Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity

Shrine, Nick; Tobin, Martin D.; Schurmann, Claudia; Soler Artigas, María; Hui, Jennie; Lehtimäki, Terho; Raitakari, Olli T.; Pennell, Craig E.; Ang, Qi Wei; Strachan, David P.; Homuth, Georg; Gläser, Sven; Felix, Stephan B.; Evans, David M.; Henderson, John; Granell, Raquel; Palmer, Lyle J.; Huffman, Jennifer; Hayward, Caroline; Scotland, Generation; Malarstig, Anders; Musk, Bill; James, Alan L.; Wain, Louise V.

doi:10.1186/s12863-016-0423-0

Table 3 CNV association with lung function with P < 0.001 for meta-analysis of 3 adult cohorts with follow up of tag SNPs in replication cohorts

From: Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity

	CNVR	CNV results					Replication^c
		Meta analysis of BHS, B58C & SHIP					Best tag SNP		SpiroMeta & CHARGE		UK BiLEVE		UK Biobank		Meta-analysis^d
		N	Beta L (SE)	Effect^b	P	Genes	SNP	r²	Beta (SE)	P	Beta (SE)	P	Beta (SE)	P	Beta (SE)	Effect^e	P
FEV₁	CNVR1073.1 (2q32.1) 640 bp deletion (2 class)	5560	-0.0467 (0.0135)	--.	5.55×10^-4	Upstream DNAJC10	rs2696127	0.766	-0.0069 (0.008)	0.38	-0.0073 (0.007)		-0.0061 (0.007)	0.37	0.0068 (0.004)	----	0.11
	CNVR217.1^a (1p31.1) 45.7kbp multiallelic (3 class)	7258	0.0268 (0.0078)	+++	5.55×10^-4	Upstream NEGR1	rs2568958	1	0.0084 (0.007)	0.24	0.0040 (0.007)	0.56	0.0072 (0.007)	0.27	-0.0065 (0.004)	++++	0.10
	CNVR4222.1^a (9p21.2) 4.01kbp deletion (2 class)	7284	-0.0868 (0.0263)	---	9.78×10^-4	Intronic LINGO2	rs10968307	0.980	0.0067 (0.031)	0.83	-0.0129 (0.026)	0.61	0.0084 (0.024)	0.73	0.0003 (0.015)	- + -+	0.99
FVC	CNVR4742.1 (10q21.1) 1.35kbp deletion (3 class)	5528	0.0599 (0.0174)	++.	5.65×10^-4	intergenic	rs1903969	0.995	0.0020 (0.005)	0.72	0.0082 (0.010)	0.40	0.0048 (0.009)	0.61		++++	0.32
	CNVR4222.1^a (9p21.2) 4.01kbp deletion (2 class)	7284	-0.1126 (0.0329)	---	6.30×10^-4	Intronic LINGO2	rs10968307	0.980	0.0342 (0.106)	0.75	-0.0150 (0.026)	0.56	-0.0126 (0.024)	0.60		- + --	0.65
	CNVR6854.1^a (16q24.2) 3.25kbp deletion (3 class)	7281	0.0389 (0.0116)	+++	7.72×10^-4	Downstream BANP	rs7501378	0.940	0.0111 (0.005)	0.017	0.0232 (0.008)	0.0037	-0.0021 (0.008)	0.79		+++-	0.0038
	CNVR7142.1^a (17q22) 2.62kbp deletion (3 class)	5519	-0.0454 (0.0136)	--.	8.20×10^-4	Downstream SCPEP1	rs880266	0.766	-0.0021 (0.006)	0.73	-0.0048 (0.008)	0.53	0.0108 (0.007)	0.14		---+	0.77
FEV₁ / FVC	CNVR94.3^a (1p36.13) 14.5kbp deletion (3 class)	4800	0.0061 (0.0016)	+.-	1.96×10^-4	Upstream CROCC	rs696095	0.263
	CNVR94.5 (1p36.13) 51.3kbp deletion (4 class)	3005	0.0045 (0.0012)	+..	2.08×10^-4	Exonic CROCC	rs696095	0.169
	CNVR94.4 (1p36.13) 106kbp multiallelic (4 class)	2951	0.0046 (0.0013)	+..	2.69×10^-4	Exonic CROCC	rs696095	0.169
	CNVR3585.1 (7q34) 560 bp multiallelic (4 class)	3082	-0.0052 (0.0014)	-..	2.89×10^-4	Intronic MGAM	rs62477625	0.644
	CNVR7927.1^a (20q13.33) 880 bp gain (3 class)	5548	0.0056 (0.0016)	++.	5.98×10^-4	upstream HAR1A; downstream HAR1B; downstream LOC63930	rs4809276	0.818	-0.0037 (0.010)	0.71	0.0083 (0.008)	0.30	0.0056 (0.008)	0.47	-0.0044 (0.005)	+-++	0.37

FEV ₁ Forced Expiratory Volume in 1 second, FVC Forced Vital Capacity (FVC). ^aCNVR class frequencies consistent with independent cohort (Additional file 1: Table S1). ^bEffect direction: BHS/B58C/SHIP (a dot signifies no result). r² correlation coefficient between CNVR copy number and SNP genotype in BHS. Replication was performed where there was a tag SNP with r² > 0.7. ^cLung function traits are rank inverse-normalised apart from FVC in SpiroMeta & CHARGE which is untransformed mL. ^dInverse-variance weighted meta-analysis for FEV₁ and FEV₁/FVC; Z-score meta-analysis for FVC. ^eEffect direction: CNVR/SpiroMeta & CHARGE/UK BiLEVE/UK Biobank. Gene annotations provided by ANNOVAR [30]

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ISSN: 2730-6844

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