A portal for sharing, analysing and visualising paediatric cancer survivorship data is enabling doctors to improve understanding of the challenges faced by these patients.
The aim of the St. Jude Survivorship Portal, created by scientists at St. Jude Children’s Research Hospital, Memphis, Tennessee, USA, is to enable researchers to make new discoveries with just “one click”, the team say.
It is a big-data platform that incorporates clinical and genomic information, integrating three dimensions of data: whole genomic sequencing, treatment exposure and outcomes.
Writing in Cancer Discovery, the team reveals that the free-to-use portal houses 1,600 phenotypic variables and 400 million genetic variants from more than 7,700 childhood cancer survivors.
Co-corresponding author Dr Jinghui Zhang, of the St. Jude Department of Computational Biology said: “In the past, people would spend weeks downloading, analysing, organising and summarising data into figures — now you can do all that in just minutes.”
Users can assemble custom cohorts by specifying clinical and genetic variables for comparative analysis. The portal provides a range of additional features, including genome exploration, statistical testing and cumulative incidence and regression analysis, with open access and free computing.
The portal builds on two significant survivorship cohorts at the hospital: the Childhood Cancer Survivor Study (CCSS) and the St. Jude Lifetime Cohort (St. Jude LIFE). The former includes 31 institutions in North America and compiles data on a range of childhood cancers. The latter is a long-term follow-up study where St. Jude patients are brought back to the hospital every five years for an assessment.
Together, these cohorts provide a rich data source for investigators to mine for new insights.
In the Cancer Discovery report, the researchers share examples of findings they made using the portal. These include comparing the use and associated outcomes for two types of platinum chemotherapy: cisplatin and carboplatin. They found cisplatin was associated with greater auditory toxicity than carboplatin.
They also discovered a novel association between mental health, age and limb amputation, finding that a teenager who undergoes amputation has increased resilience against poor mental health compared with a younger child.
The team also identified novel genetic variants in the gene MAGI3 which was strongly linked to cardiomyopathy risk in survivors of African ancestry.
“An early-career or scientist without a computing background can come to the portal with a question in mind and, with just a few minutes and a few clicks, become a kind of bioinformatics scientist or epidemiologist,” Dr Zhang said.
Source:
Matt GY, Sioson E, Shelton K, Wang J, Lu C, Zaldivar Peraza A, Gangwani K, Paul R, Reilly C, Acić A, Liu Q, Sandor SR, McLeod C, Patel J, Wang F, Im C, Wang Z, Sapkota Y, Wilson CL, Bhakta N, Ness KK, Armstrong GT, Hudson MM, Robison LL, Zhang J, Yasui Y, Zhou X. (2024) “St. Jude Survivorship Portal: sharing and analyzing large clinical and genomic datasets from pediatric cancer survivors.” Cancer Discovery, April 2024, doi: 10.1158/2159-8290.CD-23-1441.
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