Table 1. Significant hits in gene-based rare variant burden test for CLL.

Gene	p-value	FDR (q-value)	# of Cases with Rare Variants (%)	# of Controls with Rare Variants (%)	OR (95% CI)	Fisher OR (95% CI)
Discovery Cohort
CDK1	5.75 × 10-7	0.0091	8 (1.6%)	24 (0.3%)	5.8 (2.6 – 13.1)	5.83 (2.25-13.5)
ATM	1.43 × 10-6	0.011	112 (21.7%)	1296 (14.5%)	1.6 (1.3 – 2.0)	1.66 (1.34-2.06)
Extension Cohort*
CDK1	2.17 × 10-4	0.107	8 (1.2%)	26 (0.3%)	4.28 (1.93-9.51)	4.29 (1.67-9.8)
ATM	1.04 × 10-8	1.7 × 10-4	170 (26.3%)	1483 (16.6%)	1.79 (1.49-2.15)	1.79 (1.49-2.15)

^*Due to the inclusion of additional case samples, some variant allele frequencies were altered, leading to an increase in the number of variants that met allele frequency and quality control thresholds. This led to an increase in the number of controls with rare variants in the extension call set.