Table S3. Comparisons of significant gene alteration frequency differences of intra-groups of GEPNEC patients.

Gene	% (n/N)		OR (95% CI)	P
GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; OR, odds ratio; 95% CI, 95% confidence interval; ENEC, esophagus NEC; LNEC, lung NEC; GNEC, gastric NEC; DNEC, duodenum NEC; CRNEC, colorectal NEC; PNEC, pancreas NEC; BTNEC, bile tract NEC; Inf and −Inf, infinitive and −infinitive.
	ENEC vs. LNEC
TP53 (mutation)	100 (7/7)	56.1 (32/57)	0 (0−0.99)	0.036
SETD2 (mutation)	28.6 (2/7)	0 (0/57)	0 (0−0.60)	0.010
	GNEC vs. LNEC
TP53 (mutation)	87.5 (28/32)	56.1 (32/57)	0.18 (0.04−0.61)	0.002
RB1 (mutation)	28.1 (9/32)	49.1 (28/57)	2.55 (0.94−7.38)	0.033
NOTCH1 (mutation)	0 (0/32)	15.8 (9/57)	Inf (1.24−Inf)	0.024
TERT (amplification)	28.1 (9/32)	0 (0/57)	0 (0−0.24)	<0.001
IL7R (amplification)	21.9 (7/32)	0 (0/57)	0 (0−0.35)	<0.001
CCNE1 (amplification)	25.0 (8/32)	3.5 (2/57)	0.12 (0.01−0.64)	0.004
	DNEC vs. LNEC
TP53 (mutation)	100 (8/8)	56.1 (32/57)	0 (0−0.84)	0.019
KRAS (mutation)	37.5 (3/8)	3.5 (2/57)	0.07 (0.01−0.71)	0.011
IL7R (amplification)	25.0 (2/8)	0 (0/57)	0 (0−0.70)	0.013
TERT (amplification)	25.0 (2/8)	0 (0/57)	0 (0−0.70)	0.013
	CRNEC vs. LNEC
APC (mutation)	33.3 (6/18)	5.3 (3/57)	0.12 (0.02−0.63)	0.005
KRAS (mutation)	44.4 (8/18)	3.5 (2/57)	0.05 (0−0.29)	0.048
TP53 (mutation)	94.4 (17/18)	56.1 (32/57)	0.08 (0−0.56)	0.004
	PNEC vs. LNEC
RB1 (mutation)	16.7 (2/12)	49.1 (28/57)	0.21 (0.02−1.12)	0.039
KRAS (mutation)	25.0 (3/12)	3.5 (2/57)	9.02 (0.91−122.19)	0.031
	BTNEC vs. LNEC
ARID1A (mutation)	50.0 (4/8)	5.3 (3/57)	0.08 (0.01−0.79)	0.003
CTNNB1 (mutation)	37.5 (3/8)	3.5 (2/57)	0.05 (0−0.60)	0.011
TP53 (deletion)	25.0 (2/8)	0 (0/57)	0 (0−0.60)	0.013
FBXW7 (mutation)	37.5 (3/8)	1.8 (1/57)	0.03 (0−0.42)	0.005