Dell, Terascala and the Translational Genomics Research Institute (TGen) are installing state-of-the-art computing and programing specialized for human genome investigations at the National Cancer Institute (NCI).
As part of a formal collaboration, Dell is providing the Dell Genomic Data Analysis Platform, designed to deliver fast analysis of the billions of data points required when sequencing, or decoding, aspects of the human DNA and other genomic data.
TGen is providing NCI with high performance computing and bioinformatics support, as well as specialized software and tools developed over the last three years as TGen and Dell have partnered in support of pediatric cancer research programs globally, including a groundbreaking personalized medicine trial for pediatric cancer conducted by the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC).
NCI is providing TGen with access to more than 800 sequenced child-cancer genomes, which will be used in TGen’s ongoing pediatric cancer research.
“This is an enormous opportunity for the government to work with top private and research organizations to share information and expertise that will help guide physicians and medical benefit for children around the world. A system like this is critical in expediting patient care,” said James Lowey, TGen’s Vice President of Technology.
The mission of the Oncogenomics Section at the NCI is to harness the power of high throughput genomic and proteomic methods to improve the outcome of children with high-risk metastatic, refractory and recurrent cancers.
The new system at NCI will be used for four purposes:
1. House genomics data of well over 800 pediatric cancers, in a user friendly database.
2. RNAseq and immunohistochemistry database for the Stand Up to Cancer Pediatric Dream team.
3. Computational server for a precision therapy trial to be conducted with the Children’s Oncology Group.
4. Computational server for a precision therapy trial to be conducted with the Center for Cancer Research, NCI.
The research goals are to integrate the data, decipher the biology of these cancers and to identify and validate biomarkers and novel therapeutic targets and to rapidly translate findings to the clinic. This new system will host the largest collection of clinically annotated pediatric cancer genomic data ever to be released to the scientific community. Not only will this system enable state-of-the-art precision therapy trials for children and adults with lethal cancers, but also provide clinically annotated high-resolution genomics data for basic science research.
“With the advent of faster, low-cost genome sequencing technology, researchers now have a critical gateway to understanding the underlying molecular pathways for diseases. And for some diseases, every hour closer to discovery and result can mean the difference between life and death,” said Walker Stemple, Dell’s High Performance Computing Product Manager.
Terascala technology is present in several key areas of the new Dell computer cluster: TeraOS improves the reliability, ease of use, and performance of the Lustre storage in the solution; Terascala gateways enable a direct interface for the genome sequencers to the Lustre storage; and Terascala Support delivers optimized technical support across the entire storage appliance.
“We are very excited to be a contributor to this significant HPC advancement at the NCI,” said Steve Butler, CEO of Terascala. “The result is a much faster and more efficient workflow for NCI researchers. Our hope and belief is that NCI researchers will be able to accelerate their work resulting in a faster timeline in breakthroughs in the battle against cancer.”
When cancer has spread beyond the site of origin it becomes hard to cure. In addition, children with relapsed or refractory cancers have about a 20 percent chance of survival. Neuroblastoma, a rare cancer that strikes one in 100,000 children annually usually before the age of 5, is so deadly that it is responsible for one in seven pediatric cancer deaths. The cancer comes from the sympathetic nervous system, which controls heart rate, blood pressure and digestion, with aggressive tumors that are unique to each child.
To overcome these challenges, parents and physicians and scientists from the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC; https://nmtrc.org) and TGen have teamed to launch a groundbreaking personalized medicine clinical trial investigation for pediatric cancer. The trial is based on research from a group of collaborating investigators who are developing a personalized medicine process that is intended to permit near “real time” processing of information on patient tumors and prediction of best drugs for a specific patient. This process generates more than 200 billion measurements per patient that must be analyzed, shared and stored. The computation and analysis of this information can take weeks, even months, to process. The Dell solution and TGen software decreased RNA-Seq data analysis time from 7 days to 4 hours.