Table 2.

Statistics of the top genes by using different methods and alternate allele frequency thresholds.

Cohorts and genes	Methoda	n1	n2	n3	n4	P value
AF ≤8e–5
CNS (n = 336) NF1	Jointly called full genotype	12	324	6	8169	1.77e–13
	CoCoRV using in-house controls	11	325	6	8169	3.09e–12
	CoCoRV using gnomAD as controls	11	325	262	125,486	2.82e–10
ALL (n = 958) ETV6	Jointly called full genotypes	6	952	0	8175	1.31e–06
	CoCoRV using in-house controls	7	951	1	8174	9.96e–07
	CoCoRV using gnomAD as controls	7	951	5	125,743	1.06e–12
AF ≤1e–3
CNS (n = 336) NF1	Jointly called full genotype	12	324	11	8164	1.08e–11
	CoCoRV using in-house controls	11	325	11	8164	1.48e–10
	CoCoRV using gnomAD as controls	11	325	289	125,459	7.60e–10
ALL (n = 958) ETV6	Jointly called full genotypes	6	952	0	8175	1.31e–06
	CoCoRV using in-house controls	7	951	1	8174	9.96e–07
	CoCoRV using gnomAD as controls	7	951	5	125,743	1.06e–12

AF alternate allele frequency, ALL acute lymphoblastic leukemia, CNS central nervous system.

^aThe CoCoRV results were calculated based on the FET.

n₁: number of cases with potential pathogenic alleles; n₂: number of cases without potential pathogenic alleles; n₃: number of controls with potential pathogenic alleles; n₄: number of controls without potential pathogenic alleles.