Identification and validation of methylated PENK gene for early detection of bladder cancer using urine DNA

BMC Cancer

Table 2 Primer sequences for pyrosequencing and mePENK-qMSP

Pyrosequencing
Gene	Sequences (5′ → 3’)^a	Amplicon Size (bp)
CDX2	F: TGGTGTTTGTGTTATTATTAATAG R: Biotin-CACCTCCTTCCCACTAAACTA S: ATTAATAGAGTTTTGTAAATAT	129
CEI	F: TGGAAATGTAAGTAGTTTTAGTGTAT R: Biotin-AAATTTCTTAACCAAACTTCTCATAT S: TGTAAGTAGTTTTAGTGTATTAAAT	152
DMC1	F: GAGGGGGGTAAGTGGTAAAAA R: Biotin-TCCCTCAAAATCACTAAA ATTCCT S: GGGGTAAGTGGTAAAAA	165
IMP-1	F: GGATTTYGAAAYGTTATTATTTAATAG R: Biotin-AACTAAAAACRAAATATCCCAAT S: ATTTYGAAAYGTTATTATTTAATAG	126
PDE3A	F: TGGGAATTTAGTGAAGAG R: Biotin-CCACTATAAACCAACTTATCCCTAACT S: GGGTATTTTATATTATGGTAGTG	84
PENK	F: ATATTTTATTGTATGGGTTTTTTAATAG R: Biotin-ACAACCTCAACAAAAAATC S: GGGTGTTTTAGGTAGTT	322
SIM2	F: Biotin-GTGGATTTAGATTAGGATTTTGT R: CACCCTCCCCAAATTCTT S: CCTCCCCAAATTCTTC	205
VSX1	F: GGAGTGGGATTGAGGAGATTT R: Biotin-AGTAAGTTTATGGGAGGGGGATT S: TTTTTGAAATGTTGGTAAG	89
ZNF312	F: AAGAGGGATTTGGAGAGAGAA R: Biotin-TCTCAATACACCCAACCTACATAC S: GATTTGGAGAGAGAAGG	140
mePENK-qMSP
Gene	Sequences (5′ → 3’)^a	Concentration
COL2A1	F: GTAATGTTAGGAGTATTTTGTGGGTA R: CTACCCCAAAAAAACCCAATCCTA P: Cy5-AGAAGAAGGGAGGGGTGTTAGGAGAGG	0.2 µM 0.2 µM 0.1 µM
PENK	F: TCGGGTGTTTTAGGTAGTTTCGC R: ACGACTCAAATCGCCTCGCG P: Fam-TGGGGGCGATCGCGTTATTTCGG	0.2 µM 0.2 µM 0.1 µM

^a F, R, S, and P represent forward, reverse PCR primers, sequencing primers, and PCR probe, respectively. Biotin, Cy5 or Fam indicates 5’ biotinylation, 5’Cy5 conjugation, and 5’Fam conjugation, respectively

ISSN: 1471-2407