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Laboratory

Production Platforms in Human Genomics (L2PGH)

Genotyping


Responsible :  Céline Besse
E-mail: bess​e[at]​cng.fr

Published on 2 December 2019

In April 2004, the CNRGH was one of the first sites to set up single-nucleotide polymorphism (SNP) analyses on a totally automated Illumina platform. The 'Beadlab' consists of a distinct PRE-PCR laboratory and POST-PCR laboratory with independent ventilation and air-conditioning systems. The Beadlab is currently equipped with 6 Tecan automated pipetting systems and 3 iScan systems +.

                             Pre PCR

Post PCR

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Scanner slide reading

Four technicians work in the 2 laboratories under the supervision of the platform manager. The stages of the 'Infinium Assay' protocol are totally tracked by a laboratory-information management system (LIMS) from the DNA plate through the automated stages to reading on the scanners. The data generated are verified by the quality control team contributing to the generation of very high quality phenotypes. The slide processing time is 3 days, including the hybridization stage which is conducted overnight. Several batches of 96 DNA samples are processed concomitantly each day. The current throughput is 1200 DNA samples per week, equivalent to the production of over 2,000,000,000 genotypes per week.​

Infinium Assay

The whole-genome analysis technology 'Infinium Assay' is based on hybridization of the DNA with magnetic beads placed on a slide and on the elongation of a single specific base complementary to the allele under study. At the CNG, we use 'high-density' slides (~250 K to 5 M markers):  Human Core, OmniExpress, Omni 2.5 and Omni 5.0. The preselected SNP throughout the whole genome are used for association studies and studies of copy number variability.​

Slide preparation

​Other chips enable more focused analysis of exon regions or the degree of methylation of CpG sites:  Human Exome, Human Core Exome, EPIC. We also implement Illumina iSelect panels which enable creation of our proper selection of SNP to be screened with the Infinium Assay protocol in order to study the genomes of bovines, porcines and plants, or for genetic analyses of cardiovascular diseases, Alzheimer's diseases, neoplastic diseases, etc.