Genotyping

The UMGC offers several different genotyping services. The choice of platform depends primarily on the number of SNPs to be genotyped, and secondarily on the number of samples.

Our Uniplex genotyping service is ideal for projects assaying a smaller number (1-6 SNPs). The service uses allele-specific Taqman genotyping primer-probe sets, purchased as pre-designed commercial assays from Applied Biosystems (ThermoFisher). One aliquot of primer-probe cocktail is generally adequate for genotyping several hundred samples.

For a project requiring the genotyping of a moderate number of SNPs (≈ 6-500), Agena’s iPLEX platform offers effective and reliable multiplexing (up to 36 SNPs in one reaction), thereby decreasing cost and DNA usage, and increasing throughput, compared with Taqman methods. The technology combines PCR, multiplexed single-base extension, and MALDI-TOF mass spectrometry.

When a project demands high-density or genome-wide coverage, Illumina’s Infinium Beadchips provide the answer. Capable of genotyping between 3072 and over 5 million SNPs, Illumina Infinium offer the most comprehensive analysis short of sequencing.

 
# of SNPs of interest Minimum # of samples* Best Platform
1-6 SNPs 96, 192 or 384 Uniplex
6-500 SNPs 96, 192, or 384 Agena Bioscience iPLEX
3072 SNPs 1,152 Illumina Infinium

*You can submit fewer than the minimum number of samples listed, but you will still be charged for the number of samples listed. The precise minimum for Uniplex and Agena iPLEX platforms is dependent on the number of SNPs in question. Please inquire for details.