Table 1.
Basic genotype information and phenotype characteristics of the study cohorts at stages I, II and IIIa
| Sample | N | Population | # Genotyped SNPs | # Imputed SNPs | Female (%) | Age (years) | LS-BMD (g/cm2) | HIP-BMD (g/cm2) | FN-BMD (g/cm2) | Bone densitometer |
|---|---|---|---|---|---|---|---|---|---|---|
| Stage Ib (GWA meta-analysis) | ||||||||||
| OOS | 987 | Caucasian | 407 634 | 6 427 198 | 49.6 | 50.3 (18.3) | 1.03 (0.16) | 0.97 (0.16) | 0.81 (0.14) | Hologic QDR 4500W |
| KCOS | 2250 | Caucasian | 743 768 | 7 085 256 | 75.9 | 51.4 (13.8) | 1.02 (0.16) | 0.97 (0.17) | 0.80 (0.15) | Hologic QDR 4500W |
| COS | 1547 | Han Chinese | 725 883 | 5 823 600 | 50.7 | 34.8 (13.4) | 0.95 (0.13) | 0.92 (0.13) | 0.81 (0.13) | Hologic QDR 4500W |
| FHS | 3747 | Caucasian | 405 948 | 6 456 277 | 57.3 | 60.3 (10.7) | 1.22 (0.23) | 0.95 (0.17) | 0.89 (0.16) | Lunar DPX-L |
| IFS | 1488 | Caucasian | 543 932 | 7 202 569 | 100.0 | 32.7 (7.2) | — | — | — | Lunar DPX-L |
| WHI-AA | 712 | African American | 799 328 | 11 862 114 | 100.0 | 60.9 (6.9) | 1.05 (0.17) | 0.95 (0.15) | 0.83 (0.14) | Hologic QDR-2000 |
| WHI-HIS | 409 | Hispanic | 647 362 | 6 916 926 | 100.0 | 60.7 (7.2) | 0.97 (0.16) | 0.86 (0.13) | 0.73 (0.12) | Hologic QDR-2000 |
| Total | 11 140 | |||||||||
| Stage IIc (in silico replication) | ||||||||||
| RS | 4904 | Caucasian | 512 349 | 6 986 425 | 57.0 | 69.4 (9.0) | 1.09 (0.18) | NA | 0.86 (0.13) | Lunar DPX-L |
| AOGC | 1955 | Caucasian | Region-wise | Region-wise | 100.0 | 69.6 (8.6) | 1.08 (0.26) | 0.89 (0.25) | 0.79 (0.21) | Multipled |
| Total | 6859 | |||||||||
| Stage III (de novo genotyping replication) | ||||||||||
| KCOSR | 3923 | Caucasian | 3 | 0 | 57.6 | 46.8 (14.5) | 1.03 (0.15) | 0.96 (0.15) | 0.80 (0.14) | Hologic QDR |
| COSR | 2740 | Han Chinese | 3 | 0 | 57.7 | 32.3 (14.4) | 0.93 (0.12) | 0.91 (0.13) | 0.80 (0.13) | Hologic QDR 4500W |
| Total | 6663 | |||||||||
aAdapted from Supplementary Material, Table S1 of Zhang et al. (34). Although the Korean Genome Epidemiology Study (KoGES) was included in stage 2 (in silico replication) of Zhang et al. (34), because none of KoGES results were included in the in silico replication of stage I-selected poly-miRTSs, the stage II (in silico replication) of the current study only included RS and AOGC, but not KoGES. Data were presented as mean (SD). N denotes sample size for each study cohort. OOS, Omaha Osteoporosis Study; KCOS, Kansas-City Osteoporosis Study; COS, China Osteoporosis Study; FHS, Framingham Heart Study; IFS, Indiana Fragility Study; WHI-AA, Women's Health Initiative African American ancestry; WHI-HIS, Women's Health Initiative Hispanic ancestry. RS, Rotterdam Study; AOGC, Australian Osteoporosis Genetics Consortium; KCOSR, KCOS Replication; COSR, COS Replication. SNP, single-nucleotide polymorphism; poly-miRTS, polymorphism in microRNA target sites; BMD, bone mineral density; LS, lumbar spine; HIP, total hip; FN, femoral neck. ‘—’, not available. λGC ranges from 0.99 to 1.06 (34).
bAs indicated in Zhang et al. (34), 5842 825 common SNPs (either genotyped or imputed) were shared across the seven stage I genome-wide association studies and only those 41 102 poly-miRTSs were included in stage I.
cAs indicated in Zhang et al. (34), for AOGC study, genotype imputations were only performed for specific regions, and only 11 stage I-selected poly-miRTSs were included in stage II of the current study.
dEither Hologic QDR or Lunar DPX-L series was used to measure BMD.