Scientist Spotlights in Genotyping
See how other scientists are using the Axiom genotyping solution
Investigators at UK Biobank describe the biobank genotyping strategy, array design, quality control and analysis in the journal Nature.
Read the article ›
Research Director of Human Genomics, FIMM
Associate Member of the Broad Institute of MIT and Harvard
Focus: Led FinnGen, a personalized medicine project bringing together Finnish universities, hospitals, and biobanks to genotype 500,000 individuals from the Finnish population in search of the next breakthroughs in disease prevention, diagnosis, and treatment.
Products: Axiom Precision Medicine Research Array and Finnish Biobank Array
Aarno Palotie, M.D., Ph.D., is the research director of the Human Genomics program at the Institute for Molecular Medicine Finland (FIMM). He is a faculty member at the Center for Human Genome Research at the Massachusetts General Hospital in Boston and an associate member of the Broad Institute of MIT and Harvard. He is also the Chief Scientific Officer of the large FinnGen project that collects the genome and health record data from 500,000 Finnish participants.
He has a long track record in human disease genetics, holding professorships and group leader positions at the University of Helsinki, UCLA, Wellcome Trust Sanger Institute, The Broad Institute of MIT and Harvard, and Massachusetts General Hospital. He has also been the director of the Finnish Genome Center and Laboratory of Molecular Genetics in the Helsinki University Hospital. He has served in numerous national and international boards, including the FIMM board.
Thermo Fisher Scientific recently spoke with Dr. Palotie about his work with FinnGen, a personalized medicine project bringing together Finnish universities, hospitals, and biobanks to genotype 500,000 individuals from the Finnish population in search of the next breakthroughs in disease prevention, diagnosis, and treatment.
Watch the videos below, or download the transcript.
Since joining RUCDR, Dr. Brooks has worked to automate and develop the service infrastructure that provides high throughput sample management and analysis for DNA, RNA, and protein-based technologies to hundreds of labs globally. As Chief Operating Officer he oversees all laboratories within RUCDR, ensuring consistent and superior quality standards for all services. His methodologies focus on extending the use of valuable samples by extracting and renewing limited quantities of biomaterial with newly developed technologies.
Dr. Brooks has worked over the years with both academic and industry partners on the development of technologies and standards that focus on maximizing the use of biological samples while understanding both analytical and functional quality control. He has shared this information globally across many public and private biobank programs through a variety of academic and commercial activities.
“Using the Axiom platform for a product like PharmacoScan is a huge advantage because we’re only seeing an increase in the number of samples that people want to look at for pharmacogenomics and pharmacogenetics across a variety of different applications."
Dr. Brooks presented at our scientific workshop at the ISBER 2018 Annual Meeting in Dallas, Texas. His talk, “Implementation of Genetic Analysis in Comprehensive Biobank Workflows for Basic Science, Clinical Research, and Precision Medicine Applications” can be viewed in the slide deck below. Afterwards, we discussed his experience in using Applied Biosystems genotyping solutions. Check them out in the four short videos, also below.
Right Patient, Right Drug Diagnostics
Focus: PGx specialist and leader in the movement to demonstrate the feasibility and value of preemptive pharmacogenomic screening
Product: PharmacoScan Solution
Ulrich Broeckel, MD, a pharmacogenomics (PGx) specialist recently launched a new company— RPRD (Right Patient Right Drug) Diagnostics, a spin-off from the lab he leads at Medical College of Wisconsin. Dr. Broeckel is on the faculty of Medical College of Wisconsin, and is active in the Pharmacogenomics Research Network (PGRN) and the Clinical Pharmacogenetics Implementation Consortium (CPIC). He is a leader in the movement to demonstrate the feasibility and value of preemptive pharmacogenomic screening
“We are very excited to work with Thermo Fisher Scientific on this array platform, and we have been involved since the early access phase of the product. Right now, we are finishing over 600 samples and are happy with the collaboration on the content and also with the data analysis software."
