St. Jude Children’s Research Hospital scientists have unveiled an online data-sharing, analysis and collaboration portal that marks a new era of research into childhood cancer survivorship. Left to right: Leslie Robison, PhD; Nickhill Bhakta, MD, MPH; Xin Zhou, PhD; Jinghui Zhang, PhD.
St. Jude Children’s Research Hospital scientists have unveiled an online data-sharing, analysis and collaboration portal that marks a new era of research into childhood cancer survivorship.
The survivorship portal on St. Jude Cloud makes clinical and genomic data from thousands of childhood cancer survivors accessible to researchers worldwide. A poster detailing the website was presented today at the American Society of Human Genetics (ASHG) annual meeting in Houston.
“Our goal is to accelerate the rate of discovery in pediatric cancer survivorship research,” said Leslie Robison, Ph.D., chair of the St. Jude Department of Epidemiology and Cancer Control. “We are convinced the best way to achieve this is by using St. Jude Cloud to make the clinical and genomic data from the St. Jude Lifetime Cohort study available to the global research community.”
The U.S. is currently home to more than 500,000 childhood cancer survivors. The number is expected to grow as pediatric cancer survivorship rates improve.
St. Jude LIFE—the St. Jude Lifetime Study cohort—includes information from more than 5,835 childhood cancer survivors who were treated at St. Jude between 1962 and 2012. Study participants return to campus throughout their lives for screenings and tests.
The study began in 2007 to improve the lives of long-term childhood cancer survivors. St. Jude LIFE is now the largest cohort of clinically assessed childhood cancer survivors in the world.
Survivorship Portal
The Survivorship Portal combines whole-genome sequencing data of 3,006 St. Jude LIFE participants with detailed clinical data. Along with demographic information, the data include pediatric cancer diagnosis, outcome and treatment. Genotype data were generated from whole genome sequencing of 90 million curated single nucleotide polymorphisms (the most common type of genetic variation in people). This included 30% of single nucleotide polymorphisms representing novel variants not present in public databases. Information on treatment late effects and chronic health conditions, graded by severity, is also available.
The portal features two apps developed by St. Jude scientists to help researchers anywhere integrate, analyze and visualize the data. The tools, the Clinical Dictionary Browser and Genome Paint,“talk” to each other.
“This enables users to analyze genotype-phenotype associations on the fly, making the Survivorship Portal a powerful tool for discovery using cloud computing infrastructure,” said Jinghui Zhang, Ph.D., chair of the St. Jude Department of Computational Biology. “We anticipate that the rich and highly curated genomic data will be a valuable resource for the broad human genetics research community.”
Xin Zhou, Ph.D., of St. Jude Computational Biology led the team that developed the apps. He also presented the work at ASHG.
The portal includes online tutorials to help investigators get started. Additional analytic tools will be added soon. Survivorship data will be added annually.
St. Jude Cloud
The Survivorship Portal, Genome Paint and the Clinical Dictionary Browser are the latest additions to St. Jude Cloud. Launched last year, St. Jude Cloud houses more than 10,000 genomes from pediatric cancer patients, cancer survivors and catastrophic disease patients. It is the world’s largest repository of pediatric genomics data and offers a suite of unique analytic tools and visualizations.
The site was developed by scientists at St. Jude in collaboration with Microsoft and DNAnexus. The goal was to accelerate data mining, analysis and visualization capabilities in a secure cloud-based environment. To date, investigators from more than 450 institutions in 16 countries have access to St. Jude Cloud resources.
St. Jude Children's Research Hospital
St. Jude Children's Research Hospital is leading the way the world understands, treats and cures childhood cancer and other life-threatening diseases. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20% to 80% since the hospital opened more than 50 years ago. St. Jude freely shares the breakthroughs it makes, and every child saved at St. Jude means doctors and scientists worldwide can use that knowledge to save thousands more children. Families never receive a bill from St. Jude for treatment, travel, housing and food — because all a family should worry about is helping their child live. To learn more, visit stjude.org or follow St. Jude on social media at @stjuderesearch.