BCoR-L1 variation and breast cancer

Lose, Felicity; Arnold, Jeremy; Young, David B; Brown, Carolyn J; Mann, Graham J; Pupo, Gulietta M; Khanna, Kum Kum; Chenevix-Trench, Georgia; Spurdle, Amanda B

doi:10.1186/bcr1759

Breast Cancer Research

Table 1 BCOR-L1 polymerase chain reaction conditions

From: BCoR-L1 variation and breast cancer

Exon	PCR fragment	Forward primer	Reverse primer	PCR conditions	Annealing temperature^a (°C)	Size (bp)	DHPLC temperature (°C)
2	2	GGCTGGCTGCTTTAACATTC	CTCCCCAGGCCCTATTGTAT	2 U Taq, 40 pmol primers, 0.5 M betaine	54	425	62
3	3	AGGTGGTGTTGGCTCAAATC	CAACTCGACCAACCAGGTCT	40 pmol primers	54	404	62
4	4a	TGTGCATGCTATCCTGTCGT	GCTGGCAGAGGACTGAAGTT	40 pmol primers	54	450	62
4	4b	GAACTGGAGTCCCTGTGGAG	GAGGGTGGGGGTAGAAGGT	2 U Taq, 1 mM MgCl₂, 1 M betaine	54	578	63
4	4c	GTCCCCACTCCGGTTCTG	CAGGGAGCGTAAGAGTGGAG	Standard	54	442	63
4	4d	TGGTATATATCCCGCCTCCA	GTCCCTTCTGTTTGCTGCTC	40 pmol primers	54	436	57, 62
4	4e	CTTCCAACTCCACAGCCTCT	AATGGTGCTGATCAGTGCAG	2 mM MgCl₂, 0.5 M betaine	58	459	62
4	4f	CTCGCCCTTTGTCATCTTTC	GCTGGTAGGTTTCCCATTGA	2 mM MgCl₂	54	424	62
4	4g	GACAGCCAAGCACAGTGAAA	GCTGAGGGTCAAGAGGACAG	Standard	54	452	62
4	4h	CTCCTTCGTTCCAGAGCAGG	CCAGGACCAGCTCATGGGAC	Standard	59	314	61
4	4i	AGAGAGCCACCTCTGCTCTG	ACCCCTACGCTTTCCTGTTT	Standard	54	435	62
4	4j	AAGGTGGATGGTGATGTGGT	GAGGGGACAGCAGGTCATTA	Standard	54	457	62
5	5	GCAGCTCATGCCTCTAGGTC	ATCCTTGCTCGCTCACCTTA	Standard	54	446	62
6	6	GCAAAAGCGACCAAACTCTC	AATTCCCAACTCGACACCTG	2 U Taq	56	423	60
7	7	TCCTCTGTACATCCCATCCAC	GTAGAGATGCCCGAGGGTTC	2 mM MgCl₂	63	483	62
8	8	AGGCGTTGCTTTTCTGTGTT	CGCCACACACACCTTCTACA	2 mM MgCl₂	57	332	60
9	9	ATGACCCTGGTGGATGGATA	GGTTCAAGCACCAGAAGAGC	Standard	62	378	61
10	10	TGGGCAACAGAGTGAGACTG	GCAGGCAAGGTCTTTTGAGT	Standard	54	488	62
11	11	CAGGTGGTTCCCTTGTCCTA	GAGCTGTTCAAGGTGGAAGG	Standard	54	399	61
12	12	CTTCTCCCAATTCCCTTAGCC	AAAGCCAGGGAGAAGAAAGG	0.5 M betaine	54	454	60
13	13	CCCCTATATGCTCCCCTTACA	TTGCCAGGTCTTCACTTCCT	Standard	54	273	60
14	14	TTCCTCCAGCCTCCTTCAAT	CCCGGGACCTCTTGTCCT	40 pmol primers	54	595	62

^a'Touchdown' polymerase chain reaction (PCR) amplification conditions were as follows: denaturation at 94°C for 10 minutes, followed by two cycles of 94°C for 30 seconds, 30 seconds at the fragment annealing temperature (T_A) + 6°C, and 72°C for 30 seconds. The conditions remained the same for the rest of the PCR except for the T_A, which consisted of two cycles at (T_A + 4°C), then two cycles at (T_A + 2°C), and (finally) 35 cycles at the T_A. A final extension step was conducted at 72°C for 7 minutes. bp, base pairs; DHPLC, denaturing high-performance liquid chromatography.

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ISSN: 1465-542X

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