Skip to main content

Table 1 Oligonucleotide primers used for the exon 3 large rearrangement and transcript analysis

From: An entire exon 3 germ-line rearrangement in the BRCA2 gene: pathogenic relevance of exon 3 deletion in breast cancer predisposition

BRCA2 Primers

Nucleotide sequence

Size of PCR products

PCR temperature

 

Breakpoint analysis

  

C2del3-F2

5'_CAAGATCACTTCATTGATTTGTGAG_3'

4572 bp

59°C

C2del3-R2

5'_CGCTATATTTCTGTGTGCCTTTAAT_3'

  
 

Transcript analysis

  

Fragment analysis

   

Exon 02-06

 

480 bp

56°C

Rc2-01-F2

5 '6FAM_GATCCAAAGAGAGGCCAAC_3'

  

Rc2-06-R

5'_CAAACTCCCACATACCACTGA_3'

  

Exon 02-10

 

1350 bp

56°C

Rc2-01-F2

5' 6FAM _GATCCAAAGAGAGGCCAAC_3'

  

Rc2-10R

5'_TGGTAGGCTAGAAATACGTGGC_3'

  

Pyrosequencing

Allelic expression of c.-26G > A

   

Ex1-2 F

TACTCCGGCCAAAAAAGAACTGCA

  

Ex2-Ex2/4 R

TATGTCTACTATTGGGAACATTCCTTCCTG

166 pb

55°C

Ex2-Ex3/4 R

ATTGGGAACATTCCTTCCTAAGTCTA

411 pb

55°C

Ex2 R

GATCCAATAGGCATTTTTACCTACGATATTCC

89 pb

55°C

Ex2 SEQ R

TACCTACGATATTCCTCCAATG

  

Competitive quantitative PCR

   

EX2 Cpcr F

TGAAATTTTTAAGACACGCTGCAACA

 

60°C

EX2/3 Cpcr R

AAACCAATTAAGACTTATTGGTCCTAAATCT

59 bp

60°C

EX2/4 Cpcr R

ACTATTGGGAACATTCCTTCCTGCT

47 bp

60°C

EX2 Cpcr SEQ F

TTAAGACACGCTGCAA