Skip to main content

Table 2 PCR and pyrosequencing primers and primer concentrations for each selected SNP before and after concentration adjustment

From: Multiplex pyrosequencing assay using AdvISER-MH-PYRO algorithm: a case for rapid and cost-effective genotyping analysis of prostate cancer risk-associated SNPs

SNP

Quadruplex (n=4)

Multiplex PCR

Multiplex PYRO

 

Quintuplex (n=5)

 

Conc.(μM)

 
  

Primer

Initial a

Adjusted a

Primer

Conc.(μM)

rs1016343

4

F: 5’-Biot-TCAGGGCAATTACGGAATAACA-3’

0.1

0.1

5’-TGAAGCTGTGAGTAATCA-3’

0.4

  

R: 5’-AATCTAAAGAATGGGGGTCAGAG-3’

0.1

0.1

  

rs10993994

4

F: 5’-CTCTCCTCCTCTGCTCTTTTAGGT-3’

0.1

0.1

5’-TTGTTATCATTCCCAA-3’

0.4

  

R: 5’- Biot- AGGCAAAGCTGCATCAAACT-3’

0.1

0.1

  

rs16901979

4

F: 5’-GTGGGGTCTTTGTTGTGGA-3’

0.1

0.1

5’-AATGATTTAGCATTACTTAT-3’

0.4

  

R: 5’-Biot-TTATGTTCAGAGCGGTTGAATG-3’

0.1

0.1

  

rs5945619

4

F: 5’-Biot-CAGGAAGGGGAACATCACACT-3’

0.1

0.05

5’-CTTGCGGGAGTCTCA-3’

0.4

  

R: 5’- ACGGCTACTATGAGATGAGGAAAC-3’

0.1

0.05

  

rs10896449

5

F: 5’-Biot-GGGCCACAGGGAACAA-3’

0.1

0.15

5’-TGACATTCCCCTTCTTA-3’

0.4

  

R: 5’-GCCTTTTCAATGAACCCACA-3’

0.1

0.15

  

rs1859962

5

F: 5’-AATAAGAGGCTGCAGACTTTTCC-3’

0.1

0.05

5’-AAATCCCTGCCCGTG-3’

0.4

  

R: 5’-Biot-TAGGCATTCCAAAGATGAAGACTC-3’

0.1

0.05

  

rs4242382

5

F: 5’-AAAAGAGGTAACCCAGGGAACA-3’

0.1

0.075

5’-TTGTCCCTCTAGTTATCTTC-3’

0.4

  

R: 5’-Biot-GCATAGAGGGACGCTGTCAA-3’

0.1

0.075

  

rs4430796

5

F: 5’-ACGTCCCTTCCTCAGCATCTT-3’

0.1

0.3

5’-GGCAGCACAGACTGGA-3’

0.4

  

R: 5’-Biot-TGTTCCTGACATGAAGCAACTCT-3’

0.1

0.3

  

rs6983267

5

F: 5’-Biot-TCTTCCTATCTCAGCTCCCTATCC-3’

0.1

0.1

5’-AATTCTTTGTACTTTTCTCA-3’

0.4

  

R: 5’-GTTGGCTGGCACTGTCTGT-3’

0.1

0.1

  
  1. aFor each SNP, the concentrations of PCR primers were adjusted in order to select the best conditions for balancing the respective contribution of each SNP in multiplex pyro-signals