Table 3.
Numbers of COJO signals from analyses of the UKB height summary data using different LD reference samples with and without DENTIST-based QC.
| LD reference (sample size) | No DENTIST & MAF > 0.01 | DENTIST & MAF > 0.01 | No DENTIST & MAF > 0.001 | DENTIST & MAF > 0.001 |
|---|---|---|---|---|
| Benchmark | 1279 | N/A | 1310 | N/A |
| UKBv3-20K (n = 20,000) | 1296 (1.3%) | 1288 (0.7%) | 1313 (0.2%) | 1324 (1.0%) |
| UKBv3-8K (n = 8000) | 1337 (4.5%) | 1326 (3.6%) | 1337 (2.0%) | 1325 (1.1%) |
| HRS (n = 8557) | 1477 (15.5%) | 1344 (5.0%) | 1555 (18.7%) | 1362 (3.9%) |
| ARIC (n = 7703) | 1485 (16.1%) | 1372 (7.2%) | 1645 (25.6%) | 1368 (4.4%) |
| UK10K-WGS (n = 3,642) | 1417 (10.8%) | 1419 (10.9%) | 1473 (12.4%) | 1422 (8.5%) |
Benchmark: COJO analysis using the discovery GWAS (UKBv3-329K) as the reference without DENTIST. The inflation rate relative to to the benchmark is shown in the parentheses.