SNP using Sequenom

Service: Design multiplexed assays, automated PCR set up and automated, high throughput genotyping of Single Nucleotide Polymorphisms(SNPs) and Insertion/Deletions(Indels)

Platform: Sequenom MassARRAY Compact system

Application of service: Genotyping SNPs/Indels in a high throughput/multiplexed system


Technology and theory

The Sequenom MassARRAY Compact system uses Single base pair extension (SBE) and MALDI-TOF mass spectrometry for high throughput/low cost genotyping.

Mass differences are generated by SBE chemistry and the resultant products separated via mass spectrometry. Dependent on which of the 4 base pairs (ACGT) are added to an extend primer determines the final mass of the primer oligonucleotide. The small differences in mass generated from this addition (9-40 daltons) can easily be distinguished on the Compact.

Using iPLEX technology it is possible to multiplex up to 29 SNP assays, right from PCR through SAP clean, extension and mass spectrometry. Assay design software enables primers to be designed and plexes formed automatically and laboratory automation ensures a uniform high throughputGenotypes are called in real time and confidence scores assigned.

Sample throughput

90,000 genotypes per day can be generated (29plex x 384 samples x 8 chips per day).

Sample requirement

30ng of DNA@15ng/µL per plex.