Table 1.

DNA primer and probe sequences used in steps 1 + 2 of QM-MSP

	Primer		Primer		Amplimer
Gene	abbr.	Forward primer (5′ → 3′)	abbr.	Reverse primer (3′ a 5′)	size (bp)
APC	Ext:	AAA ACC CTA TAC CCC ACT AC	Ext:	GGT TGT ATT AAT ATA GTT ATA TGT	163
APC	FM:	AAT ACG AAC CAA AAC GCT CCC	RM:	TAT GTC GGT TAC GTG CGT TTA TAT	78
APC	FU:	TAA ATA CAA ACC AAA ACA CTC CC	RU:	GTT ATA TGT TGG TTA TGT GTG TTT	79
APC	MP:	CCC GTC GAA AAC CCG CCG ATT A	UP:	TTC CCA TCA AAA ACC CAC CAA TTA AC
BRCA1	Ext:	TAT TTT GAG AGG TTG TTG TTT AG	Ext:	AAA CAT CAC TTA AAC CCC CTA T	241
BRCA1	FM:	TTT CGT GGT AAC GGA AAA GCG	RM:	CCG TCC AAA AAA TCT CAA CGA A	86
BRCA1	FU:	TGG TAA TGG AAA AGT GTG GGA A	RU:	CCC ATC CAA AAA ATC TCA ACA AA	73
BRCA1	MP:	CTC ACG CCG CGC AAT CGC AAT TT	UP:	CTC ACA CCA CAC AAT CAC AAT TTT AAT
BRCA2	Ext:	GTT GGG ATG TTT GAT AA G GAA T	Ext:	ATC ACA AAT CTA TCC CCT CAC	262
BRCA2	FM:	TTT GAT TTT CGG GTG GTG CGT	RM:	TCA AAA ACT CGC GCC ACA AAC	82
BRCA2	FU:	ATT TTT GGG TGG TGT GTG TGT T	RU:	TCA AAA ACT CAC ACC ACA AAC C	78
BRCA2	MP:	AAC CAC GTA ACG CCG TAA CGC GA	UP:	AAC CAC ATA ACA CCA TAA CAC AAC AC
CDH1	Ext:	TAA TTT TAG GTT AGA GGG TTA T	Ext:	AAC TCA CAA ATA CTT TAC AAT TC	214
CDH1	FM:	AGG GTT ATC GCG TTT ATG CGA G	RM:	ACA ACC AAT CAA CAA CGC GAA C	82
CDH1	FU:	GAG GGT TAT TGT GTT TAT GTG AG	RU:	CAC AAC CAA TCA ACA ACA CAA AC	84
CDH1	MP:	CCC AAA ACG AAA CTA ACG ACC CGC	UP:	CTC CCC AAA ACA AAA CTA ACA ACC CAC
CyclinD2	Ext:	TAT TTT TTG TAA AGA TAG TTT TGA T	Ext:	TAC AAC TTT CTA AAA AAT AAC CC	286
CyclinD2	FM:	TTT GAT TTA AGG ATG CGT TAG AGT ACG	RM:	ACT TTC TCC CTA AAA ACC GAC TAC G	83
CyclinD2	FU:	TTA AGG ATG TGT TAG AGT ATG TG	RU:	AAA CTT TCT CCC TAA AAA CCA ACT ACA AT	78
CyclinD2	MP:	AAT CCG CCA ACA CGA TCG ACC CTA	UP:	AAT CCA CCA ACA CAA TCA ACC CTA AC
ERα	Ext:	TTG GAG GTT TGG GAG TTT AG	Ext:	ACA ATA AAA CCA TCC CAA ATA C	298
ERα	FM:	AGG GCG TTC GTT TTG GGA TTG	RM:	CGC CGA CAC GCG AAC TCT AA	82
ERα	FU:	TGG TGG AGG GTG TTT GTT TTG	RU:	ATC CCA CCA ACA CAC AAA CTC	93
ERα	MP:	CGA TAA AAC CGA ACA ACC CGA CGA	UP:	CCC AAT AAA ACC AAA CAA CCC AAC AA
HIN1	Ext:	GTT TGT TAA GAG GAA GTT TT	Ext:	CAC CGA AAC ATA CAA AAC AAA ACC AC	286
HIN1	FM:	TAG GGA AGG GGG TAC GGG TTT	RM:	CGC TCA CGA CCG TAC CCT AA	74
HIN1	FU:	AA G TTT TTG AGG TTT GGG TAG GGA	RU:	ACC AAC CTC ACC CAC ACT CCT A	123
HIN1	MP:	ACT TCC TAC TAC GAC CGA CGA ACC	UP:	CAA CTT CCT ACT ACA ACC AAC AAA CC
RARβ	Ext:	GTA GGA GGG TTT ATT TTT TGT T	Ext:	AAT TAC ATT TTC CAA ACT TAC TC	239
RARβ	FM:	AGA ACG CGA GCG ATT CGA GTA G	RM:	TAC AAA AAA CCT TCC GAA TAC GTT	82
RARβ	FU:	TTG AGA ATG TGA GTG ATT TGA GTA G	RU:	TTA CAA AAA ACC TTC CAA ATA CAT TC	83
RARβ	MP:	ATC CTA CCC CGA CGA TAC CCA AAC	UP:	AAA TCC TAC CCC AAC AAT ACC CAA AC
RASSF1A	Ext:	GTT TTA TAG TTT TTG TAT TTA GG	Ext:	AAC TCA ATA AAC TCA AAC TCC C	198
RASSF1A	FM:	GCG TTG AAG TCG GGG TTC	RM:	CCC GTA CTT CGC TAA CTT TAA ACG	74
RASSF1A	FU:	GGT GTT GAA GTT GGG GTT TG	RU:	CCC ATA CTT CAC TAA CTT TAA AC	75
RASSF1A	MP:	ACA AAC GCG AAC CGA ACG AAA CCA	UP:	CTA ACA AAC ACA AAC CAA ACA AAA CCA
TWIST	Ext:	GAG ATG AGA TAT TAT TTA TTG TG	Ext:	CCT CCC AAA CCA TTC AAA AAC	273
TWIST	FM:	GTT AGG GTT CGG GGG CGT TGT T	RM:	CCG TCG CCT TCC TCC GAC GAA	78
TWIST	FU:	GGT TTG GGG GTG TTG TTT GTA TG	RU:	CCC ACC TCC TAA CCA CCC TCC	104
TWIST	MP:	AAA CGA TTT CCT TCC CCG CCG AAA	UP:	AAA CAA TTT CCT TCC CCA CCA AAA CA

QM-MSP, quantitative multiplex-methylation specific PCR. Primer abbreviations: Ext, external methylation independent primers used in the first step of QM-MSP; FM, forward methylated primers; RM, reverse methylated primers; FU, forward unmethylated primers; MP, methylated probe sequence labeled with VIC fluorophore; UP, unmethylated probe sequence labeled with FAM fluorophore.