Falcon Perspectives: Capitalizing on the Genomics Data Flood

//Falcon Perspectives: Capitalizing on the Genomics Data Flood

Falcon Perspectives: Capitalizing on the Genomics Data Flood

With the coming data flood, how can precision medicine capitalize?

If you are as interested as we are at Falcon Computing to answer this question, then why don’t you join us in diving through the highlights of 2018 for each of the ecosystem participants. This is our review of the key initiatives that helped us get a wholesome perspective of this space.Could you change the way pediatric medicine is practiced with valuable data you have aggregated? That’s the question St. Jude’s Children’s Hospital asked itself after they had built a database of over 5,000 whole-genomes (each record could easily be over 80GB in size), 5,000 whole-exomes and 1,200 RNAseq datasets of pediatric cancer data. Having an anonymized database of these records would be of great benefit for research and so St. Jude’s decided to partner with bioinformatics startup DNAnexus and cloud-savvy Microsoft to build a platform that would democratize access to their data. DNAnexus could be considered one of the most successful in the space if we base it on its growth and the $100 million that they have been able to raise, but they are just the beginning of this trend. As the need for other bioinformatic solutions are needed, the next DNAnexus may be possible thanks to initiatives such as the establishment of Blavatnik Harvard Life Lab at Longwood after a $200 million donation received by Harvard Medical School. This new initiative will provide a place for high-potential biotech startups to connect in a collaborative space that will benefit from other initiatives at the medical school.
Improving health care practices of its citizens may not be priority number one for a country until you read the statistics such as the ones published by CMS (Centers for Medicare & Medical Services). Using the US as an example, the combined spend of Medicare and Medicaid, the two publicly funded health coverage agencies, was short of $1.3 trillion -over 6% of GDP in 2017. So how are governments going to minimize future health care spending? A recent global strategy has been around national genome banks to provide better data access to find ways to provide precision medicine to the world’s rapidly growing population. Many are familiar with Genomics England and their recently completed challenge to sequence 100,000 genomes. Looking to expand their efforts, this year the US, Ireland and Israel among others fully kicked off their own population-scaled sequencing project. In the US, the All of Us Research Program opened its doors for enrollment in May and soon after in September it provided $28 million in funding to three research centers to provide sequencing services. The selected centers include Baylor College of Medicine, The Broad Institute (famous for establishing the GATK Best Practices pipeline for genome sequencing), and Northwest Genomics at the University of Washington. In Ireland the goal is to recruit 400,000 volunteers or close to 10% of the population and last week Israel announced their 100K genome sequencing project. We are looking at massive databases for each of these projects, getting the most value out of each record will be itself the biggest challenge.While Next Generation Sequencing (NGS) can easily become the table topic at your upcoming holiday parties, single-cell sequencing should be added to this list. In 2013 single-cell sequencing won Method of the Year by Nature and soon after The Human Cell Atlas kicked-off. Their mission is to create a comprehensive reference map of all human cells. Can you imagine the size of this task when you have to go through 10 billion cells that need to be mapped and categorized? To help with this effort, the Chan-Zuckerberg Initiative provided $15 million in funding to map every cell in a healthy human body. This particular set of funds are spread across 85 global research projects at 53 institutes that include Georgia Institute of Technology, the Broad Institute and University of Eastern Finland. Research institutions are looking to solve great problems but taking the learnings into practice is not always easy. An even harder problem is providing care to a more diverse population as studies have so many control variables you must also control who gets to be part of clinical trials. To help with that, the National Cancer Institute (NCI) announced the expansion of their eligibility criteria for cancer clinical trials at the end of November. The news was applauded as it now provides an opportunity for patients under 18 years of age along with patients with other existing health conditions to also be part of the participating pool.Who could have ever predicted that before 2020, as consumers, we would be using DNA sequencing for things like nutrition and weight-loss recommendations and even to figure out which wine is best for our unique palate- don’t believe me? Check out companies like EverlyWell and Vinome. The popularity of these at-home kits and the expected growth of this market is a good sign of the general population’s perception of DNA testing. To confirm this, at the end of last year, Wamber Genomic Advisors which polled 530 consumers about their views on genetic testing. On that survey, 75% of participants agreed that genetic testing can help individuals lead a healthier lifestyle and potentially prolonged life. It is no surprise then why 100,000 people have signed up to the All of Us program this year and why Veritas Genome sold out 1,000 sequencing packages in less than 6 hours during their recent thanksgiving promotion. Veritas did not only pull a great marketing stunt, it also proved that the demand for whole genome sequencing is there once the price is right. As sequencing companies rapidly work to achieve the $99 per genome goal, what will stop the every-day patient from adding WGS to their annual check-ups or holiday wish list?It would be interesting to see a current and broader study such as the one published in March of 2017 in the journal Pulmonary Circulation that discussed the knowledge and practices of health practitioners. This particular study focused on specialist treating pulmonary arterial hypertension (PAH). Of the 223 participants, only 13% scored themselves with an 8 or more, in a scale of 1 to 10, when asked how knowledgeable they considered themselves on the genetics of PAH. While other research has shown PAH can be a familial disease tied gene BMPR2, close to 80% of participants responded that they never or rarely refer their patients with PAH to a genetic counselor. How come participants were almost never referring  their patients to genetic testing? One of the main reasons for this is the lack of genetic counselors, the responders said. The Bureau of Labor Statistics expects that genetic counselor jobs will grow by more than 20% over the next 8 years but the number of accredited master’s programs that can fulfill such demand is short of 40 across the US and Canada. This will help with bringing new talent in the space but what will be more complicated will be to more thoroughly educate the current care providers that can start guiding conversations with patients as genetic home-kits expand their products to be more than ancestry services.Key players in the future of precision medicine are the insurance providers. Today, when a patient requires more than one genetic test, the cost can quickly exceed $7,000, a large expense for the average patient when it is not covered under insurance. On top of the upfront costs, patients can require medicine that can cost more than $15,000 a month out of pocket when looking at some of the patients going through cancer treatment. Before this year, genome sequencing coverage was almost non-existent. In March, the Centers for Medicare & Medicaid Services (CMS) took a first step by adding a policy to cover genomic sequencing for patients with advanced cancer. Another first step was taken by LifeMark Partners, an independent insurance broker, to provide 250,000 Americans with a complementary cancer genomic profile when purchasing a new policy. To support the value of genetic testing, a study published in the Journal of the National Cancer Institute (NCI), discussed the value of general population scanning for breast and ovarian cancer gene mutations instead of only looking at high-risk patients. Preventive medicine can become the next wave of cost-saving initiatives for insurance agencies as more studies like the one mentioned demonstrate the economic value of gene sequencing. The next question to ask would be how many insurance providers have been developing a platform secure and scalable enough to manage such large data sets on which they can build their models? Our educated guess, not many.

Did you see the pattern?

Whether it is to build predictive models for preventive health or to lower the cost of healthcare across nations, the volume of whole genome data being generated is rapidly increasing (case in point is the NCBI WGS Bank). Data collaboration is at the core of the engine that will help us unlock and capitalize precision medicine for the masses. Being able to share, compare, and validate results will be driven by accuracy and the speed at which insights can be generated.

If you are entering a journey of large data processing and NGS data analysis, you should check out Falcon Computing’s available solutions and connect with us to learn more about our acceleration pipelines for fast and accurate bioinformatics.

 

By |2018-12-19T20:23:03+00:00December 19th, 2018|Blog|0 Comments