For St. Jude, Advancing Cures for Pediatric Cancer Means Accelerating Genomic Discovery and Collaboration

Angela Blog Author




Historically, cancer research has been slowed by an inability to make genomic data rapidly accessible to research collaborators. Last week, St. Jude Children’s Research Hospital took a big step toward solving this problem with its launch of St. Jude Cloud, an online platform that allows researchers to access the world’s largest public repository of pediatric cancer genomics data. Developed in partnership between St. Jude, Microsoft, and DNAnexus, St. Jude Cloud provides a flexible cloud platform for rapid data mining, analysis and visualization capabilities.

St. Jude has long been a leader in advancing cures for pediatric cancer and other life-threatening diseases, and continues to develop new approaches to revolutionize the way medicine is practice. St. Jude Cloud is the latest unique tool developed in the fight to advance cures for pediatric diseases. DNAnexus is proud to serve as the technology platform that brings together St. Jude researchers and their partners in a secure and collaborative ecosystem.

Collaboration fuels scientific advancements, and St. Jude Cloud is already doing just that. In a paper that was recently published in Nature, St. Jude researchers lead by Jinghui Zhang, PhD, discovered mutations connected to UV damage in a B-cell leukemia. This was a very surprising finding and led the team to ask whether other leukemia samples not included in the original study might have a similar mutational pattern. Scott Newman, PhD, used St. Jude Cloud to reproduce the original experimental findings in just a few days whereas the original research took more than two years to complete.

Using St. Jude Cloud, Newman was able to conduct large-scale data analysis enabling him to identify the same UV-linked mutational signature in pediatric B-Cell leukemia patients over four days. Discovering these additional samples further helped researchers understand the possible link between UV damage and a blood cancer and potentially leads to the development of new therapies. Learn more about the St. Jude Cloud and its research capabilities via Q&A with Newman featured in the St. Jude Progress.

Like St. Jude Cloud, DNAnexus delivers fit-for-purpose community portals to advance scientific research through a secure and collaborative online environment that has been independently audited and certified. DNAnexus community research portals allow members to focus on discovery and innovation, removing the burden of secure data management, distribution, and data analysis. Other community research portals powered by DNAnexus include the FDA’s precisionFDA platform for advancing regulatory standards for NGS-based drug and devices, and the microbiome research platform, Mosaic, which facilitates the translation of microbiome research into clinical applications.

Learn more about DNAnexus community portals and determine which use case is right for you.

We’re coming to the Windy City for AACR

American Association for Cancer ResearchWe are excited to be attending our very first American Association for Cancer Research 2018 Annual Meeting in Chicago, April 14th – April 18th alongside thousands of oncology researchers and clinicians. We will be exhibiting at booth 2845, located next to the St. Jude Children’s Research Hospital booth.

Last month we announced our partnership with St. Jude and Microsoft to analyze and store half a petabyte of pediatric cancer genomic data and attended HIMSS 2018 to promote the partnership alongside 43,000 IT & Healthcare professionals. At AACR, we will be highlighting our capabilities around portals which provide customized spaces for users to securely collaborate and globally scale their scientific research through removing the heavy lifting around secure data access, management, and analysis.

St. Jude Cloud, utilizing DNAnexus and deployed in Microsoft Azure , is a data-sharing resource for the global scientific community allowing researchers to mine, analyze and visualize NGS data for pediatric cancer and other life-threatening diseases. The portal enables St. Jude and researchers worldwide accelerated scientific discoveries around pediatric diseases by comparing a vast multitude of datasets in a regulated and compliant platform.

See what we have planned at AACR below! If you’re eager to schedule a meeting ahead of time with us, St. Jude Children’s Research Hospital, or Microsoft, email us!

DNAnexus Activities at AACR


Come visit the DNAnexus booth 2845 to get live demonstrations of the DNAnexus platform and DNAnexus Portals. Visit St. Jude Children’s Research Hospital booth 2844, for live demos of St. Jude Cloud and the Childhood Solid Tumor Network. Our scientific experts will be onsite to answer how our solutions could accelerate your cancer research.

Monday, April 16th

Tuesday, April 17th

Meet & Greets

Also in the booth will be times for scientific “meet-ups” with leading researchers from St. Jude Children’s Research Hospital and Microsoft Genomics. We’ll be providing more information in the upcoming weeks for the sessions via Twitter, (so make sure to follow us!).

