The importance of a large sample cohort for studies on modifier genes influencing disease severity in FAP patients

Talseth-Palmer, Bente A; Wijnen, Juul T; Andreassen, Eva K; Barker, Daniel; Jagmohan-Changur, Shantie; Tops, Carli M; Meldrum, Cliff; Spigelman, Allan; Hes, Frederik J; Van Wezel, Tom; Vasen, Hans FA; Scott, Rodney J

doi:10.1186/1897-4287-11-20

Hereditary Cancer in Clinical Practice

Table 1 Logistic regression and Kaplan-Meier analysis

From: The importance of a large sample cohort for studies on modifier genes influencing disease severity in FAP patients

Logistic regression model (n = 139)						Analysis endpoint - CRC			Analysis endpoint - Adenomas
*APT5A1* SNP: Genotype		Total n (%)	Cancer free (n)	CRC (n)	Adenomas (n)	OR (95% CI)	p-value	Kaplan-Meier analysis p-value*	OR (95% CI)	p-value	Kaplan-Meier analysis p-value*
rs13381709:	CC	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	CT	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	TT	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
rs1800636:	CC	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	CT	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	TT	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
rs1800637:	TT	58 (42)	50	8	44	1.0		0.5385	1.0		0.2362
	TC	56 (40)	46	10	41	1.36 (0.49-3.74)	0.553	0.5385	0.87 (0.37-2.02)	0.746	0.2362
	CC	25 (18)	23	2	14	0.54 (0.11-2.76)	0.462		0.40 (0.15-1.09)	0.074
rs1800639:	GG	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	GT	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	TT	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
	TT	57 (41)	49	8	44	1.0		0.3183	1.0		0.2561
	TC	57 (41)	46	11	42	1.52 (0.56-1.12)	0.406		0.95 (0.42-2.19)	0.913
	CC	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
	Failed genotyping	2 (1)
rs2298787:	TT	57 (41)	50	7	42	1.0		0.3208	1.0		0.4143
	TC	59 (42)	47	12	44	1.82 (0.66-5.03)	0.245	0.3208	1.05 (0.46-2.41)	0.913	0.4143
	CC	23 (17)	22	1	13	0.32 (0.04-2.80)	0.306		0.46 (0.17-1.28)	0.138
rs2578187:	GG	114 (82)	99	15	78	1.0		0.9719	1.0		0.5744
	GA	24 (17)	19	5	20	1.74 (0.56-5.35)	0.336	0.9719	2.31 (0.74-7.24)	0.152	0.5744
	AA	1 (1)	1	0	1	-	-		-	-
rs2578189:	CC	89 (64)	78	11	67	1.0		0.0014	1.0		0.3898
	CT	45 (32)	38	7	28	1.31 (0.47-3.64)	0.609	0.0014	0.54 (0.25-1.17)	0.118	0.3898
	TT	5 (4)	3	2	4	4.73 (0.71-31.52)	0.109		1.31 (0.14-12.38)	0.812
rs7244921:	TT	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	TC	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	CC	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
rs8088881:	TT	58 (42)	50	8	44	1.0		0.3179	1.0		0.2493
	TC	57 (41)	46	11	42	1.49 (0.55-4.04)	0.429		0.89 (0.38-2.07)	0.788
	CC	23 (17)	22	1	13	0.28 (0.03-2.41)	0.249		0.41 (0.15-1.15)	0.090
	Failed genotyping	1 (1)
rs8089150:	AA	57 (41)	50	7	42	1.0		0.3208	1.0		0.4143
	AG	59 (42)	47	12	44	0.82 (0.66-5.03)	0.245	0.3208	1.05 (0.46-2.41)	0.913	0.4143
	GG	23 (17)	22	1	13	0.32 (0.04-2.80)	0.306		0.46 (0.17-1.28)	0.138
rs8092674:	CC	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	CT	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	TT	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
rs8093880:	CC	57 (41)	49	8	43	1.0		0.3322	1.0		0.3575
	CT	55 (40)	45	10	42	1.36 (0.49-3.75)	0.551		1.05 (0.44-2.50)	0.909
	TT	23 (17)	22	1	13	0.28 (0.03-2.36)	0.241		0.42 (0.15-1.18)	0.099
	Failed genotyping	4 (3)
rs8094902:	TT	59 (42)	51	8	44	1.0		0.3183	1.0		0.2561
	TC	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3183	0.95 (0.42-2.19)	0.913	0.2561
	CC	23 (17)	22	1	13	0.29 (0.03-2.46)	0.256		0.44 (0.16-1.22)	0.115
rs8095031:	TT	59 (42)	51	8	44	1.0		0.3234	1.0		0.2221
	TC	57 (41)	46	11	42	1.52 (0.56-4.12)	0.406	0.3234	0.95 (0.42-2.19)	0.913	0.2221
	CC	22 (16)	22	1	12	0.30 (0.04-2.58)	0.275		0.41 (0.15-1.14)	0.087
	Failed genotyping	1 (1)
rs8095608:	AA	58 (42)	51	7	43	1.0		0.3183	1.0		0.3738
	AG	58 (42)	46	12	43	1.90 (0.68-5.24)	0.214		1.0 (0.44-2.30)	1.000
	GG	22 (16)	21	1	12	0.35 (0.04-2.99)	0.336		0.42 (0.15-1.17)	0.096
	Failed genotyping	1 (1)

*Log-Rank p-value.
Demographics of the genotype frequencies in Australian FAP patients with CRC, patients with adenomas and cancer/adenoma free individuals. Logistic regression model was used to test risk of CRC associated with each SNP, while Kaplan-Meier estimator analysis was used to test association between age of diagnosis of CRC/adenomas and genotype. Two different analysis was performed; one using CRC as endpoint of analysis and one using adenomas as endpoint of analysis.

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ISSN: 1897-4287

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