A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines

Table 1 Primer sequences, regions examined for methylation, and the methods used to detect methylation

Region	Method	Position	Size (bp)	Forward primer (5'-3')	Reverse primer (5'-3')	Pyrosequencing primer (5'-3')
1	COBRA Bisulphite sequencing	-966 to -733	233	AGTTTGGTTTYGGGYGATTTAT TTTGT	CCCAAAAAACACCTATCTAAATA AACT
2	Bisulphite pyrosequencing	-110 to +217	327	TTATGGTTGTAGTTTTYGAGAG GAGAGAAT	CTACAAAAACCRCAACAAATAC AACTACAAACTAA (round 1) CCCAAACAACTACACTAAACAT ACTCAA (nested)	GAGAGGAGAGAATTG
3	COBRA Bisulphite sequencing	-80 to +234	314	TTTAGTAGAGTTTGTGGTTTGG GGATTT	CAAACTTCCATCATAACTACAA CTTCC
4	qMSP	+237 to +368	132	AGTTGAGTCGTTGTGAGGCGA GGTCG	CAAACCGACCGACTCCCCGAAAACG
5	Bisulphite sequencing	+554 to +836	283	GTTGTAGTTTTAGGGAGGGGGT	CRCCRCTACCAAACCTCTAACTACTA
6	Bisulphite sequencing Bisulphite pyrosequencing	+801 to +971	171	GGTTTTTTTTGTAGGATGGAAA TGGT	CRCCRCTACCAAACCTCTAACTACTA	AAATGGTTTTGGATTT

Six regions of the PTEN CpG island were investigated for methylation in this study using various methods. Listed are the regions assayed, the method used for the detection of DNA methylation, the position of the region analysed relative to the transcription start site of the PTEN gene (NM_000314) located at Chr10:89613175 (NCBI36/hg18, March 2006 freeze), the size of each amplicon, and primer sequences (including pyrosequencing primer sequences)

ISSN: 1480-9222