Thermo Fisher Scientific Custom Microarrays Drive Large-Scale Genotyping Study

Thermo Fisher Scientific announced facilitation of the next phase of the FinnGen precision medicine study that aims to deepen the overall understanding of chronic disease mechanisms in the Finnish population and to enable development of targeted therapies. The latest stage is focused on analyzing more than 50,000 samples in six months toward fulfilling the overall goal of a half-million individual samples with Thermo Fisher’s custom microarray technology. The FinnGen study represents one of the largest longitudinal precision medicine studies of its kind. The project endeavors to analyze genetic information from 500,000 individual blood samples collected by a nationwide network of biobanks and marry it with national health records. Launched in 2017 and funded by pharmaceutical partners and Business Finland, a Finnish funding agency for innovation, the research program is leveraging Thermo Fisher’s Applied Biosystems Axiom Genotyping Solution, which has been custom designed to meet FinnGen’s specific requirements.

Genetic data from retrospective and prospective samples have been analyzed during the ongoing program, which includes pre-planned pauses every six months to ensure the information gathered from the more than 102,000 individuals to date is saved cumulatively on a regular basis. The FinnGen project focuses on patients to maximize the number of disease cases and on the elderly to capture a long history of health record data for the study. “The availability of health record information from birth to death, the powerful microarray technology we selected and strong collaboration from all the parties involved in the FinnGen project is key to achieving breakthroughs in disease prevention, diagnosis and treatment,” said Aarno Palotie, Ph.D., research director of the Human Genomics Program at HiLIFE in the University of Helsinki/Institute for Molecular Medicine Finland (FIMM) and a faculty member at the Center for Human Genome Research at the Massachusetts General Hospital in Boston, and associate member at the Broad Institute of MIT and Harvard, “Together, with hundreds of thousands of Finns, we are on a journey of discovery into shared heritage.”

The Finnish population is uniquely suited for such an in-depth genetic study because it has evolved from a small founder population with little consanguinity, enabling the original genotype to mostly remain conserved. The low level of variants in the population structure increases the chances that the potential disease association findings have statistical significance. FinnGen brings together Finnish universities, hospitals, the National Institute for Health and Welfare (THL), biobanks, international pharmaceutical companies and companies like Thermo Fisher for the effort. Determining how best to produce the optimum genotype data for such a large-scale endeavor was critical. A genome-wide association design (GWAS) supported by a scalable, and customizable high-throughput microarray platform was the path chosen. “We needed a genotyping pipeline of the highest quality that provided an unrivalled post-lab analytic work flow,” said Palotie. “In our case, customization was an important component due to the unique needs of the Finnish population, where the population isolate structure has resulted in an enrichment of coding, potentially deleterious variants. Thermo Fisher successfully fulfilled all of our criteria, providing us with a validated, trustworthy industry-level pipeline, which meant that we could just provide our samples and receive high-quality genotypes.”

Thermo Fisher developed FinnGen’s custom Axiom genotyping array through its Microarray Research Services program in Santa Clara, CA. The site is also where all genotype calling is being performed for the project after DNA is first extracted in Finland. “We are proud to be active collaborators in this exciting study, and to contribute our powerful genotyping platform to help uncover the incidence and effects of variations relative to disease states in a founding genotype,” said Shantanu Kaushikkar, director of Product Management for Thermo Fisher Scientific. “Axion arrays are consistently selected for their flexibility and reputation of delivering high-quality data.” – Medical Buyer Bureau