A genome-wide detection of copy number variations using SNP genotyping arrays in swine

BMC Genomics

Table 2 Results of quantitative real-time PCR analysis of the 12 confirmed CNVRs

CNVR_No.	Chr.	Start^a	End^a	Primer_ID	Positive samples				Negative samples				validated	Genes
					Frequency	Type	Number of samples	Confirmed samples	Confirmed rate	Number of sample	Confirmed samples	Confirmed rate
6	1	91513835	91584145	17-2	0.0148	gain	7	7	1.0000	5	0	0.0000	Yes	--
				17-8			7	0	--	5	0	--	No	--
11	1	160653704	160713406	4-1	0.0675	loss	32	32	1.0000	15	1	0.0667	Yes	--
				4-4			32	32	1.0000	15	1	0.0667	Yes	--
20	1	274307988	274570232	5-3	0.0274	loss	13	0	--	11	0	--	No	C5
				5-7			13	12	0.9200	11	2	0.18	Yes	TRAF1
22	1	276291234	276800847	3-1	0.0738	both	35	31	0.8857	11	1	0.0909	Yes	ORs
				3-5			35	35	1.0000	15	6	0.4000	Yes
161	14	52620825	52720705	6-3	0.0211	loss	10	10	1.0000	11	8	0.7273	Yes	--
				6-6			10	10	1.0000	11	8	0.7273	Yes	--
259	2	4834400	5424602	7-3	0.0759	both	18	16	0.8889	12	6	0.5000	Yes	EFEMP2
				7-5			36	31	0.8611	12	6	0.5000	Yes	DPF2
276	2	137644872	137915976	15-4	0.0928	gain	8	0	--	4	0	--	No	ORs
				15-5			38	26	0.6842	19	9	0.4737	Yes
				15-6			8	7	0.8750	4	1	0.2500	yes
285	3	87641425	87711895	16-2	0.0422	gain	20	18	0.9000	12	8	0.6666	Yes	--
				16-5			20	19	0.9500	18	10	0.5556	Yes	--
314	5	59744851	60461526	13-1	0.0084	loss	4	3	0.7500	12	0	0.0000	Yes	CD4
				13-5			4	3	0.7500	8	0	0.0000	Yes	GAPDH
325	6	37641317	38387857	8-2	0.0211	loss	10	10	1.0000	8	2	0.2500	Yes	FTL
				8-5			10	10	1.0000	8	2	0.2500	Yes	IRF3
344	7	29445530	29634684	9-4	0.0105	loss	5	0	--	7	0	--	No	-
				9-6			5	5	1.0000	16	10	0.6250	Yes	-
373	9	4203824	4364337	2-2	0.0928	loss	28	28	1.0000	17	4	0.2353	Yes	ORs
				2-7			29	29	1.0000	17	2	0.1176	Yes
Mean									0.9269			0.3182

^a The Sus scrofa assembly (9.0) (http://www.ensembl.org/Sus_scrofa/Info/Index) was used to indicate the position of the CNVRs.

ISSN: 1471-2164