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Genotyping

Genotyping is a rapid, cost-effective method for identifying regions of susceptibility to human diseases.

The Centre National de Recherche en Génomique Humaine (CNRGH) at the CEA (French Atomic Energy Commission) disposes of three platforms which can meet the needs of all types of genotyping projects :

- Illumina platform : Very high throughput platform that uses Infinium genotyping assay technology for whole genome studies, genome-wide association studies and also replication studies with a large number (several thousand) of variants

- Sequenom platform : Medium throughput platform that uses MALDI-TOF technology (Matrix-Assisted Laser Desorption/Ionisation Time of Flight) for medium throughput replication studies (several dozen variants)

- Applied Biosystems 7900-HT platform, which uses TaqMan labelling chemistry for genotyping of several variants in a large number of samples
The figure below depicts the Infinium whole-genome genotyping assay (the main genotyping application used at the CNRGH).

The aim of the first stages is to prepare the genomic DNA to make it compatible with the genotyping BeadChips to which a specific probe is attached for each of the variants to be studied.
The next stage consists of hybridisation and nucleotide extension to confer allelic specificity to each variant. The chips are then read on a scanner.
Genotyping is performed using the GenomeStudio software which determines the genotype for a given variant according to the contrast ratio of the colours detected.

Maximum output of our Illumina platform :
- using 12-DNA Chips : 2304 DNAs per week
- using 4-DNA Chips : 384 DNAs per week


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