Dell HPC systems power TGen’s fight against pediatric cancer

Editor’s Note: Below is a guest blog post from James Lowey, the Translational Genomics Research Institute (TGen) Director of High-Performance Biocomputing. You can read James’ full bio here, and here’s his guest post.


What a huge difference a year makes.

Exactly a year ago this week, the Translational Genomics Research Institute, where I work as TGen’s Director of High-Performance Biocomputing, announced a partnership with Dell and the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC) to make a significant leap in the ability of doctors to treat children with cancer.

As part of this partnership, Dell announced a major commitment of funding, employee engagement  and cloud computing technology to support pediatric cancer research programs globally, including the world’s first personalized medicine trial for pediatric cancer conducted by NMTRC.

Dell’s High Performance Computing (HPC) is supporting TGen’s work on the NMTRC personalized medicine clinical trial, enabling ever-faster diagnosis and treatment for some of the most aggressive types of cancer in children for whom time is extremely precious.

Neuroblastoma strikes one in 100,000 children annually, usually before the age of 5, and despite it being so rare, it is so deadly that it is responsible for one in seven pediatric cancer deaths.  It attacks the sympathetic nervous system, which controls heart rate, blood pressure and digestion, with aggressive tumors that are unique to each child.

Using Intel and Dell technology, we’ve been able to make a real difference in the time it takes to analyze Next Generation Sequencing samples, significantly minimizing the time it takes to discover the genetic flaws in the 3-billion-letter DNA code of these patients.

We need to get this information into the hands of physicians in a timely way, enabling them to improve the outcomes for children with cancer. Armed with this information, an oncologist can prescribe the best possible drugs to knock down and, perhaps some day, cure these types of cancers.

With the Dell team, we at TGen have worked together to push the performance envelope.

I will deliver details of these advances at Supercomputing 12, or SC12, the International Conference for High Performance Computing, Networking, Storage and Analysis. My presentation is set for 12:15 p.m. Tuesday, Nov. 13, at The Salt Palace convention center in Salt Lake City.

This “Birds of a Feather” session — Genomics Research Computing: The Engine that Drives Personalized Medicine Forward — will include information based upon practical experience on how to optimize bioinformatics, algorithms and HPC architectures for use in genomics analysis.

Specifically, I will elaborate on what the Dell/TGen teams have done to reduce critical analysis times in these clinical trial studies from as many as 7 days to just 1.

For example, it used to take up to 2 days just to copy data to HPC resources, and as many as 5 days to align that data using the resources that were available to TGen. By leveraging Dell technologies and expertise, that work can be done in just 1 day.

That is a substantial time savings when young lives are on the line.

About the Author: James Lowey