Table 2.

Methylation changes in NBL2 repeats in Wilms tumors and ovarian carcinomas relative to controls somatic controls as determined by hairpin sequencing or Southern blot analysis

	Summary of genomic sequencing resultsa		NBL2 methylation scores from SB with the indicated DNA digestsb				Global DNA methylationc
Sample	Hypermeth. (%)	Hypometh. (%)	Hha I	Ava I	Hpa II	Bst UI	%C methylated
Ovarian carc. D	22	50	−2	↓	↓	↓	3.31
Ovarian carc. E	33	47	−1	↓	↓	↓	2.94
Wilms tumor 9	33	26	+1	↓	↓	↓	3.09
Wilms tumor 4	50	30	+1	↓	↓	NC	2.88
Ovarian carc. N	63	11	+2	NC	↓	↑	3.76
Wilms tumor 67	78	9.3	+1	↓	↓	↓	3.45
Ovarian carc. O	81	9.3	+2	↓	↓	↑	3.73
Wilms tumor 21	86	4.9	+3	↑	↑	↑	3.90
Ovarian carc. Q	87	14	+3	NC	↓	↑	3.57
Wilms tumor 16	89	5.3	+3	↑	↑	↑	3.67
ICF B LCL	19	53	−3	↓	↓	ND	ND
Pat C LCL	63	12	+2	↓	NC	ND	ND

^aHypermethylation in NBL2 at the the normally unmethylated CpG6 and CpG14 was calculated as the overall percentage of these two sites with symmetrical methylation and hypomethylation, as the overall loss of symmetrical methylation at the normally methylated CpG2, 3, 5, 8, 10, 11, and 12.

^bHha I site methylation scores were from previous SB analyses with phosphorimager quantitation (12). Negative values, overall hypomethylation at Hha I sites; positive values, overall hypermethylation at these sites. For the other CpG methylation-sensitive enzymes, downward and upward arrows denote hypomethylation and hypermethylation, respectively. NC, no change in methylation relative to the somatic controls; ND, not determined.

^cGlobal genomic methylation levels determined by HPLC analysis of DNA digested to mononucleosides (11). Depending on the tissue, somatic controls have 3.43–4.04% of genomic C residues methylated.