Table 2.

Gene-set level rare, deleterious variant (RDV) burden in the study cohorts.

	TCGA-dbGaP Cohort		BioMe Cohort
	Cases (6371)	Controls (6647)	Cases (1571)	Controls (6200)
	94 Cancer predisposition genes
# Variants	274	186	88	192
# Genes	57	48	35	51
# Unique individuals	464 (7.28%)	326 (4.90%)	136 (8.66%)	439 (7.08%)
OR (p-value) [95% CI]	1.51 (4.58e-08) [1.30–1.75]		1.24 (0.04) [1.01–1.51]
	95 DNA damage repair genes
# Variants	254	181	82	160
# Genes	41	36	29	35
# Unique individuals	374 (5.87%)	269 (4.05%)	108 (6.87%)	273 (4.40%)
OR (p-value) [95% CI]	1.50 (8.30e-07) [1.28–1.77]		1.59 (1.17e-04) [1.26–2.00]
	299 Somatic cancer driver genes
# Variants	231	154	88	169
# Genes	59	52	40	59
# Unique individuals	377 (5.92%)	272 (4.09%)	125 (7.96%)	294 (4.74%)
OR (p-value) [95% CI]	1.46 (4.04e-06) [1.24–1.72]		1.72 (2.00e-06) [1.38–2.14]
	22 Fanconi Anemia genes
# Variants	115	58	32	69
# Genes	15	13	8	13
# Unique individuals	163 (2.56%)	85 (1.28%)	52 (3.31%)	103 (1.66%)
OR (p-value) [95% CI]	2.05 (6.14e-08) [1.58–2.70]		2.01 (1.07e-04) [1.42–2.80]