Thermo Fisher Scientific recently spoke with Dr. Broeckel about his work in pharmacogenomics research.
Thermo Fisher: Can you tell us about your vision for pharmacogenomics?
Broeckel: We now know that a growing number of gene-drug pairs and other genetic variations can affect a patient’s reaction to a drug. CPIC, which is a great resource for the community, publishes guidelines to help clinicians understand how the available genetic test results should be used to optimize drug therapy. CPIC has, to date, published specific genetic testing guidelines for over 30 drugs. The US FDA publishes a list of nearly 200 FDAapproved drugs with pharmacogenomic information in their labeling, and many of these drugs are listed with specific actions that should be taken based on patient-specific biomarker information. This includes seven drugs that have black-box warnings—the strongest guidance the FDA requires. These lists are growing all the time.
In the beginning, markers were discovered one-by-one, and tests were developed accordingly—one test for each target. Reimbursements followed this development pattern and covered individual, one-target tests. But a patient may need multiple tests, each of which may take several days, thus delaying treatment. On the positive side, this onetest/ one-target process delivers a manageable amount of information to the physician.
To read the rest of the interview, download the PDF.
Department of Surgery, Perelman School of Medicine, University of Pennsylvania
Focus: One of the founders of a consortium dedicated to improving transplant outcomes by better understanding the genetics and complications of transplant rejection
Product: Axiom Transplant Genotyping Array
Brendan Keating is a faculty member of the Department of Surgery (Division of Transplantation) in the Perelman School of Medicine at the University of Pennsylvania. Dr. Keating studies miRNA, mRNA, and DNA of heart, liver, lung, and kidney transplant donors and recipients. The goal of his work is to deliver individualized treatment of immunosuppression therapies post-transplant and predict genetic signals that may underpin graft rejection and complications of rejection. He is the principal investigator of GWAS for solid organ transplant studies at the Children’s Hospital of Philadelphia.
Dr. Keating is also one of the founders and leaders of the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN). This consortium is dedicated to improving transplant outcomes by better understanding the genetics and complications of transplant rejection.
“The fact that the arrays from Thermo Fisher Scientific are so easy to modify is important. The Axiom platform is much more malleable and customizable than other technologies we have worked with before. The technology performed very well with the difficult-to-genotype HLA markers.”
We interviewed Dr. Keating about his work with iGeneTRAiN, covering topics such as research goals, microarray design, and how he and the consortia came to partner with Thermo Fisher Scientific with the aim of improving transplantation success.
Robert Turner Professor of Diabetes at the University of Oxford and Consultant Endocrinologist at the Oxford University Hospitals Trust, Oxford, UK
Focus: How genetic studies can now integrate the power of imputation with our knowledge of population, disease, and biological function to answer some of the remaining questions about the future role of genetics in precision medicine.
Product: UK Biobank Axiom Array
Mark McCarthy is Robert Turner Professor of Diabetes at the University of Oxford and Consulting Endrocrinologist at the Oxford University Hospitals Trust, Oxford, UK. His research team has a long-standing interest in the genetics of complex traits including type 2 diabetes (T2D), obesity and growth. They have played a leading role in international efforts, such as the Wellcome Trust Case Control Consortium, that have applied genome-wide association and next-generation sequencing approaches to study these traits.
The research work of Professor McCarthy’s team has, with international collaborators, identified at least 50 new regions involved in susceptibility to type 2 diabetes and a similar number impacting on other traits. This work has provided novel biological insights into the pathogenesis of these conditions of underpins future efforts to translate genetic findings into clinical practice with which they are closely involved.
“There’s no doubt that designing a scaffold using an imputation-aware, multi-marker tagging approach is a much more efficient way to achieve coverage."
Below, Professor McCarthy outlines how the intersection of biobank capabilities, new study designs, and technological advances will improve our understanding of complex trait genetics.
