Table 2.
Oligonucleotides for Amplification of Informative SNP Markers and Analytes Produced by MALDI-TOF MS Genotyping
| SNP Marker name | SNp position on AF354168 | Amplification primersa | PROBE primerb | Probe mass (m/z) | Amplicon length (bp) | Termination mixture | Analyte products | Analyte masses (m/z) |
|---|---|---|---|---|---|---|---|---|
| DLK1_406.1 | 47113 | cacctgcttgtcctctctcc | gaagccagagagcccgcg | 5543.7 | 328 | ddA/ddC | gaagccagagagcccgcga | 5840.9 |
| acttggtgcctcattcat | gaagccagagagcccgcggc | 6146.1 | ||||||
| DLK1_INTR1.1 | 54626 | cacagcacactgcctagctc | acaacaaacgtcaggccc | 5446.6 | 270 | ddC/ddG | acaacaaacgtcaggcccg | 5759.8 |
| cgccttacctatgagccttc | acaacaaacgtcaggccctc | 6024.0 | ||||||
| 9571-268.2 | 103894 | tggcaggagagacggttaat | gaaaggatctgacaggtgg | 5941.9 | 515 | ddA/ddC | gaaaggatctgacaggtggc | 6215.1 |
| gaaaacgtgaacccagaagc | gaaaggatctgacaggtggtc | 6519.3 | ||||||
| Meg3.1 | 139107 | aggagaacaaaggccacctc | cacgtagcaacccgctcg | 5429.6 | 229 | ddA/ddG | cacgtagcaacccgctcga | 5726.8 |
| ttcctttgtccctgtcaagc | cacgtagcaacccgctcgcg | 6032.0 | ||||||
| Meg3_enh2 | 151581 | gtgtagaagccgccattg | atgggatccccatgttga | 5514.6 | 355 | ddA/ddC | atgggatccccatgttgaa | 5811.9 |
| ggtgccccagagtgaaa | atgggatccccatgttgaga | 6141.1 | ||||||
| Meg3.13 | 157968 | ttgctaagcgtcccagtc | tgctcacccatccctccccac | 6183.1 | 539 | ddC/ddG | tgctcacccatccctccccacg | 6496.3 |
| acatctgaggctggtcactg | tgctcacccatccctccccacaag | 7122.7 | ||||||
| Meg3.12 | 158139 | ttgctaagcgtcccagtc | gaaagaggaggaattctgtg | 6270.1 | 539 | ddC/ddG | gaaagaggaggaattctgtgc | 6543.3 |
| acatctgaggctggtcactg | gaaagaggaggaattctgtgtg | 6887.6 | ||||||
| Meg3.10 | 158394 | ttgctaagcgtcccagtc | caatgaaaagcttgaag | 5251.5 | 539 | ddC/ddG | caatgaaaagcttgaagc | 5524.7 |
| acatctgaggctggtcactg | caatgaaaagcttgaagag | 5877.9 | ||||||
| Meg3.9 | 158520 | acacgtaagcatggcagatg | ggacacagaattcatctg | 5507.7 | 337 | ddA/ddT | ggacacagaattcatctga | 5804.9 |
| gcctcgaaaggcgaaaata | ggacacagaattcatctgca | 6094.1 | ||||||
| Meg3.8 | 158616 | acacgtaagcatggcagatg | ccctctgaatggtcatcc | 5410.6 | 337 | ddA/ddT | ccctctgaatggtcatcct | 5698.8 |
| gcctcgaaaggcgaaaata | ccctctgaatggtcatccct | 5988.0 | ||||||
| Meg3.7 | 158663 | acacgtaagcatggcagatg | gggtcagactccccaggccc | 6064.0 | 337 | ddA/ddT | gggtcagactccccaggccca | 6361.2 |
| gcctcgaaaggcgaaaata | gggtcagactccccaggcccgct | 6970.6 | ||||||
| Meg3.5 | 158998 | atggacaagcgataggtgct | atctcctatgtatcca | 4791.2 | 382 | ddA/ddC | atctcctatgtatccaa | 5088.4 |
| aaggactgtgggttttgtgc | atctcctatgtatccagc | 5393.6 |
a
Universal sequence (agcggataacaatttcacacagg) placed at 5′ end of the second locus specific primer listed.
b
PROBE primer is in sense direction relative to the first amplification primer.