The Genomics Platform is equipped with the Illumina and the Affymetrix systems.

Illumina BeadStation

The Platform is equipped with an Illumina iScan instrument coupled to the Autoloader2. Assays are robotized on Tecan Freedom EVO instruments to improve throughput and technical consistency. This complete benchtop solution for genetic analysis enables a wide range of sample throughput.


  • Genotyping (GWAS)

    Illumina proposes a range of BeadArrays with various numbers of SNPs interrogated, depending on the requirements of the projects. After whole genome amplification, Infinium assays are used: amplified DNA is hybridized onto arrays containing oligonucleotides with 3’ end positioned directly adjacent or overlapping the SNP site. SNP detection is performed by single base extension using dual colored assays (details in Illumina website). Infinium products comprise BeadArrays covering up to 4.3 million of SNPs and numerous CNVs. Custom or semi-custom arrays can also be designed.

  • Methylation analysis

    Illumina has developped a robust methylation profiling platform that provides quantitative methylation measurement at the single-CpG-site resolution. Thanks to the Infinium assays, up to 850’000 methylation sites can be analyzed at a time.

Protocol used and input material
Genotyping and methylation
  • For whole-genome genotyping arrays and methylation arrays, 10 µL of DNA (un-treated or bisulfite treated, respectively) at 50 ng/µL are required.
 Illumina iScan

 Illumina iScan
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Affymetrix GeneChip system

The Platform is equipped with two complete GeneChip instrument systems, each including a hybridization oven, two Fluidics 450 washing/staining stations, and a 7G scanner.

The Affymetrix technology is based on targets hybridization with oligonucleotides synthetized directly on arrays by photolithography. Arrays contain hundreds of thousands of oligonucleotide probes packed at extremely high densities.


  • Gene expression analysis

    For standard RNA-based applications (gene expression) including miRNA, Affymetrix proposes microarrays covering numerous species, including human, mouse, rat, as well as numerous widely used model organisms (details in Thermo Fisher Scientific website).

    Arrays contain probes covering multiple exons (Clariom S or Gene arrays) or every exon (Clariom D or Exon arrays) with the aim of increasing sensitivity and enabling to capture alternative splicing events. Some older designs contain probes designed toward the 3’ of the transcripts.

    New target preparation protocols enable RNA profiling on FFPE samples.

  • Constitutional cytogenetics

    For high resolution cytogenetic analysis, CytoScan arrays are available, providing high resolution and specificity for CNV, LOH, cnLOH and relevant mutations in cancer genes (details in Thermo Fisher Scientific website).

Protocol used and input material
Gene expression
  • For classical protocol, a minimum of 50 ng of total RNA is required.
  • For lower input (down to 0.5 ng), a pico-kit is used.
Affymetrix GeneChip instruments

 Affymetrix GeneChip instruments

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