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French Medical Genomics Initiative's Pilot Sequencing Platforms Set to Commence Operations


NEW YORK (GenomeWeb) – Two pilot genomic platforms — one serving northern France, the other serving the south — will begin sequencing patient samples in the first quarter of next year as part of the country's national personalized medicine project.

The establishment of the platforms is a milestone for the Plan France Médecine Génomique 2025 (PFMG), a €670 million ($764 million) initiative the French government announced two years ago. The new platforms, outfitted with Illumina NovaSeq instruments, are each expected to generate roughly 18,000 genomes from patient samples by 2021, data that will be stored in a centralized database and will inform future research.

"By the first quarter of 2019, we will be fully operational and producing sequences," said Jean-Yves Blay, director of Centre Léon Bérard, a comprehensive cancer center based in Lyon in southern France.

"The data will be generated at one hospital in Lyon and curated and analyzed by multiple institutions," Blay said. "All data will be sent to a central repository in a single place, and this will become a public resource for both researchers and private partnerships."

Blay is the scientific manager for Auragen, one of the two pilot platforms that will begin operations next year. The consortium includes participants from four university hospitals in the region: CHU de Clermont-Ferrand, CHU Grenoble Alpes, Hospices Civils de Lyon, and CHU de Saint-Etienne. In addition, it counts two cancer centers, the Centre Jean Perrin and the CLB, and a cancer research institute, Institut de Cancérologie de la Loire Lucien-Neuwirth, among its members.

The sequencing platform is housed and administered by the genetic service of Hospices Civils de Lyon. Informatics and other reference tools will be coordinated by the CLB for cancer genomes and by CHU Grenoble for genomes associated with constitutional diseases.

Blay noted that Auragen received €150 million of the initial €670 million investment in PFMG to fund its operations through 2025. The Auragen platform is expected to produce 18,000 genomes — 9,000 related to cancer, 9,000 for rare diseases — within its first two years of operations.

The specific indications handled by the center — cancers or rare diseases of interest — are under discussion. Still, Blay noted that by commencing its sequencing operations, whole-genome sequencing will for the first time become universally available to all patients across France.

"France has had whole-genome sequencing installed for the past decade, but following this plan, we will have easier access to this infrastructure to help patients," Blay said.

Under the original PFGM plan announced in 2016, France was supposed to support a dozen sequencing platforms like Auragen. However, two years into the project and with just two pilot sequencing platforms ready to come online, Blay suggested that there may be fewer platforms in operation by 2025 than originally envisioned.

"My impression is that we have to adapt to the context, which is rapidly evolving," said Blay. "In 2025, we will certainly have a large data repository, informed by two platforms, perhaps others."

The other platform that is set to begin operations next year is the Sequencing Omics Information Analysis (SeqOIA) cooperative health group, which involves Assistance Publique-Hôpitaux de Paris, the Institut Curie, the Gustave Roussy Cancer Center, and Institut Imagine. In July, SeqOIA selected Integragen as its industry partner for the project. The company, based in Evry, a suburb of Paris, said in a statement at the time that it would receive €18 million over the next five years to provide SeqOIA with access to exome as well as whole-genome and RNA sequencing data from patients with cancer and rare diseases.

Dominique Stoppa-Lyonnet, the head of the department of genetics at Institut Curie, said that the introduction of the SeqOIA and Auragen platforms in France will create infrastructure that will change the way sequencing has been used in medical genetics in the country to date.

"NGS is implemented in many genetics laboratories already," Stoppa-Lyonnet noted, "but it is mainly used for multigene panel analysis. The idea of the 2025 plan is to introduce it for whole-genome analysis, as well as for exomes, also."

Echoing CLB's Blay, Stoppa-Lyonnet said it was unclear if the country would see a dozen platforms like the ones run by Auragen and SeqOIA in operation by 2025. However, she said it is likely that other platforms will be developed to more directly serve other parts of France. She noted that currently, SeqOIA will serve labs across northern France, in cities like Brest, Rouen, and others, while Auragen will sequence samples for labs across the south in cities like Nice, Marseilles, Toulouse, and Bordeaux. "Labs in these cities use NGS for multigene panels and some for exomes, but very few are able to do whole-genome sequencing yet," she said.

Another issue that France will confront as its pilot platforms begin to generate sequence data is its clinical utility, Stoppa-Lyonnet pointed out. "Analysis of whole-genome data is still limited," she said. "But in a few years' time, it may be easier."

Integragen CEO Bernard Courtieu said that his company is participating in SeqOIA solely as an industry partner. In this role, the firm will run the samples and report back data to the platform's IT team. He noted that the SeqOIA team is closely in touch with Auragen in the south. "It is important that both platforms have a certain degree of homogeneity in their processes," he said. "It would be inappropriate to have different choices of technology, IT, and so on."

According to Courtieu, such harmonization also must remain true to the "values of the French healthcare system," which guarantees equal access to healthcare. "It is important that there isn't one platform here with its own setup and another that has different standards and processes," he said. "So there is a very strong collaboration between Auragen and SeqOIA."

While the new pilot platforms should enable French patients' universal access to whole-genome sequencing, Courtieu noted that the country has accrued "significant experience in providing genomics to researchers and clinicians" in the past decade. "The 2025 plan was based on the understanding that genomics was ready to move to the clinic, and that large-scale genomics was something that was required or was soon to be required for at least cancer care and rare diseases and probably for other types of diseases," he said.

"The goal was to be able to provide these services to patients wherever they are in France," he said. "I think this is something that is fairly innovative and ambitious in terms of how it compares with other countries."

Stoppa-Lyonnet also stressed that the French project was medical in nature, and not a research project. "It is a very important difference," she said. "The idea is to introduce genomics into patient care."

There are multiple patient-focused genomics projects underway in Europe at the moment, each of which has taken a different approach to introducing genomics into the healthcare system. Finland, for example, last year announced plans to genotype 500,000 people as part of a five-year, €59 million project. Estonia also set aside money to genotype 100,000 people this year as part of its personalized medicine project, and some disease risk is already being reported back to certain patients in pilot programs. Also, Denmark recently established a National Genome Center to provide a national sequencing infrastructure and to manage a centralized database.

Closer to France, Switzerland set aside CHF 40 million ($41 million) in 2016 to create a national infrastructure for sharing clinical data, including genomics data, throughout the country. And Genomics England, launched more than five years ago, recently announced the completion of 100,000 genomes related to cancer and rare diseases for patients within the country's National Health Service, and is widely seen as a pioneer program in Europe.

The idea of data consolidation, standardization, and sharing is certainly core to PFMG 2025, too. As outlined in a 2016 report published by Aviesan, the French National Alliance for Life Sciences and Health that is overseeing the project, the 2025 plan calls for the establishment of a so-called National Center for Intensive Calculation for processing and analyzing the data generated by the new sequencing platforms. The plan also calls for creating standardized, interoperable electronic patient medical records in France to support the analysis of genomic and clinical data.

"The idea is to build a center that can store all the data from all the sequencing that can be used later for research analysis, algorithms, and artificial intelligence, and also for the healthcare professionals who need to access information from patients," said Ines Amado, deputy director at Aviesan. According to Amado, the new center is not yet operational, though it is being created.

She described it as a "physical center" that will be remotely accessible to researchers.

Amado noted that though all of the ongoing medical genomics projects in Europe are different, those involved in PFMG 2025 are in touch with colleagues in other countries. For example, the initiative has signed a memorandum of understanding with Genomics England to foster collaboration.

"Every country will have its own choices, but it helps to communicate because we can learn from each other," Amado said.