Table 2.

FPR and power of COJO before and after DENTIST-based QC in simulations.

Analysis method (LD reference)	FPR for common-causal (%)	FPR for rare-causal (%)	Power for common-causal (%)	Power for rare-causal (%)
Benchmark	0.1 ± 0.11	0.2 ± 0.16	78.8 ± 0.9	30.6 ± 1.4
COJO without DENTIST (UKB-8K-1KGP)	1.0 ± 0.50	2.7 ± 0.50	79.0 ± 0.9	30.6 ± 3.0
COJO with DENTIST (UKB-8K-1KGP)	0.2 ± 0.13	1.63 ± 0.43	80.0 ± 1.2	29.4 ± 1.6
COJO without DENTIST (HRS)	7.9 ± 1.37	28.4 ± 1.37	78.5 ± 1.2	27.6 ± 2.9
COJO with DENTIST (HRS)	0.5 ± 0.18	2.68 ± 0.55	78.8 ± 1.2	23.0 ± 1.6
COJO without DENTIST (ARIC)	7.1 ± 1.32	28.7 ± 1.38	77.6 ± 0.9	26.3 ± 2.9
COJO with DENTIST (ARIC)	0.4 ± 0.17	3.50 ± 0.63	76.8 ± 1.0	23.2 ± 1.6

Benchmark: COJO analysis using the discovery GWAS as the reference without DENTIST. Shown are mean ± standard error.