BRCA promoter methylation in sporadic versus BRCA germline mutation-related breast cancers

Breast Cancer Research

Table 2 Methylation probe characteristics of the methylation-specific multiplex ligation-dependent probe amplification assay (ME053 BRCA1-BRCA2 X1-0914; MRC-Holland)

Gene	Probe ID	Length	Chromosome position	5′ Probe	3′ Probe	Start	End	CpG site	CpG loci ID
BRCA1	BRCA1.1	165	17q21.31	CCTCTGAGAGGCTGCTGCTTAGCGGTAGCCCCTT	GGTTTCCGTGGCAACGGAAAAGCGCGGGAATTACAGA	41277415	41277483	41277429	cg04110421
BRCA1	BRCA1.2	230	17q21.31	CATGCATCTGAGAAACCCCACAGCCTGTCCCCCGTCCAGGAA	GTCTCAGCGAGCTCACGCCGCGCAGTCGCAGTTT	41277407	41321886	41277395	cg16630982
BRCA1	BRCA1.3	252	17q21.31	GTGGGGTTTCTCAGATAACTGGGCCCCTGC	GCTCAGGAGGCCTTCACCCTCTGCTCTGGGTAAAGGT	41277286	41277352	41277323	cg08993267
BRCA2	BRCA2.1	130	13q13.1	CCATCTTGTGGCGCGAGCTTCTGAAACTA	GGCGGCAGAGGCGGAGCCGCTGTGGCACTGCT	32889614	32889670	32889621	N/A
BRCA2	BRCA2.2	149	13q13.1	TGCGGGTTAGTGGTGGTGGTAGTGGGTT	GGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGG	32889801	32889865	32889836	N/A
BRCA2	BRCA2.3	160	13q13.1	CCTCTGAGAGGCTGCTGCTTAGCGGTAGCCCCTT	GGTTTCCGTGGCAACGGAAAAGCGCGGGAATTACAGA	32889665	32889746	32889672 + 32889683	N/A
BRCA2	BRCA2.4	217	13q13.1	CTTCCGGGTGGTGCGTGTGCTGCGTGTCGC	GTCACGGCGTCACGTGGCCAGCGCGGGCTTGT	32889557	32889618	2889608	N/A

N/A Not available
The chromosomal locations are based upon GRCh37/hg19. The first nucleotides of the 5′ probe may not be complementary to the target DNA, because it contains the stuffer sequence. The CpG loci ID are as determined by the Infinium HumanMethylation450 BeadChip Array (Illumina, San Diego, CA, USA)

ISSN: 1465-542X