TABLE A5.

Univariable Associations Between Genomic Alterations and RFS

	RFS
		MSK (n = 101)				TCGA (n = 357)
Gene	N Alt, No. (%)	HR (95% CI)	P	q	N Alt, No. (%)	HR (95% CI)	P	q
CDKN2B.Del	13 (13)	1.89 (0.95 to 3.75)	.068	0.4	116 (32)	1.18 (0.88 to 1.58)	.3	0.7
CDKN2A.Del	13 (13)	1.89 (0.95 to 3.75)	.068	0.4	118 (33)	1.13 (0.84 to 1.51)	.4	0.7
CDKN1A	13(13)	1.96 (0.92 to 4.19)	.08	0.4	26 (7.3)	0.88 (0.49 to 1.58)	.7	0.9
ARID1A	24 (24)	1.62 (0.90 to 2.92)	.11	0.4	71 (20)	1.25 (0.89 to 1.75)	.2	0.7
KMT2D	16(16)	1.55 (0.80 to 2.99)	.2	0.4	74 (21)	0.97 (0.69 to 1.36)	.8	>0.9
KDM6A	28 (28)	1.44 (0.83 to 2.48)	.2	0.4	78 (22)	1.18 (0.85 to 1.64)	.3	0.7
TP53	63 (62)	1.3 (0.76 to 2.23)	.3	0.6	1 67 (47)	1.02 (0.77 to 1.35)	.9	>0.9
ELF3a	10 (14)	1.53 (0.62 to 3.76)	.4	0.6	23 (6.4)	1.31 (0.78 to 2.18)	.3	0.7
Unknown	27
KMT2C	10 (9.9)	0.73 (0.33 to 1.63)	.4	0.6	32 (9.0)	0.77 (0.45 to 1.33)	.4	0.7
CREBBP	12(12)	1.3 (0.66 to 2.57)	.4	0.6	29 (8.1)	0.98 (0.58 to 1.65)	>.9	>0.9
PIK3CA	13(13)	0.79 (0.34 to 1.85)	.6	0.8	70 (20)	0.78 (0.55 to 1.12)	.2	0.7
TERT	63 (62)	0.91 (0.54 to 1.52)	.7	0.8	-	-	-	-
RB1	20 (20)	0.89 (0.47 to 1.68)	.7	0.8	59 (17)	1.15 (0.79 to 1.67)	.5	0.7
STAG2	11 (11)	0.93 (0.40 to 2.17)	.9	0.9	38 (11)	0.53 (0.30 to 0.95)	.034	0.4

NOTE. Bold values are statistically significant.

NOTE. Only alterations with >10% alteration prevalence in the MSK chemotherapy-resistant cohort were evaluated. False discovery rate corrected for multiple testing. All alterations in table are mutations unless specified.

Abbreviations: HR, hazard ratio; MSK, Memorial Sloan Kettering; RFS, recurrence-free survival; TCGA, The Cancer Genome Atlas.

^aDel. N = 74.