Big Data Brings Hope to Small Patients
Accelerating pediatric cancer treatments through molecular diagnosis and tailored treatment.
Neuroblastoma sometimes forms before a child is born, but it usually isn't found until later, when the tumor begins to grow and affect the body? When diagnosed, speed is of the essence. Translational Genomics Research Institute (TGen) is working to show how the genomic sequencing possible today can make personalized medicine a reality in clinical settings when every moment counts. TGen joined forces with Dell and Intel to move next-gen whole genetic sequencing (WGS) from research into clinical practice. Fourteen children were fighting deadly, fast-growing neuroblastoma cancer. Over 60 percent of these patients did benefit clinically from this groundbreaking pediatric clinical trial, run by TGen.
Fourteen children, most of them under five, were fighting deadly, fast-growing neuroblastoma cancer. They found hope through a groundbreaking pediatric clinical trial, supported by TGen. Speed was crucial because all of them were either non-responsive to treatment or relapsed, with poor prognoses. The goal was to biopsy and characterize their tumors, generate RNA profiles, and match promising drugs to each individual—all within 21 days. Over 60 percent of the children benefitted clinically from this study.
High performance computing made it possible to accomplish this ambitious goal, cutting the best-case two-month timeframe by more than half, and improving the odds for these young patients.
These kinds of Life Sciences computational challenges require a multidisciplinary approach. Working with Dell on infrastructure, Intel on processing power, and other technology leaders on storage and networking solutions, TGen was able to streamline sample preparation and sequencing from 12 days to five, slash data analysis from days to hours, and show the feasibility of delivering results to the Tumor Board in roughly 10 days. The trial demonstrated that next-gen sequencing, a key enabler for personalized medicine, is a viable tool in a time-constrained clinical setting. This proof-of-concept trial was so successful that the work is set to continue in an expanded follow-on trial with more than 100 children.
Personalized medicine using molecular diagnosis holds special promise for our youngest patients and also offers new options for anyone suffering from a difficult-to-diagnose or non-responsive condition. It arms clinicians with the insight to pinpoint diagnosis faster and tailor therapies for each individual, increasing the chances of successful treatment. It has the potential to end the frustrating and expensive “diagnostic odyssey.” It links clinical treatment decisions to molecular diagnosis, which can reduce side effects while improving outcomes. And beyond treating disease, it can help us make better lifestyle decisions based on genomic markers.
All 14 were able to be treated using the molecular guided therapy and we found no serious or adverse side effects.Dr. Giselle Sholler, Chair, Neuroblastoma and Medulloblastoma Translational Research Consortium, Haworth Family Endowed Director of Innovative Therapeutics Clinic, Head Pediatric Oncology Translational Research Program, Pediatric Oncology, Helen DeVos Children’s Hospital, and Associate Professor Michigan State University and lead sponsor of the clinical trials.
Supplied the computing power to support 25 TFLOPs with Intel® Xeon® processors, Lustre* storage and file technology, and large data set application expertise.
60 percent of the kids benefited clinically from the molecular guided treatment, showing prolonged stability.
See how TGen is solving complex problems for patients through genomic testing with Dell and Intel, which provide high performance computing resources that help doctors and researchers understand data and ultimately treat and prevent disease.
Personalized medicine—marked at times by both excessive hype and dour skepticism—is a reality today, albeit one with a still modest reach. One of the best examples is an FDA-approved, first-of-its-kind pediatric clinical trial in which children with a deadly, fast-growing cancer (neuroblastoma) have their tumors biopsied and characterized by modern molecular medicine tools (microarrays and next-generation sequencing).
Used next generation sequencing technology (Illumina) and secondary analysis (Genomics codes and apps) in order to deliver quantitative RNA profiles (gene expression) faster, with richer data, and with an expanded dynamic range versus microarrays (previous technology). Used as input for oncologists to analyze and then suggest the best treatment based on mapping the unique mutations to the right drugs.
Supplied PowerEdge* servers for the HPC infrastructure that drove the secondary analysis, the Luster* HPC storage systems, domain expertise, and financial support.
Worked alongside Dell and TGen offering software optimization support to accelerate Bowtie 2* (used to align the large sequencing reads), and the processing power to drive the project.
Analytics Sophisticated SW is used to accelerate diagnosing diseases. Intel-balanced compute storage and faster code optimization allows clinicians to tailor treatment accordingly in a fraction of the time and cost for diagnosing and treating diseases through data analytics.
Intel and Oregon Health & Science University (OHSU) are teaming up to develop next-generation computing technologies that advance the field of personalized medicine by dramatically increasing the speed, precision, and cost-effectiveness of analyzing a patient’s individual genetic profile.
With nearly USD 450 million annually in research expenditures, Arizona State University is a research leader. ASU partnered with Dell to create the NGCC, ASU's next generation cyber capability to advance big data and high performance computing research in complex adaptive systems.