This special report sponsored by Dell Technologies, takes a deep dive into HPC and AI for life sciences in the era of genomics. 2020 will be remembered for the outbreak of the Novel Coronavirus or COVID-19. While infection rates are growing exponentially, the race is on to find a treatment, vaccine, or cure. Governments and private organizations are teaming together to understand the basic biology of the virus, its genetic code, to find what can stop it.
Significant amounts of computing power are aimed at this problem, including using the most powerful high performance computing (HPC) systems in the world today. Finding a cure or eliminating COVID-19 will not only benefit the worldwide population, but will also be the foundation for tackling the next pandemic, which some scientists say will happen in the not too distant future.
This technology guide, insideHPC Special Report: HPC and AI for the Era of Genomics, highlights a lineup of Ready Solutions created by Dell Technologies which are highly optimized and tuned hardware and software stacks for a variety of industries. The Ready Solutions for HPC Life Sciences have been designed to speed time to production, improve performance with purpose-built solutions, and scale easier with modular building blocks for capacity and performance.
Introduction
2020 will be remembered for the outbreak of the Novel Coronavirus or COVID-19. While infection rates are growing exponentially, the race is on to find a treatment, vaccine, or cure. Governments and private organizations are teaming together to understand the basic biology of the virus, its genetic code, to find what can stop it. Significant amounts of computing power are aimed at this problem, including using the most powerful high performance computing (HPC) systems in the world today.[1] Finding a cure or eliminating COVID-19 will not only benefit the worldwide population, but will also be the foundation for tackling the next pandemic, which some scientists say will happen in the not too distant future.[2]
Artificial Intelligence (AI)
Slavé Petrovski, Head of Genome Analytics and Informatics at AstraZeneca’s Centre for Genomics Research (CGR) explains that there is a wide range of uses for AI within this field. He says that the approximately three billion base pairs that make up the human genome can be analyzed through AI to find genetic variations. The next step is to determine the level of confidence to be placed in the differing data to decide if it represents a biological genetic variant.
AI is being combined with traditional HPC simulations to predict more accurate results. Based on previous completed computations, an algorithm is able to determine what the next input or result could be. For example, if protein A shows a possible affinity to kill the Coronavirus, then does protein B (or others) have a better chance or could be more effective?
There are a number AI uses within genomics research that can identify and facilitate drug target interaction. By combining analytical and automated processes with the ongoing study of genomics, a more complete understanding of this field will progress. AI can lead to greater insights into the patterns and anomalies in the data, where humans may not see the correlations at first. By using machine and deep learning techniques, new and more effective medicines can get to patients faster and will be better targeted to fight diseases.
Produvia, a research company, has identified five areas where AI will benefit genomic research moving forward:
- Extract genomic and epigenomic variants of clinical utility
- Identify genes
- Predict genomic associations
- Predict protein functions, and
- Predict sequence the specificity of DNA and RNA-binding proteins.
Precision Medicine
While AI can benefit genomic research, the end goal is to create treatments that specifically attack the genetic code of the infection or disease, and to create treatments that are tailored to an individual’s genetic makeup. To do this requires significant data, computing power, and collaborations that combine expertise from many disciplines.
With a combination of faster and more accurate genomic sequencing with faster computer systems and new algorithms, the movement of discovering what medicine will work best on individual pathogens and patients has moved from research institutions to bedside doctors. Physicians and other healthcare providers now have better, faster and more accurate tools and data to determine optimal treatment plans based on more data. This is especially true for pediatric cancer patients.
Personalized or precision medicine holds the key to innovative approaches to manage diseases on an individual level. Various decisions regarding the management of healthcare to each pathogen and/or individual is customized, based on the knowledge of the genetic or cellular information. Diagnosis of diseases, and the resulting treatments can be tailored for each person. However, a number of challenges exist as this scientific field moves forward, such as regulatory oversight, intellectual property rights and patient privacy.
Worldwide, many countries are dedicating resources and efforts to learn more about genomics and how to apply this knowledge to personalizing medicine. Figure 1 shows the worldwide effort to bring precision medicine to those in need. Figure 2 shows how the cost of decoding a human genome has come down, even faster than Moore’s Law.
Over the next few weeks we will explore these topics surrounding HPC and AI for life sciences in the era of genomics:
- Introduction, Artificial Intelligence (AI), Precision Medicine
- COVID-19, Benefits to Organizations
- Challenges, Case Studies, Dell EMC Ready Solutions for Life Sciences
Download the complete insideHPC Special Report: HPC and AI for the Era of Genomics, courtesy of Dell Technologies.
[2] Scientists in race to protect humanity from future pandemics
