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

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

Description meSDC2 LTE-qMSP meSDC2-qMSP
SDC2
Primer sequencesa
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 probea 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 sequencesa 5′-GTAATGTTAGGAGTATTTTGTGGITA-3′
5′-AAAGATTCGGCGACCACCGACTAICCCAAA AAAACCCAATCCTA-3′
F: 5′-TGGTGATGGAGGAGGTTTAGTAAGT-3′
R: 5′-AACCAATAAAACCTACTCCTCCCTT AA-3′
COL2A1 probea 5′-Cy5-AGAAGAAGGGAGGGGTGTTAGGAGAGG-3′ 5′-TET-ACCACCACCCAACACACAATAACAAACA CA-3′
COL2A1 amplicon size 86 bp 133 bp
  1. Bold identical nucleotide sequences with meSDC2-qMSP assay, italics universal sequence, I inosine nucleotide, F and R indicate forward and reverse primers, respectively
  2. aCpG dinucleotide sites are underlined