BMC Cancer

Table 2 CpG dinucleotides examined by methylation-specific polymerase chain reaction

From: The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers

					Primer position*		Intensity ratio†
Gene	Chromosome locus	CpG sites (kb)*	CpG ratio	GC%	U	M	U	U/M‡	M
CDH1	16q22	0	0.73	70	-78	-76	0.92	0.49/0.51	0.94
RABGEF1	7q11	-0.2	1.00	67	-285	-283	0.9	0.46/0.54	0.91
STAG1	3q22	-0.4	0.95	62	-493	-490	0.93	0.51/0.49	0.91
MYBPC2	19q13	-1.2	0.61	61	-1,226	-1,224	0.92	0.48/0.52	0.94
		-0.6	0.83	67	-742	-742	0.9	0.51/0.49	0.88
VDR	12q13	-0.7	0.71	58	-728	-727	0.92	0.51/0.49	0.92
		+0.1	0.84	63	+45	+45	0.95	0.51/0.49	0.94
ESR2	14q23	-0.9	0.66	59	-983	-986	0.85	0.48/0.52	0.91
MLH1	3p22	-1.0	0.43	49	-1,098	-1,098	0.93	0.51/0.49	0.95
		-0.6	0.85	63	-660	-655	0.94	0.48/0.52	0.93
FLJ43855	16p11	-1.1	0.62	55	-1147	-1147	0.89	0.48/0.52	0.90
PTEN	10q23	-1.4	0.66	62	-1,425	-1,425	0.93	0.52/0.48	0.91
		-0.9	0.86	62	-953	-953	0.94	0.51/0.49	0.93
CDKN2A	9p21	-1.5	0.77	65	-1,580	-1,575	0.9	0.47/0.53	0.93
		0	1.10	65	-85	-85	0.91	0.47/0.53	0.91
		+0.8	0.48	51	776	775	0.93	0.51/0.49	0.96
PAX5	9p13	-1.0	0.50	63	-1,056	-1,054	0.92	0.52/0.48	0.90
RUNX2	6p21	-3.8	0.25	36	-3,883	-3,883	0.9	0.48/0.52	0.93
		-3.0	0.71	55	-3,061	-3,061	0.91	0.49/0.51	0.92
		-0.7	0.81	62	-852	-850	0.93	0.52/0.48	0.92
		+1.6	0.63	53	1573	1573	0.92	0.47/0.53	0.94
RUNX3	1p36	-1.7	0.82	60	-1,790	-1,790	0.89	0.46/0.54	0.9
		-0.5	0.94	75	-559	-559	0.91	0.48/0.52	0.9
		-0.1	1.07	76	-219	-217	0.92	0.5/0.5	0.93
		+1.0	0.79	59	952	952	0.91	0.49/0.51	0.93
KIAA1752	16q12	+0.4	0.42	41	391	391	0.92	0.48/0.52	0.94
MUC8	12q24	+2.0	0.42	59	1,909	1,909	0.94	0.49/0.51	0.95
MAGEA2	Xq28	0	0.56	64	-81	-75	0.9	0.54/0.46	0.91
DDX53	Xq22.11	0	0.53	59	-71	-102	0.94	0.48/0.52	0.94
TFF2	21q22	-0.2	0.32	57	-251	-251	0.96	0.5/0.5	0.96
SERPINB5	18q21	-0.3	0.62	51	-315	-308	0.93	0.51/0.49	0.94
MSLN	16q13	-0.8	0.52	57	-827	-827	0.92	0.47/0.53	0.93

*The genomic position was calculated from the May 2004 human reference sequence.
†The relative proportion of unmethylation (U) and methylation (M) band intensity against the total band intensity.
‡U/M indicates a PCR mixture containing the same amount of the universal methylated and unmethylated DNA.

Back to article page

ISSN: 1471-2407

Contact us

Submission enquiries: bmccancer@biomedcentral.com
General enquiries: ORSupport@springernature.com