Feasibility of quantifying SDC2 methylation in stool DNA for early detection of colorectal cancer

Clinical Epigenetics

Table 2 Comparison of meSDC2 LTE-qMSP with meSDC2-qMSP

Description	meSDC2 LTE-qMSP	meSDC2-qMSP
SDC2 Primer sequences^a	5′-GT A G A A A T T A A T A A G T G A G A G G G C-3′ 5′-AAAGATTCGGCGACCACCGAACG A C T C A A A C T CG A A A A C T CG-3′	F: 5′-TAGAAATTAATAAGTGAGAGGGCGT-3′ R: 5′-GACTCAAACTCGAAAACTCGAA-3′
SDC2 probe^a	5′-FAM-TTCGGGGCGTAGTTGCGGGCGG-3′	5′-FAM-AGTAGGCGTAGGAGGAGGAAGCGA-3′
SDC2 amplicon size	124 bp	121 bp
Real time PCR reagents	AptaTaq DNA Master, 5X	Rotor-Gene Probe PCR Kit
Thermal cycling condition	LTE: 95 °C 5 min; 95 °C 15 s, 60 °C 1 min, 35 cycles; heating and cooling rates were 15 and 20 °C/s. qMSP: 95 °C 5 min; 95 °C 15 s, 60 °C 1 min, 40 cycles; heating and cooling rates were 15 and 20 °C/s.	qMSP: 95 °C 5 min; 95 °C 10 s, 62 °C 15 s, 72 °C 20 s; 40 cycles; heating and cooling rates were 15 and 20 °C/s.
Control gene	COL2A1	ACTB
Primer sequences^a	5′-GTAATGTTAGGAGTATTTTGTGGITA-3′ 5′-AAAGATTCGGCGACCACCGACTAICCCAAA AAAACCCAATCCTA-3′	F: 5′-TGGTGATGGAGGAGGTTTAGTAAGT-3′ R: 5′-AACCAATAAAACCTACTCCTCCCTT AA-3′
COL2A1 probe^a	5′-Cy5-AGAAGAAGGGAGGGGTGTTAGGAGAGG-3′	5′-TET-ACCACCACCCAACACACAATAACAAACA CA-3′
COL2A1 amplicon size	86 bp	133 bp

Bold identical nucleotide sequences with meSDC2-qMSP assay, italics universal sequence, I inosine nucleotide, F and R indicate forward and reverse primers, respectively
^aCpG dinucleotide sites are underlined

ISSN: 1868-7083