The Genomics Programme

Genomics is the study of the genome, i.e. all of an individual's genetic material. Large-scale genome analysis has already identified a number of genes involved in the development of various types of cancer and variants associated with a predisposition to certain cancers.

The study of genetic modifications in tumour cells should result in the development of new diagnostic tools and the identification of better therapeutic strategies by pinpointing the predictive markers for a response to a type of therapy so that only responsive patients are treated. Thus, it could give rise to “personalised medicine”.

On 27 April 2006, the President of the French Republic launched the first national cancer genomics programme, co-ordinated by INCa.
This theme was taken up again in the second Cancer Plan, which was launched in November 2009, with its focus on extensive sequencing of a particular number of tumours (Measure 5-4 of the 2009-2013 Cancer Plan).

The national cancer genomics programme

Co-ordinated by INCa, this programme draws on the expertise of the French National Genotyping Centre (part of the Genomics Institute, within the French Atomic Energy Commission (CEA)), the Jean Dausset Foundation (Centre for the Study of Human Polymorphisms, (CEPH)) which is responsible for centralising the collections, DNA preparation and quality control as well as sample preservation. Canceropôles (cancer hubs) are also participating in this programme, which is unfolding in an international context.

The primary objectives are focused around large-scale studies designed to identify genetic factors involved in a predisposition to cancer by mapping Whole Genome Association (WGA) studies. Lung and kidney cancers, studied in the Specialised National Excellence Programmes (PNES), are the initial priority targets for these genetic studies. Breast cancer, prostate cancer and melanoma were also included in the programme.

For lung cancer, a WGA study funded by INCa was conducted on around 2000 people from six Central European countries. It has enabled us to identify a locus strongly associated with lung cancer, at chromosome area 15q25. This locus was replicated in five different studies on lung cancer. The association zone contains several genes, three of which code for sub-units of the nicotinic acetylcholine receptor (CHRNA5, CHRNA3 and CHRNB4). These findings were detailed in a scientific publication in April 2008 (Hung et al., A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature, 452, 633-637). Other findings have been published identifying a new lung cancer susceptibility locus on chromosome 5p15.33, including the telomerase reverse transcriptase gene (TERT) and cleft palate gene CLPTM1L (Cleft lip and palate transmembrane 1 like) (MacKay et al. Lung cancer susceptibility locus at 5p15.33. Nature genetics, 40, 1404-1406). In the extension of this programme, two projects were selected for their scientific excellence in an INCa call for proposals. These projects will help determine the functional and clinical significance of these WGA results.

The first project aims to gain a mechanical understanding of the role of the identified genes in lung carcinogenesis and to determine their relevance as biomarkers for early detection, diagnosis, prognosis and therapeutic response prediction.
The second project includes an analysis of the interaction between the genetic variations identified in the WGA study and tobacco use and occupational exposure to certain carcinogens, in a cohort comprising over 5000 cases and a similar number of control subjects.

In 2009, the French National Cancer League, in partnership with INCa, launched a call for proposals for human tumour genome studies in adults and children. This is part of the Tumour ID Card programme.