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The Future of Genomic Medicine VII: Making Genetic Information Clinically Actionable
Los Angeles, CA March 12th 2014 – The California sunset marked an appropriate ending to the Future of Genomic Medicine VII conference held in La Jolla, CA on March 6th and 7th. Yet, even more impressive than the scenery within which the conference was nestled is the exciting discoveries and future prospects of the work being conducted by the fields leading experts. The following post highlights some of the insights gained from discussions with enthused attendees we spoke with after the conference.
As Dr. Eric Topol took the stage Thursday morning urging attendees to post a flurry of tweets (#FOGM14), the conference was well on its way to being one of the day’s hottest Twitter trends. Still, the insights shared by attendees on social media paled in comparison to the information conveyed by the distinguished presenters representing a spectrum of industries.
Seeking to Unlock New Information Hidden in the Genome
“I think we all, doctors and patients alike, need to be open to the possibility that a patient can be a coauthor of medical information,” Kim Goodsell proclaimed to the packed audience of clinicians, researchers, and other attendees on Thursday morning. In her 30s, Kim, a highly active individual regularly engaged in competitive athletics and outdoor expeditions, found herself on an entirely new kind of journey. Her unique medical voyage encompasses many of the themes prevalent throughout the FOGM conference, from efforts to understand the underlying genetic basis of disease to unlocking the clinical power of the genome.
After being plagued with debilitating arrhythmia, the product of a rare heart disease known as arrhythmogenic right ventricular cardiomyopathy (ARVC), Kim received a defibrillator allowing her to continue living a highly active lifestyle. She continued engaging in athletic endeavors for many years, until her deteriorating motor skills left her “barely able to hold a fork”. Ultimately, Kim sought attention from the world’s leading doctors at both the Mayo Clinic and Scripps Health. Her diagnosis was a rare neurological disorder called Charcot-Marie-Tooth disease (CMT) and affecting only 1 in 2,500 individuals. Kim was certain a connection must exist between her two extremely rare diseases. As Dr. Eric Topol would later explain, she had a better probability of “getting hit by an asteroid than developing both diseases (4 in 10 milliion)”. Thus began her search to identify a “unified field theory” underlying all of her symptoms.
A persistent patient urging her cardiologists and neurologists to look outside of their specialized fields to identify a common thread, Kim remained adamant in her efforts despite dismissal from doctors. Always one to seek out a challenge, she began researching her condition turning to the field of genomics where she identified the LMNA gene. Mutations in the gene explained all of her symptoms and though it seemed unlikely to her doctors at Mayo, Kim agreed to pay the $3000 it would cost to have the genetic test. Her suspicions were confirmed.
Kim has subsequently written up her case history to serve as an example of the previously undiscovered genetic link and is listed as a co-author on the publication to be presented at the upcoming Heart Rhythm Society meeting. Her ability to uncover a novel genetic connection and reverse the effects of her symptoms by eliminating risk factors from her diet demonstrates the clinical impact genetic information is slowly starting to have on the empowered patient. Kim Goodsell represents a glimpse into the “patient of tomorrow”, equipped with genetic information and a strong desire to self-educate.
“…The truth is access to genomic information at a reasonable price is already here. We’ve achieved our dream of having the $1000 genome. The question now is how to interpret this data once we have it and what other factors need to be considered to merit a clinical response.” – Molecular Pathologist, Top 10 University
While Kim Goodsell’s efforts to identify the genetic underpinnings of her condition are unique from a patient perspective, many of the conference’s presenters are engaged in demanding research to understand the genetic basis of a variety of diseases. Two topics of particular interest involved efforts to understand cancer genetics and the connection between age related disease and genetic factors.
A pioneer in the field of cancer genetics, Bert Vogelstein joined via phone from Johns Hopkins University to inform attendees on the current state of the “war against cancer”. With successful efforts to identify the “drivers and passengers” of cancer through genetic tumor profiling, Bert stressed the importance of the next steps in this war: defeating the enemy. Of the various methods for treating cancer, including traditional surgery and targeted treatment, Bert notes that many cancers, such as colorectal tumors, take nearly 30 years to develop leaving ample time for a “pre-emptive strike”. “It is only in the last 3 years that metastasis occurs, giving 27 years to detect and attack these tumors,” he emphasized. Further applications of genomic sequencing for cancer treatment were highlighted by Elaine Mardis and Robert Nussbaum, each discussing current efforts to employ genomic information into the clinic. As she has done every year at this conference, Elaine provided an update on the work she has been heading at the genome center at the University of Washington, outlining the benefits of the integrated use of NGS (Whole genome sequencing for SNP / CNV / indel analysis; Exome sequencing for validation and increased depth for clonality analysis; Transcriptome for overexpression, gene fusion, expressed SNVs).
