Allelic imbalance at the HER2/TOP2A locus in breast cancer

Diagnostic Pathology

Table 1 Panel of selected Single Nucleotide Polymorphisms (SNPs)

SNP nr	dbSNP-ID (rs)	SNP-ID (hCV)	Base (17q)	SNP	Minor allele frequency
SNP nr	dbSNP-ID (rs)	SNP-ID (hCV)	Base (17q)	SNP	CEU	CHB	JPT	YRI
1	7214151	30187206	34,761,298	C/T	0.38	0.04	0.45	0.46
2	7503195	437172	34,976,041	A/G	0.38	0.04	0.45	0.45
3	876493	7452397	35,078,071	G/A	0.36	0.23	0.43	0.43
4	4795408	30547514	35,361,153	A/G	0.47	0.43	0.47	0.39
5	4794822	31651885	35,410,238	T/C	0.42	0.38	0.39	0.39
6	868150	471861	35,466,885	A/G	0.42	0.34	0.44	0.45
7	2015561	7479296	35,846,755	G/A	0.46	0.44	0.42	0.00
8	4890114	27932396	35,857,075	T/C	0.46	0.44	0.42	0.00
9	8065040	11876205	36,073,767	A/G	0.37	0.43	0.43	0.36
10	10491123	29903401	36,086,722	A/G	0.37	0.44	0.44	0.47
11	7502428	29885409	36,133,740	C/T	0.47	0.44	0.43	0.41

SNP-ID (rs) = reference SNP ID number. SNP-ID (hCV) = Celera SNP ID. Base (17q) = the nucleotide position on chromosome 17(q). The HER2 gene is positioned at base 35,097,919-35,138,441, the TOP2A gene at 35,798,321-35,827,695 (SNP browser software Version 4.0, Applied Biosystems). SNP 1-6 were located up- and downstream of the HER2 gene within the HER2 smallest region of amplification [33]. The remaining 5 SNPs (7-11) were located up- and downstream of the TOP2A gene. The particular nucleotide variation is referenced in “SNP”-column. Minor allele frequencies are indicated for different populations: CEU, CEPH (Centre d'Etude du Polymorphisme Humain) from Utah; CHB, Chinese from Beijing; JPT, Japanse from Tokyo and YRI, Yoruba from Ibadan Nigeria

ISSN: 1746-1596