Table 1.
Loci and Primers (With T7 Tags, Lower Cases) for Initial Technical Validation by MassArray
| ACGT Location | Forward Primer With T7 Balance (Top) Reverse Primer With T7 Tag (Bottom) |
|---|---|
| Chr4 145913471 | aggaagagagAGTTTTTATGTTTTTTGTAAGGTTATTTGA cagtaatacgactcactatagggagaaggctCCAAACTCCTAATCCCAATCTAAC |
| Chr7 147043670 | aggaagagagTTGGGGGTTTTTAATTAAGATAGTTT cagtaatacgactcactatagggagaaggctTTCCCTCTAATATATCCCATTTTACC |
| Chr12 62103733 | aggaagagagAGTATTAGGGTTAAGTATTGAATAAATTTA cagtaatacgactcactatagggagaaggctAATCAAAATAAAAAATCAAAAAAAA |
| Chr11 4347732 | aggaagagagTTTAGGTATATATTATTATATTTGATTTTT cagtaatacgactcactatagggagaaggctAATTACCACAAAACCTAACAC |
| Chr2 38354047 | aggaagagagAGAGTGGTATTTGTGTTAGAGAGGA cagtaatacgactcactatagggagaaggctTTCCAAAAAAAACCAAAAAAAA |
| Chr6 64724205 | aggaagagagTGTTTTTGTAATTTAGATAAGATTATTTTA cagtaatacgactcactatagggagaaggctAATCACATATCACTAACCAAACAATATC |
| Chr2 165155478 | aggaagagagGGGTGATAGGAAGTTGTAGAGATTAGA cagtaatacgactcactatagggagaaggctAAAAAAACACTACCCAAACTTAAATAACA |
| Chr11 3036940 | aggaagagagGGGTATTTGTTTAAGATATTTTTGATTTAT cagtaatacgactcactatagggagaaggctACAATAACCAAATAAAAAACACACCA |
| Chr12 101338922 | aggaagagagTGGTGTTTTAGTTGTTAAAATGTTATAGG cagtaatacgactcactatagggagaaggctCAAAAATATTCCCCAAATATCAAAA |
| Chr18 55862932 | aggaagagagTAGAAAAATAGGGAGAATGTGATATT cagtaatacgactcactatagggagaaggctATATCTAACTTCCCTACACCCACTAAAA |
| Chr1 25839243 | aggaagagagTTTTAGGATTGAATAAAATTTTAAGA cagtaatacgactcactatagggagaaggctATTTAATTTACTCATTCTCTCTATATAC |
Individual sites representing 0%, 25%, 50%, 75% or 100% methylation, that were consistent between the 2 assayed samples, were chosen for validation by Sequenom's MassArray to generate a standard by which to make calls on methylation levels. Primers were designed using MethPrimer and T7 tags were added as per the Sequenom guide.