Genotyping

MCIC support for genotyping includes:

  1. Illumina sequencing based methods for marker discovery, validation and genotyping in genome-wide association study (GWAS). Support includes
  2. Genotyping of microsatellites by fragment length analysis of fluorescent PCR products using the Benckman CEQ8800 capillary electrophoresis instrument

Fluidigm Access Array System
The Access Array System provides a platform for SNP and other sequence variation detection across hundreds of loci and samples. By using the Integrated Fluidic Circuits (IFCs) and controllers, up to 480 uniquely tagged amplicons per sample can be synthetized at once. Uniquely tagged amplicons from up to 384 samples are then pooled and sequenced simultaneously in a single sequencing run. These amplicon libraries are compatible for sequencing on all major next-generation sequencing platforms such as MiSeq (available at the MCIC), HiSeq, IonTorrent PGM, and PacBio SMRT.
The process involves:
    1. Design and acquisition of custom primer sets from
    2. FluidigmPreparation of amplicon libraries on the Fuidigm Array System
    3. Sequencing on the platform of your interest at the MCIC


Beckman CEQ capillary electrophoresis instrument
The CEQ8800 is an 8 capillary instrument for AFLP (Amplified restriction Fragment Length Polymorphic) fingerprinting. It has diode lasers that excite infrared dyes, and has four detection channels. For fragment analysis, alleles in each sample can be labeled with up to three separate dyes, the fourth dye is used for the size standard. Collected data are analyzed with the CEQ800 Fragment Analysis Software that estimates DNA fragment sizes and amounts and identifies alleles represented by specific DNA fragments.
   - Instructions for sample submission for CEQ8800 fragment analysis
   - Sample submission form for CEQ800
   - Submit sample for CEQ8800 frgment analysis