For those on the front lines of treating cancer, speed and precision are key to patients’ survival. Pediatric cancer researchers have been making incredible strides in accelerating delivery of new diagnostic and treatment options through collaborative clinical care and personalized medicine. Supercomputer-powered genetic diagnosis is being used to harness the power of high throughput genomic and proteomic methods and is playing a key role in improving the outcome for children with genetic diseases. Through use of high performance computing (HPC) systems, researchers are able to quickly run extremely complex algorithms that analyze terabytes of genetic and molecular data from the patient and from research databases.
Personalized medicine is attempting to change cancer treatment as it currently exists by providing and adapting treatments so they are specific to the individual and to that child’s cancer. Personalized cancer treatment uses data that specifically describes the differences between the patient and the tumor from both genomic and proteomic standpoints. The approach merges science and medicine with computational and analytical capabilities to study the biology of the pediatric patient and their individual genomic differences, and then leverages the technology to put all of the information together and make a treatment decision. Oncologists are able to select an appropriate treatment that is likely to be the most effective in destroying the specific tumor, while being least harmful to the patient.
Center for Pediatric Genomic Medicine
Roughly 4,100 genetic diseases affect humans, and these are the main causes of infant deaths. But identifying which genetic disease is affecting a critically-ill child isn’t easy. The Center for Pediatric Genomic Medicine (CPGM) at Children’s Mercy Hospital in Kansas City, MO, has been using supercomputer power to help save the lives of critically ill children and is working to someday achieve a fast genomic diagnosis for every patient. In 2010, the center’s work was named one of Time magazine’s top 10 medical breakthroughs, and received an HPC Innovation Excellence Award from the IDC HPC User Forum in November 2014.
Led by Dr. Stephen Kingsmore, CPGM was the first genome center in the world to be created inside a children’s hospital and one of the first to focus on genome sequencing and analysis for inherited childhood diseases. While most genome centers focus on research, the CPGM develops new clinical tests as a starting point for next‐generation medical treatments to improve outcomes in patients at Children’s Mercy and around the world. By using Targeted Gene Sequencing and Custom Analysis (TaGSCAN) and STAT-seq whole genome analysis, Children’s Mercy has dramatically reduced the overall diagnosis time and substantially helped affected children and their families.
“For one infant suffering from liver failure, the center used 25 hours of supercomputer time to analyze 120 billion nucleotide sequences and narrowed the problem down to two genetic variants. This allowed the doctors to begin treatment with corticosteroids and immunoglobin. Thanks to this highly accurate diagnosis of the problem and pinpointed treatment, the baby is alive and well today,” explains Steve Conway, Research Vice President, High Performance Computing, IDC. “For 48 percent of the cases the center works on today, supercomputer-powered genetic diagnosis points the way toward a more effective treatment. The center’s five-year goal is to provide a fast, accurate diagnosis for every critically-ill child that comes under their care.”
Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC)
Parents, physicians and scientists from the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC) teamed with Translational Genomics Research Institute (TGen) to launch a groundbreaking personalized medicine clinical trial investigation for pediatric cancer. NMTRC is a group of 18 universities and children’s hospitals based at the Helen Devos Children’s Hospital in Grand Rapids, MI, that offers a nationwide network of childhood cancer clinical trials. These trials are based on research from closely collaborating investigators who are developing a personalized medicine process intended to permit near-real-time information processing on patient tumors and prediction of best drugs for a specific patient.
NMTRC’s trials process generates hundreds of billions of measurements per patient that must be analyzed, shared and stored. Computation and analysis of this information can take weeks, or even months, to process. However, in a ground-breaking collaboration with TGen, Dell and Intel, NMTRC was able to use TGen’s highly specialized software and tools, along with Dell’s Genomic Data Analysis Platform and cloud technology, to decrease the research team’s data analysis time from 10 days to just six hours.
“TGen’s partnership with Dell has enabled patients to receive targeted care faster, cutting down on the computer analysis time with a 12-fold improvement in performance,” said James Lowey, TGen’s Vice President of Technology.
Hospital for Sick Children (SickKids) Centre for Computational Medicine
The SickKids Centre for Computational Medicine is working “to better understand the makeup of a human organism,” analyzing terabytes of data to predict the minute differences from one person to the next. The only way to determine the nuances that differentiate us from one another is to analyze this data with algorithms, and HPC has become essential in allowing researchers to discover the tiny distinctions that are otherwise impossible to find.
The Scalar Decisions Data Centre at the Peter Gilgan Centre for Research and Learning at SickKids grew out of an alignment between technical vendors that created a sophisticated architecture able to do 107 trillion calculations per second — one of the largest systems dedicated to health research. Key technologies of this system include
- compute nodes: SGI C-Series
- storage: EMC Isilon X400 System, SpectraLogic T950 Tape System
- network: Mellanox InfiniBand SX6036 with Ethernet Gateway Functions and SX1024 Ethernet Switches
- management, provisioning and monitoring: Bright Cluster Manager
- scheduling and workload management: Adaptive Computing Moab HPC Suite
- project management: Scalar certified PMI Project Manager, single point of call solution
“We went from 1,200 to approximately 7,000 cores. Storage capacity has gone up drastically, from 550 terabytes to two petabytes. We have moved from an Ethernet network to an InfiniBand network, which is considerably faster and meets the requirement of 80 gigabytes per second from the compute nodes to the storage,” explains Jorge Gonzalez-Outeirino, Ph.D., Facility Manager of the Centre for Computational Medicine at SickKids.
The one-size-fits-all approach to pediatric medicine is changing. The idea of personalized medicine, made possible by the growing understanding of the human genetic makeup and high performance computing, is allowing for customized care, fitted to a child’s unique genetic makeup. Medical and IT collaborations have become an essential part of this new approach, and are helping to remarkably accelerate diagnosis and treatment and to truly make a difference in the outcomes for pediatric cancer patients.