Untangling the Mysteries Behind the Human Genome: The Key to Customized Patient Care

 
Our Interconnected Planet

NCI and their Next-Generation Approach to Medical Research

The field of human genomics research is becoming increasingly active. With the speed of next generation genomic sequencing that is now possible, it is now feasible to create new genomics-based personalized medical services, offering patients more advanced diagnosis. These data can also be used to create a large database of genomics data which can then be used to develop national health policies that benefit society. Understanding the genetic factors that account for human diseases is one of the most important reasons for studying the human genome. Even though many genetic disorders are not yet treatable; early or pre-diagnosis can help improve the quality of life or even extend the lifespan of patients. Current clinical trials on genetic therapies for cystic fibrosis, hemophilia, and other genetic disorders offer the promise of eventual treatments that may give patients a life free from debilitating symptoms. Diagnostic tests can also help couples make informed decisions about whether to risk passing specific disease-related genes to their children. Using genetic testing in conjunction with in vitro fertility; doctors can specifically select embryos that do not carry the dangerous gene. Truly, the human genome holds the key to advancing personalized medical care in a myriad of ways.

Other benefits of studying human DNA and genetics include helping scientists to examine phylogeny to better understand where humans came from and how we relate with one another as an evolutionary species. It can help clarify the connections between different groups of people and give historians and anthropologists a clearer picture of historic human migration patterns. In more mainstream uses, a person’s genome can give clues to their personal ancestry and help him better understand his or her genealogy. Genetic testing has been widely used to verify or rule out relatedness of individual persons or populations. In the area of criminology, human genetic information has been used to either match or rule out a suspect’s DNA to biological evidence found at a crime scene, to identify victims and to exonerate convicted individuals using newer genetic methods that were not available at the time of the initial conviction. When genetic material has been available, individuals have been freed years, even decades after being wrongly incarcerated, all thanks to breakthrough research. Paternity testing has also become a very common legal application of genetic testing.

The potential ethical, social, and legal implications of genetic testing and analysis are numerous and new applications of the technology give rise to new areas of controversy including, for example, human genetic enhancement; altering human DNA to enhance athletic ability or intelligence, or any of a wide variety of physical characteristics. On the other hand, while society sorts out the ethics, being able to alter the human genome at the embryonic level will signal an end to currently incurable genetic diseases such as Down’s syndrome, congenital deafness and congenital heart defects.

This growing field of medical research currently uses gene sequences to understand, diagnose and treat human diseases and promises to revolutionize clinical practice in the coming years, through medical care customized to a patient’s unique genetic makeup. NCI is playing an active and increasingly important role in supporting this next-generation sequencing approach to medical research. Genomic medicine relies on the sequencing of thousands of whole genomes, each of which produces around 200 gigabytes of data which depend on NCI’s capability for fast computation for analysis and storage for archive. Medical research of this kind, working at the population scale, requires large numbers of de-identified genomic sequences to be gathered in one place, like the Garvan Institute of Medical Research’s Medical Genome Reference Bank (MGRB).

The MGRB stores the genomes of thousands of disease-free Australian seniors to provide a rigorous sample with which to compare the genomes of patients with rare diseases and cancer. Setting a new record for processing, the MGRB aligned 1200 human genomes overnight, making full use of the data bandwidth available at NCI.

As part of this effort, NCI is using Mellanox’s interconnect solutions to allow for faster inter-node connectivity and access to storage, providing Australian researchers and scientific research organizations with critical on-demand access to NCI’s high-performance cloud. This cloud facilitates scientific workloads with a deployment that combines the Mellanox CloudX solution with OpenStack software to support high performance workloads on a scalable and easy to manage cloud platform. CloudX simplifies and automates the orchestration of cloud platforms and reduces deployment time from days to hours. The NCI deployment is based on Mellanox 40/56 Gb/s Virtual Protocol Interconnect adapters and switches supporting both InfiniBand and Ethernet. NCI also has Mellanox’s 100Gbit/s EDR InfiniBand interconnect for its new Lenovo NextScale supercomputer. This powerful combination of storage and compute power enable NCI to deliver extremely complex simulations and more accurate predictions, all with the aim of improving the human condition.

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About Gerald Lotto

Jerry recently joined Mellanox in 2016 as Director HPC and Technical Computing, with more than 30 years of experience with scientific computing. An early adopter of InfiniBand, Jerry built the first HPC teaching cluster in the Harvard’s Department of Chemistry and Chemical Biology with an InfiniBand backbone during the early InfiniBand days. In 2007, he helped to create the Harvard Faculty of Arts and Sciences Research Computing group. In an unprecedented collaborative effort between 5 Universities, industry and state government, Jerry also helped to design the Massachusetts Green High Performance Computing Center in Holyoke, MA which was completed in November 2012. In mid-2013, Jerry left Harvard University to join RAID, Inc as Chief Technology Officer working to help companies, universities and government design, build, integrate and use HPC and technical computing technologies throughout the United States.

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