Genetic Services Platform
Applications for pilot or collaborative projects to be run on the GSP should be made using the corresponding forms (see below for definitions of the 2 types of projects). The completed documents should be submitted to both Florence Le Calvez-Kelm () and James Mckay ().
Click to download the 'Pilot Project form' (accessible only from inside IARC).
Click to download the 'Collaborative Research Project form' (accessible only from inside IARC).
The feasability of the proposed projects will be discussed with GCS scientists. If the project is receivable, a meeting between GSP members and the project leader will be organized to define the objectives of the project, the number of samples to study, the techniques to use, the workplan, and others technical details related to the project.
GSP can undertake 2 types of projects:
Pilot projectsA pilot project is a small-scale validation project that is run on an existing available platform (Illumina, Taqman, LightScanner (HRM) or 96-capillary sequencer) to validate the quality of samples and/or to conduct preliminary analyses on new sets of genes, polymorphisms or customized Illumina kits (for example, this can include the set-up of laboratory conditions for the mutation screening of a new gene on 96 samples, or the test of 1 or 2 customized Illumina arrays on 96 or 24 samples, respectively, depending on the scale of the corresponding research project and the requested array format). Those validation projects are the preliminary steps required for any research project to be undertaken on the platform.
A pilot project can also consist in developing new applications on an existing platform (for example, the validation of the whole genome expression profiling process and the analysis of the raw data on the existing Illumina platform).
GSP can reasonably undertake 5-6 pilot projects a year using GSP dedicated funds. The level of pilot funding depends on the methods and applications but should not exceed 5,000 euros per project.
Collaborative research projectsA collaborative research project is a small-scale study for which GSP can provide expertise and technician support to an extent of 30 workable days per project. Availability of the GSP technician is likely to vary a bit depending on the demand. For large-scale projects requiring more technical support, collaborators should consider having a person from their group contributing to the laboratory work.
The design, the feasibility and the organisation of a project should be discussed with GSP members.
For any collaborative research project, collaborating groups will be responsible for the cost of consumables. Depending on the platform used, groups can be asked to contribute to the maintenance contract costs.
Groups should confirm IRB approval related to the collaborative research project has been obtained before any samples are processed by GSP.
GSP members involved in the collaborative research projects will expect to have the opportunity to contribute to writing and interpretation of scientific manuscripts and be co-authors in project-related publications.
Until now, GSP capacities enabled to undertake all proposed projects. If there is an increasing demand, GSP could propose 2-3 calls per year for pilot/collaborative projects. Project proposal would be then reviewed by scientists of the GEN section for approval.
The principal capabilities of GSP are:
1. Whole-exome sequencingPaired-end or Forward ECC SOLiD 5500XL Human whole exome sequencing from tumor DNAs (somatic analysis) or blood DNAs (germline analysis).
(Fragment Library Preparation 5500 Series SOLiD Systems, TargetSeq Exome Enrichment System with multiplexing of libraries prior to capture; 1.5ug to 3ug DNA required)
2. Targeted sequencingIon Torrent PGM targeted sequencing analysis of candidate genes on tumor DNAs, Germline DNAs and circulating DNAs from plasma samples.
(Amplicon resequencing with Qiagen GeneRead assays or custom assays, NEBNext® Fast DNA Library Prep Set, Ion OneTouchTM 200 Template Kit v2 DL, Ion PGM 200 Sequencing Kit; few ng DNA or WGA DNA required)
3. Whole transcriptome analysis (RNA-seq)Paired-end or Forward SOLiD 5500XL Human whole transcriptome analysis from tumor DNAs, cell lines DNAs.
(SOLiD Total RNA-seq kit, 200-500ng rRNA depleted total RNA)
4. Single Nucleotide Polymorphisms (SNP) genotyping and Copy Number variation analysis- Illumina Infinium assays
(Whole Genome Genotyping and CNV analysis - Catalog arrays: HumanOmni1-Quad, Human 1M-Duo, Human660W-Quad, Human CyotSNP-12 ; 3 000 to 1 000 000 markers Custom Infinium iSelect arrays; 200-400ng of gDNA required)
- Illumina Goldengate assays
(384-SNPplex, 768-SNPplex or 1536-SNPplex genotyping custom arrays-Catalog arrays: Cancer Panel array; 250ng of gDNA or WGA DNA required)
- TaqMan Analysis on the ABI HT7900 instrument (Simplex analysis in 384-well plate format; 10ng of gDNA or WGA DNA required per SNP)
- High Resolution Melting Curve Analysis (HRM) on the Idaho Lightscanner instrument
(Simplex analysis in 384-well plate format; 30ng of gDNA or WGA DNA required per SNP)
5. Mutation scanning of candidate genesPre-screening using High Resolution Melting Curve Analysis (HR-Melt) on the LightScanner instrument followed by Sequencing on the 96-capillary Sequencer (Spectrumedix, Transgenomics) of the samples showing aberrant melting profiles (100ng to 300ng of gDNA or WGA DNA required depending on the size of the gene).
6. Gene expression profiling- DASL Illumina Goldengate (for Paraffin embedded tissues; 250ng of RNA)
(Custom DASL assays or Catalog arrays (whole genome, human cancer panel))
- Whole genome Gene Expression assay (for non-degraded RNA; 250ng to 500ng of RNA)
NB: Quality control and quantification of extracted RNAs will be performed using Agilent 2100 bioanalyzer.
Note that the Bioanalyzer can also check the integrity of miRNAs.
7. Whole Genome Methylation profiling- Infinium Whole Genome Methylation profiling (HumanMethylation450 DNA arrays, 500ng gDNA; HumanMethylation27 DNA arrays, 200ng gDNA)
More details are given here in the pdf document (accessible only from inside IARC).