Using UK Biobank’s genotyping array as an example, Professor McCarthy discusses how new genetic studies can now integrate the power of imputation with our knowledge of population, disease, and biological function to answer some of the remaining questions about the future role of genetics in precision medicine.
Thermo Fisher: Arguably, the GWAS era began in earnest with the 2007 Wellcome Trust Case Control Consortium (WTCCC) paper5. What have been the key successes in complex trait genetics since then?
McCarthy: There were earlier GWAS successes, for example, in age-related macular degeneration6 and inflammatory bowel disease7, but in terms of scale and scope, WTCCC marked the point where, for many in the field, the potential of GWAS became clear. The key success has been that the GWAS approach has proved to be so robust. This is, in part, because you are testing a relatively simple hypothesis, specifically, whether or not you see a difference in allele frequencies between cases and controls at a given variant. This has been sufficient to pick up many common variant signals without the need for complex analytical strategies. Another important point, particularly in retrospect, is that the field applied strong benchmarks, early on, for defining statistical significance. Few of the signals that reached these thresholds have subsequently proven to be false. This is very welcome when we remember the quite dismal era of candidate gene studies when almost nothing replicated.
These genomic studies also encouraged rapid development of collaborations and the formation of large international consortia. As a result of this data aggregation, the field found a way to move rapidly towards robust signals, avoiding years wasted while individual labs published under-powered studies. This was a major advance in the field and has since had impact on other areas of biological sciences.
All of this showed that high-throughput, large-scale genomics can be done and produces robust results. Out of that came thousands of loci for hundreds of traits.
To read the rest of the interview, download the PDF.
Cofounder and Chief Scientific Officer of AKESOgen, USA
Focus: Has created state-of-the-art CLIA compliant and CAP-accredited labs to meet the needs of high-throughput genetic, genomic, and biomarker studies.
Product: Axiom Precision Medicine Research Array
Mark Bouzyk, PhD, is co-founder and Chief Scientific Officer of AKESOgen, a genomic services company that works with scientists engaged in clinical and basic research around the world. Prior to founding AKESOgen, Bouzyk developed Emory University’s genomics facilities and served as director of Emory’s Center for Medical Genomics. Dr. Bouzyk was also the director of genetic laboratory sciences at GlaxoSmithKline for nearly a decade. He has worked on applying genetic testing technology in the clinical environment and has created state-of-the-art CLIAcompliant and CAP-accredited labs to meet the needs of high-throughput genetic, genomic, and biomarker studies.
“The VA who created the project chose Thermo Fisher to build a custom genotyping microarray tailored to specific genetic- and disease-related targets identified by VA scientists and physicians."
Thermo Fisher Scientific recently spoke with Dr. Bouzyk about his work in precision medicine research.
Thermo Fisher: Can you give us an overview of your company AKESOgen?
Bouzyk: The first thing people wonder about is where our name came from. We took it from Akeso, who is the Greek goddess of healing and curing, because ultimately that’s what we are working toward. We founded the company in 2010 and have established and expanded it through grants and contracts, with no outside investment funding. This year we were again named to Inc. magazine’s list of America’s fastest-growing companies, and we are ranked as the 23rd fastest-growing health care company. We are CLIA-compliant, CAP-accredited, and have a GxP-enabled quality management system, enabling us to work with investigators in the clinical and clinical trials areas. We have a 14,000 sq. ft. facility, where we have put an infrastructure in place that covers all the bases for genomics and precision medicine research and development. We support three sectors: academic, government, and pharmaceutical research, with an emphasis on looking at disease risk factors; the diagnostic sector, where we carry out cancer diagnostic testing and are about to launch capabilities for Alzheimer’s testing; and we support clinical trials by performing genomics testing.
To read the rest of the interview, download the PDF.
Listen to Dr Bouzyk’s webinar on genotyping to enable large-scale precision medicine research studies.
For Research Use Only. Not for use in diagnostic procedures.