We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy.
A mass spectrometry (MS) based multiplex genotyping method using solid phase capturable (SPC) dideoxynucleotides and single base extension (SBE), named the SPC SBE, has been developed for mutation detection.
SNP markers were typed on the RH panel with a 384 SNP multiplex genotyping assay using the GoldenGate Assay.
We have thus developed and validated a multiplex genotyping platform using the Bioplex suspension array for detecting a panel of ATP binding cassette (ABC) drug transporter polymorphisms.
The Bioplex 200 Luminex system (Bio-Rad, Hercules, CA, USA) was used for HPV detection and genotyping using multiplex bead-based hybridisation with Luminex technology as described by Schmitt et al (2006).
Assays that failed to multiplex were genotyped using TaqMan 5′ exonuclease (Applied Biosystems, Foster City, CA) and ABI PRISM 7900 Sequence Detector System.
Assays failing to multiplex were genotyped using the TaqMan 5' exonuclease [Applied Biosystems (ABI), Foster City, CA, USA] with primers from ABI using radioactive labeled probes detected with ABI PRISM 7900 Sequence Detector System [ 46].
Sequences were obtained from GenBank (accession no AF222861 and FJ788664 for porcine COL10A1 and MMP3, respectively) and assays were designed to permit genotyping using a multiplex SNP genotyping platform (Beckman Coulter).
Finally, due to the low amount (5 ng) of genomic DNA required for the 50-plex PCR (compared to 25 ng for each of the 7-reaction-multiplex PCRs), we have attempted APEX genotyping using our improved methodology on DNA derived from plasma samples.
For SNP and functional markers, multiplex genotyping was conducted using the SNPstream system (Beckman Coulter, California, USA).
