HudsonAlpha’s Genomic Medicine Conference: Embracing A Brave New World

By Benjamin Ross

April 11, 2018 | Coinciding with the Institute’s 10-year anniversary, HudsonAlpha hosted their second Genomic Medicine Conference this week on their campus in Huntsville, Ala. For two and a half days researchers, geneticists and healthcare professionals told their stories about how genomic data has impacted their respective professions and how the data they have been collecting influences their patients.

“I feel like we’re finally grown up,” Andy Crouse, IP and Industry Partnerships Developer at HudsonAlpha, said when addressing the attendees about the future of the biotechnology institute. “We have grown up problems now.”

Shawn Levy, Faculty Investigator for Technology Development & Automation, Informatics & Genomic Variation at HudsonAlpha, spoke about genomic technologies and their application in clinical research. The Genomic Services Lab at HudsonAlpha, which Levy oversees, has worked with over 4,000 projects, Levy said, including the Michael J. Fox Foundation funded Parkinson’s Progression Markers Initiative (PPMI). “We’re sequencing about 8,000 longitudinal samples for Parkinson’s for biomarkers of disease progression,” Levy said. “What’s important about that number is [that] we need to be concerned about the overall integrity of the data across this large-scale perspective, as well as avoid bias whenever possible.”

Levy reflected on how far genomics has come in the past decade, especially genome sequencing. “The idea of whole genome sequencing was still a basic concept [10 years ago], and even exomes were still a reach in terms of genome capacity,” he said. Contrast to 2018, Levy says the HudsonAlpha location will be sequencing over 70,000 whole genomes by the end of the year.

Looking ahead at new technologies, Levy singled out 10x Genomics’ recently announced ability to look at single-cell work as well as investigate functional genomics and identify cellular phenotypes.

“What this opens up in terms of possibilities is the ability to both look at [cells] on an individual basis, identify antigen, anti-cell, and then also ask what are the alpha and beta cell, or what are the alpha and beta cell receptors that corresponds with the detection of that antigen,” Levy said. “When you think about that for a minute, what this means from a molecular perspective is the opportunity and potential to understand what specific alpha and beta chain sequencing corresponds to a specific antigen. The applications of that are tremendous from an autoimmune perspective, from a cancer immunotherapy perspective.”

The medical community must be ready for the day when genetics permeates all of medicine, Nancy Cox, Division of Genetics Director at Vanderbilt University Medical Center (VUMC), told those attending the conference. This will require education and understanding on the part of the researchers, physicians and patients. Such a task has been the focus of Cox’s career for years and she admits to a certain amount of satisfaction in where the field of genetics is heading.

“It’s a really fun thing to be at a point in my career where what I do might actually matter and help patients,” she said.

The work of Vanderbilt’s BioVU biobank is an accomplishment Cox is quick to point to when discussing continued successes in genetic research. “We have 10-15 years of electronic health records (EHRs) on the patients that we have, and more than 250,000 samples with 120,000 having genome interrogation that allows us to impute the transfections and metabolomes (at least the parts of those that are genetically determined), and that’s what we do using G-texts.” Researchers at VUMC can then associate those transcript levels with the entire medical record of a patient.

“Where we are right now is trying to prove the value of getting genetics, genomics information into the health records of every patient,” Cox said. This is an arduous task, she continued, in part because of how our current healthcare system works. “We have to make sure, not just that physicians know how to use the information, but that the information has true value. We have to convince payers of the value of that information, despite the costs.”

At Illumina, Erica Ramos represents genetic counseling, a branch of healthcare several attendees said is an area in desperate need of attention.

Ramos, Associate Director of Market Development at Illumina and President of the National Society of Genetic Counselors, says that genetic counselors, much like the whole medical industry, is being pushed in one direction by consumer-directed testing.

“How many people in this room have had a patient come to them asking about 23andMe or Ancestry or raw data?” Ramos asked the audience, to which more than half the room raised their hands. “I suspect that’s going to happen more and more, and I don’t care what specialty you’re in.”

This trend isn’t one that’s going away anytime soon, with Ancestry reporting earlier this year that it has tested more than seven million people, and 23andMe not far behind at three million. The emergence of consumer-directed tests represents to Ramos a shift in the perception of who’s in charge from a medical perspective. It also raises more questions about what genetics can tell researchers about the implications and dynamics of disease development.

“We’ve never looked at [these consumer-directed tests] from the perspective of using calculated, geographic ancestry to guide things like carrier testing or other types of testing,” Ramos said. “Hopefully that research is starting to come.”

“The future of genomics is now,” Vandana Shashi, Professor of Pediatrics at Duke University School of Medicine, said. “We need to start understanding how we can move forward based on what we’ve learned so far.”

In order to implement genomics into clinics across all medical fields, Shashi believes we need data on clinical relevance to answer the questions of whether or not genomics really works and what the outcomes are if it does work.

“Is it worthwhile to do all of these genomic investigations if we cannot establish it’s economically feasible and medically effective?” Shashi said. “There has to be data coverage that is broadly applicable, and there needs to be medical personnel who are comfortable handling this information.”

With so many questions still up in the air, Shashi is concerned with the perception that the community has been overhyping the potential for this technology.

“We are overstating the benefits and underestimating the risks,” Shashi said, warning that researchers need to be cognizant of this. “Some degree of hype is necessary for innovation and funding, but we need to be realistic.”

Even in the rare disease community, where Shashi primarily focuses, patients have been disappointed with diagnoses based on their preconceived notions of what it means to have their genes sequenced.

One way to address this, Shashi believes, is to provide more clinical support to physicians regarding how they process genomic data. “Maybe we need [Continual Medical Education] opportunities in genomic medicine, and education about genomics should be incorporated in medical school and residences.”