Genome-wide rare copy number variation screening in ulcerative colitis identifies potential susceptibility loci

BMC Medical Genetics

Table 1 Summary of association statistics

Locus:	Deletion 13q32.1						Duplication 7p22.1						Duplication 8q24.3
Breakpoints:	chr13:94,781,525-94,797,285						chr7:5,786,323-5,905,210						chr8:140,390,975-140,524,875
Previously reported:	DGV(Variation_49277)						DGV(Variation_53516)
CNV size:	15.8 kb						119 kb						134 kb
Covered or close genes:	ABCC4, CLDN10						ZNF815, OCM, RNF216, RSPH10B						KCNK9
	cases		controls		P-value	OR	cases		controls		P-value	OR	cases		controls		P-value	OR
	wt	cc	wt	cc		(95 % CI)	wt	cc	wt	cc		(95 % CI)	wt	cc	wt	cc		(95 % CI)
Germany (discovery) Affy6.0	897	5	1563	1	0.027	8.71	899	3	1564	0	0.043	Inf	898	4	1564	0	0.018	Inf
						(0.97 - 411)						(0.72 - Inf)	0.45		0.00			(1.15-Inf)
Germany (replication) TaqMan	445	6	1272	2	0.005	8.56	453	0	1279	0	>0.05		452	1	1377	0	>0.05
						(1.52-87.2)
WTCCC2 (UK) Affy6.0	2391	5	4880	6	>0.05		2393	3	4886	0	0.061		2391	5	4884	2	0.058	3.40
																		(0.66 - 21.9)
Norwegian Affy6.0	251	1	272	0	0.36		252	0	272	0	>0.05		252	0	272	0	>0.05
Lithuanian TaqMan	442	2	1131	2	>0.05		438	0	1139	1	>0.05		445	0	1134	0	>0.05
in silico controls European-ancestry combined results	–	–	4501	5	----		–	–	5788	1	-----		–	–	6724	3	-----
	4426	19	13619	16	1.2 × 10 ⁻³	2.64	4435	6	14928	2	2.7 × 10 ⁻³	8.41	4438	10	15955	5	8.7 × 10 ^{- 4}	4.62
	0.43 %		0.11 %			(1.3–5.2)	0.13 %		0.01 %			(1.4–88)	0.22 %		0.03 %			(1.5–15)
Bonferroni corrected					3.6 × 10 ⁻³						8.1 × 10 ⁻³						2.6 × 10 ⁻³
MARV					4.3 × 10 ⁻³						6.2 × 10 ⁻³						2.8 × 10 ⁻³

Frequencies are presented panel-wise and combined for the 3 relevant CNVs. P-values were calculated by two-sided Fisher’s exact tests for CNV carriership. Odds ratios (OR) with 95 % confidence intervals (95 % CI; inf = infinite) are listed when P-values are smaller than 0.05. cc refers to CNV carrier individuals and wt (wildtype) to non-carriers. To account for population structure and low frequencies, the M.A.R.V. analysis method [29] was applied to the overall study sample

ISSN: 1471-2350