While cancer has remained a dominant focus in the genomic medical revolution, age related illness grabbed an unexpected spotlight at this year’s FOGM conference. Dr. Eric Topol gave an exciting glimpse into these efforts by announcing the launch of Scripps Health’s “Wellderly Study”, an effort to uncover the protective genetic factors associated with health in thousands of elderly volunteers. Further excitement around identifying age related health factors was expressed as Craig Venter took the stage to share his thoughts on synthetic biology and to discuss his new venture Human Longevity. A massive undertaking, the company, in partnership with UCSD and other organizations, aims to sequence 140,000 genomes of volunteers over the next ~2 years (40,000 this year) to identify the underlying factors of healthy aging. Employing two Illumina HiSeq X Ten Sequencing Systems to begin this endeavor, the ultimate goal of Human Longevity is to compile the most extensive database of genotypes, phenotypes, and microbiomes. As Craig later explained, “the only way we’re ever going to understand human physiology is to put all of this stuff together.” While the declining cost of sequencing is enabling these unprecedented genomic endeavors, the next question is how to cope with all of the resulting data and how to incorporate this information into the clinic.
“Can we objectively integrate diverse annotations into a single score,” asked Jay Shendure, Associate Professor of Genome Science at the University Of Washington School Of Medicine. Jay, like many other presenters at FOGM VII, is currently engaged in efforts to understand how to integrate the endless flow of patient information into meaningful clinical answers. The need to develop and adopt a standardized method for annotating genomic information is an essential missing piece to the clinical application of the human genome. While there is still a great deal of work required in annotating genetic variants to allow for pre-testing of risks, attempts to understand the genetic basis of disease have proven successful thus far. Other areas of clinical interest discussed at this year’s conference included the role of genetics in drug response and the effects of the microbiome on patient health. However, the question remains: once we produce this unprecedented amount of genomic information how can it be made accessible and actionable?
It is no secret that the technological uptake of the medical industry is slow. However, interest from some of Silicon Valley’s “best and brightest” is positioned to have an unparalleled catalyzing effect in some key areas of genomic medicine. Leveraging their expertise in technology for mass consumption, Cloudera’s Jeffrey Hammerbacher and 23andMe CEO Anne Wojcicki both presented their current undertakings to address the way in which physicians and patients interact with their genetic information. Jeffrey Hammerbacher, the archetypal “data scientist” previously responsible for building the data storage and analysis infrastructure of Facebook, described his current endeavors at Mount Sinai Hospital to build computing instruments for the aggregation and analysis of huge pools of patient medical information. Implementing these advanced tools has the potential to radically transform the way in which physician’s interact with information, including the patient genome, to draw meaningful answers. While Jeff’s goal is ultimately to empower the physician with patient data, Anne Wojcicki hopes to have a similar empowering effect on the patients themselves.
Anne’s company, 23andMe, has made genetic sequencing accessible and engaging to consumers across the nation. For the cost of only $99 and a container of saliva, individuals can access previously unattainable information, from health risk probabilities (prior to the FDA crackdown) to ancestry information. Her unmatched price point and trendy marketing has allowed the company to accrue the most extensive database of genetic information in the world, with around 650,000 genotypes to date. Yet, even more impressive than this enormous collection of patient SNPs, 23andMe has also built a highly active network of engaged patients, regularly taking health and haplotype surveys and expressing interest in their health. As many of the science and technology writers presenting at FOGM explained, there is an essential unmet need to make genetic information easily consumable and attractive for mass adoption. In the words of Chris Gunter, consultant at the Marcus Autism Center, “science is full of drama,” express this to the public and get them interested.
This year’s FOGM VII conference brought a broad range of views, from academic researchers and industry scientists to technological visionaries and science journalists, all with a shared interest in the power of the human genome. While presenters provided hints at the integration of genetic information into the clinic, the process has proven slow due to issues primarily with regards to decentralized data and annotation standards. With a community rallying to address these issues, the future of genomic medicine appears truly bright. As research and countless clinical cases have proven, the efficacy of genetics in understanding patient health is not to be underestimated. With the $1000 genome finally a reality, it will not be long before the number of patients sequenced reaches a tipping point. The focus now is how to collect and interpret this data to create meaningful change in patient health.
Author: Eric Lakin, Analyst at DeciBio, LLC
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