The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls

Table 2 Primers and product sizes for the detection of polymorphic HML-2 proviruses

Locus^a(synonym)	Forward (5’➔3’)	Reverse (5’➔3’)	Size (bp)^bsolo/pre	PredictedBsr1 Fragment size (bp)
1p31.1-I	AACTACGTGAAGAATGAAGA	AATAAAGCTGAGATAAGAGG	1239	1752
3q13.2-I	GCTCGGATTTCAACATCCAT	TCGTCCGACTTGTCCTCAATG	1821	1985
3q13.2-II	GCTCGGATTTCAACATCCAT	TATTGGTGACAGAGAGATGCAG	1847/879
6q14.1-I	TCGTCGACTTGTCCTCAATG	CTGCCAGTCTCAGGTGTTTG	1075	1758
6q14.1-II	CCCCTGCTTATTGATGCTCTACG	TGAGGCTGAATGTGTGGAGTCC	1526/556
7p22.1a-I	TACTGAACGATGCTGACGTTTGG	TTTGAACCATTATCACCCTA	1407	2067
7p22.1b-T	GTCTGCAGGTGTACCCAACAG	TTTGCCCCATTATCACCCTA	1216	1981
7p22.1-II	CCTCCTGGTTCAAGGGATTCTC	GCTTTCGGGACTTCAACATTGG	1387/419
8p23.1a-I	CTTGTGTTTTCATTACAATCTATT	TTCAGTCATTCTATCATTAAGATTC	1667	2513
8p23.1a-II	CAGTCTATAGATGTGGATGCCT	AGCACTGAATCCAAACTCATAT	1320/352
10p12.1-I	CCACCATCTGAGAAGTGTGATG	AATGGAGTCTCCYATGTCTACT	1342	1846
10p12.1-II	CCACCATCTGAGAAGTGTGATG	GGCAACAAAGGGTTCATATGAGAA	1508/540
11q22.1-I	CCATGCTCAGAAAGGAAACA	TAGCTTCTTCCGAGCACACA	1168	2076
11q22.1-II	CCATGCTCAGAAAGGAAACA	ACCATCTGTCCTTCCACCAG	1661/693
12q13.2-I	CGGAGAATTCCACCTTCAAA	CTCGAGCGTACCTTCACCCTAG	1377	2392
12q13.2-II	CGGAGAATTCCACCTTCAAA	TGCATTGTGGTCATCCATTT	1488/520
12q14.1-I	GGAAACCCTTCCAACATTCCA	CCCCATTATCACCCTAGCTTC	1299	1755
12q14.1-II	GGAAACCCTTCCAACATTCCA	TGAGGCTGAATGTGTGGAGTCC	1101/133
19p12b-I	TGCATGGGGAGATTCAGAACC	TCGGGATCTCTCGTCGACTTGTCC	1210	5287
19p12b-II	TGCATGGGGAGATTCAGAACC	CGTGTTAGCCAGGATGGTCT	310/1278

^a‘I’ specifies primers for the 5’LTR; ‘II’ specifies primers for either the solo LTR or empty site.
^bProduct sizes were estimated using in silico PCR (UCSC Genome Browser) of primer pairs. Product sizes for alleles for the 10p12.1, 12q13.2, and 19p12b proviruses were estimated manually by adding the distances to the distance to the nearest BsrI site in the host genome regions flanking each integration site and in the respective provirus for that site.

ISSN: 1742-4690