Presentation showcasing the DNAnexus Platform

Scott Newman, Group Lead, Bioinformatics Analysis at St. Jude Children’s Research Hospital, will be giving a presentation at AACR showcasing how major cloud-computing infrastructure is necessary to making complex bioinformatics pipelines easily accessible and providing intuitive visualizations for data mining in the Cloud. You can read the abstract and see the meeting agenda on the AACR website.

Track: Computational Methods and Resources for Cancer Research
Access, visualize and analyze 5,000 whole-genomes from pediatric cancer patients on St. Jude Cloud
Sunday, April 15th
3:05 – 3:20
Room N228 – McCormick Place North (Level 2)

Visit us at booth 2845 to learn more about DNAnexus, see a live demo of the platform or portals. If you would like to schedule a meeting, make sure to email us!

The Case for Rapid Genome Sequencing – Saving Critically Ill Newborns

Andrew, Alpha, and EJ Authors

From its inception, genomics has captured public imagination for its promise to save lives and improve the human condition. The rapid Whole Genome Sequencing (rWGS) work published by Rady Children’s Institute for Genomic Medicine (RCIGM) in Nature Genomic Medicine represents as near a manifestation of that promise as any.

Genomics Rady Childrens
Source: Rady Children’s

Genetic disorders and congenital anomalies affect 6% of live births. Severe occurrences convert a time of joy into an urgent, chaotic race for answers to save a newborn’s life and ease the child’s suffering. The paper describes RCIGM’s diagnosis of 42 infants admitted to the NICU, over the first nine months of their rWGS operation.  Of those infants, 43% were diagnosed by sequencing (compared to 2% by traditional methods). Consequently, there was a change in medical management in 72% of those cases. In some instances, this adjustment resulted in immediate, life-saving, targeted treatment that helped children avoid unneeded, high-risk, and costly surgeries.

On an economic basis, the sequencing program was strongly justified – reducing the inpatient cost between $800,000 – $2,000,000 by improving patient outcome, avoiding futile procedures and ending the diagnostic odyssey.

The study, which was part of RCIGM’s Rapid Newborn Diagnostics Program and a larger National Institute of Health (NIH) research program led by Dr. Stephen Kingsmore, MD, DSc, President and CEO of RCIGM, took place between July 2016 and March 2017.

Achieving these results demand broad and exceptional expertise from RCIGM – spanning patient consent, sample accessioning, sequencing, analysis, and diagnostic turnaround of results in a high-pressure environment within a very short time frame (2 – 5 days), all the while remaining compliant to CAP/CLIA standards. The scientific challenge is especially great as causal variants in newborns are far more likely to have never been encountered before due to their lethality, more likely to arise de novo, and typically involve complex, hard to call structural variants.

RCIGM has clearly demonstrated the model of rWGS to save lives, suffering, and expense. The next challenge is to expand the reach of the program to achieve the greatest impact. Now there are plans to implement the Rady’s program at other regional hospitals such as Children’s Minnesota, Children’s Hospital of Orange County , Children’s Hospital Colorado, and Nicklaus Children’s Hospital in Miami (with more expected to follow over time). DNAnexus is excited to be a part of this monumental effort to transform pediatric medicine, powering RCIGM’s rWGS analysis and providing the key infrastructure to link up the pipeline partners.

“I believe this is a monumental publication that clearly demonstrates the diagnostic and clinical utility of whole genome sequencing with hard numbers. We are very motivated to propel this technology into pediatric institutions around the country and grow the evidence base. We are excited to be working with DNAnexus to scale our operations and help create a secure and seamless logistical framework.” said Dr. Narayanan Veeraraghavan, Director of Informatics & IT at RCIGM.

As RCIGM’s rWGS program expands to clinical partners around the country, they will be able to leverage the scalability, flexibility and security offered by the DNAnexus Platform. The DNAnexus platform is well suited to support such collaborative efforts, enabling secure sharing of data and tools in an efficient manner.

I strongly encourage you to read the paper. It contains descriptions of several cases. Though identities are withheld and the work is highly professional and academic, the details tell a deeply human story –  a risky procedure avoided at the last minute, a child saved from a likely condition of neurological impairment. The story refreshes the vision of hope from the early days of genomics as the first draft of the genome was completed – the promise that through effort and ingenuity, we can secure a healthier and safer future for our children.