affymetrix 500K and MIPS 50K combined | version 3 Illumina Infinium II HumanHap550 SNP chip array |
| Genotyping center | NIA Genetic Laboratory | Broad Institute | Cedars-Sinai Medical Center | Affymetrix Core Laboratory | Erasmus Medical Center |
| Genotype calling | Illumina BeadStudio | Birdseed | Illumina BeadStudio | BRLMM | Beadstudio v.3.1.14 |
| Exclusion on SNPs used for imputation | call rate < 97%, HWE p<1e-6, MAF <1%, Mishap p < 1e-9, A/T and G/C SNPs, Mismatches between Illumina, dbSNP and/or HapMap position | call rate <90% MAF < 1% pHWE < 10−6 |
call rate <= 97% HWE p< 10−5 2 replicate errors or Mendelian inconsistencies(for reference CEPH trios) heterozygote frequency =0, not in HapMap |
call rate < 97% HWE p<1e-6 Mishap p < 1e-9 Mendelian errors > 100 |
Call rate <90% No MAF/HWE filter |
| Exclusion on a per sample basis | Sex mismatch, Sample failure, Genotype mismatch with reference panel | call rate < 95%, sex mismatch, 1st degree relatives, genotype mismatch with reference panel, outliers based on IBS clustering or Eigenstrat | call rate < 95% sex mismatch sample failure | Call rate < 97%, subject heterozygosity > 5 SD away from the mean, large Mendelian error rate | call rate<97.5% sex mismatch, excess autosomal heterozygosity >0.336, outliers identified by the IBS clustering analysis |
| Imputation | MACH (version 1.0.16 | Mach1 v1.0.16 | BIMBAM10 v0.99 | MACH (version 1.0.15) | Mach 1.0 |
| Imputation Backbone (NCBI build) | Hapmap release 22 CEU(build 36) | July 2006, phased haplotypes, HapMap release 21 (build 35) | HapMap CEU using release 21A, build 36 | HapMap (release 22, build 36, CEU) | HapMap release 22 CEU(build 36) |
| Data handling and statistical tests | PLINK and R | PLINK, Mach2QTL | R | R packages kinship, gee, coxph | Plink, Probable, Mach2QTL, |
Abbreviations: AGES, Age, Gene/Environment Susceptibility (AGES)--Reykjavik Study; ARIC, The Atherosclerosis Risk in Communities Study; CHS, The Cardiovascular Health Study; FHS, The Framingham Heart Study; RS, the Rotterdam Study; MAF, minor allele frequency; HWE, Hardy-Weinberg equilibrium.