Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

Table 1 PCR amplification conditions for the MS-HRM assays

Gene	MgCl₂ concentration (mmolL⁻¹)	Primer concentration (nmolL⁻¹)	Cycling time (sec)	Annealing temperature (°C)
APC	2.5	F - 200	10, 15, 20	58.5
APC	2.5	R - 300	10, 15, 20	58.5
BRCA1	4.0	F - 250	10, 10, 20	61.0
BRCA1	4.0	R - 250	10, 10, 20	61.0
CDH1	2.5	F - 200	10, 10, 20	63.5
CDH1	2.5	R - 200	10, 10, 20	63.5
CDH13	3.0	F - 300	10, 20, 25	58.0
CDH13	3.0	R - 400	10, 20, 25	58.0
CDKN2A (P16)	2.5	F - 300	10, 10, 20	70.0
CDKN2A (P16)	2.5	R - 200	10, 10, 20	70.0
GSTP1	2.5	F - 200	10, 10, 20	64.5
GSTP1	2.5	R - 200	10, 10, 20	64.5
MAL	2.5	F - 200	10, 10, 20	59.0
MAL	2.5	R - 200	10, 10, 20	59.0
MGMT	4.0	F - 250	10, 20, 20	60.0
MGMT	4.0	R - 250	10, 20, 20	60.0
MLH1	3.5	F - 200	10, 15, 20	59.0
MLH1	3.5	R - 300	10, 15, 20	59.0
TP73	3.0	F - 300	10, 15, 20	55.0
TP73	3.0	R - 200	10, 15, 20	55.0
RARβ	3.0	F - 200	10, 10, 20	66.0
RARβ	3.0	R - 300	10, 10, 20	66.0
RASSF1A	3.0	F - 300	15, 25, 20	65.0
RASSF1A	3.0	R - 200	15, 25, 20	65.0
TWIST1	2.5	F - 200	10, 10, 20	52.0
TWIST1	2.5	R - 300	10, 10, 20	52.0
WIF1	3.0	F - 400	10, 20, 25	53.0
WIF1	3.0	R - 400	10, 20, 25	53.0

ISSN: 1471-2407