OpenPBTA: A Revolutionary Genomic Resource for Pediatric Brain Tumors
Researchers from a number of prestigious institutions like Children’s Hospital of Philadelphia (CHOP), Children’s Brain Tumor Network (CBTN), Pacific Pediatric Neuro-Oncology Consortium (PNOC), and Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Lab came together to create the Open Pediatric Brain Tumor Atlas (OpenPBTA). OpenPBTA is a cutting-edge genomic resource for pediatric brains tumors that is accessible to anyone seeking to discover new therapeutic targets and to translate research into clinical practice. It is the first large-scale, collaborative open analysis of genomic data providing a cloud-based resource for researchers seeking more comprehensive data on pediatric brain tumors.
Pediatric Brain Tumors – The Need for Comprehensive Data
Pediatric brain tumors are the leading cause of cancer-related deaths in children in the United States. These tumors differ in severity, with some having a nearly universal fatal prognosis, while others have relatively high long-term survival rates, but all brain tumors have a negative impact on patients and their families.
Limited access to tissue samples and patient-derived cell lines has been a significant barrier to understanding the differences between pediatric brain tumors at a molecular level. That sought-after data could lead to better diagnostic techniques and targeted therapies that could treat these tumors.
Genomic and Clinical Data of 1000 Pediatric Brain Tumors
CBTN and PNOC began extracting and preparing approximately 6,000 tumor samples in 2011, with over 68,000 subsamples. Over 1,000 of these tumors were sequenced to create the initial release of the Pediatric Brain Tumor Atlas (PTBA) in 2018. The data was made available to researchers so they could study which variants could be driving specific brain tumors.
With the help of the Alex’s Lemonade Stand Foundation Childhood Cancer Data Laboratory, researchers created an open-source version of this atlas, the Open Pediatric Brain Tumor Atlas (OpenPBTA), which could analyze this data. At the time of the study, OpenPBTA contained genomic and clinical data from over 1000 pediatric brain tumors and 22 cell lines derived from CBTN and PNOC patients. OpenPBTA provides a real-time open framework to genomically characterize pediatric brain tumors.
OpenPBTA’s Role in Identifying Genetic Variants Linked To Poorer Outcomes
Loss of the tumor suppressor gene TP53 is a significant marker of poor overall survival in fast-growing brain and spinal cord tumors, called ependymomas, and certain diffuse midline gliomas. Gene dysregulation has also been implicated in high-grade hypermutant gliomas. The OpenPBTA model of real-time co-collaboration supported by PNOC and CBTN has not only fueled new discoveries, but also innovative ways to perform the required science in the name of accelerated collaborative innovation for children affected by brain tumors.
OpenPBTA’s revolutionary approach could serve as a model for other cancers, pediatric or otherwise. It enables experts from across the world to come together and gain a deeper understanding of the leading cause of cancer-related death in children and young adults.
Expanding Horizons – OpenPBTA’s Contribution to Medical Research
The Open Pediatric Brain Tumor Atlas has the potential to revolutionize the treatment of pediatric brain tumors. Using OpenPBTA will help researchers to develop innovative treatments to target pediatric brain tumors’ unique genetic structures and test these treatments more rapidly.
OpenPBTA facilitates the development of better diagnostic methods and safer therapies with fewer negative impacts on patients. By providing complete and sound genomic data, OpenPBTA paves the way for a more precise understanding of how pediatric brain tumors work and how genetic irregularities lead to these malignancies.
The potential for expanding the OpenPBTA model of real-time co-collaboration across other forms of cancers is enormous. OpenPBTA has introduced a viable and practical solution to the challenge of accessing robust genomic data.
The Outcome
The Open Pediatric Brain Tumor Atlas enables researchers to collaborate to achieve better treatments for pediatric brain tumors. The platform is the first step in treating these tumors that afflict children and young adults. OpenPBTA provides a unique resource to perform genomic characterizations of the complexities of pediatric brain cancers, in real-time, co-collaboratively. It is an essential tool to enable experts worldwide to work towards developing targeted treatments, diagnostics, and therapies that improve survival rates and patient outcomes.
Summary
OpenPBTA is a first-of-its-kind, open source, reproducible analysis platform for pediatric brain tumors. The platform is accessible to anyone seeking to discover new therapeutic targets and to translate research into clinical practice. Researchers have used the initial release of the Pediatric Brain Tumor Atlas (PTBA) in 2018 to identify genetic variants linked to poorer outcomes. OpenPBTA contained genomic and clinical data from over 1000 pediatric brain tumors and 22 cell lines derived from CBTN and PNOC patients. Loss of the tumor suppressor gene TP53 is a significant marker of poor overall survival in fast-growing brain and spinal cord tumors, called ependymomas, and certain diffuse midline gliomas. Gene dysregulation has also been implicated in high-grade hypermutant gliomas.
Additional Piece
The Future of Open Science and Collaborative Research
The Open Pediatric Brain Tumor Atlas represents a turning point in the field of pediatric brain tumor research. The collaborative model created by OpenPBTA allows experts worldwide to come together and work towards creating effective treatments for patients. It empowers researchers from different cultures, disciplines, and countries to work seamlessly together, and by doing so, create more effective treatments.
Experts around the world can now access the complete set of genomic data that they need to decode pediatric brain tumors’ intricacies. OpenPBTA’s cloud-based framework helps scientists to co-collaborate with ease and speed up the discovery process, reducing the time to research and develop new treatments.
OpenPBTA is not just a groundbreaking genomic resource; it has also raised the bar for open science and effectively demonstrated new models of medical research that are more accessible, interoperable, and reusable by other researchers.
Quick Facts
The Open Pediatric Brain Tumor Atlas:
Offers an open-source, reproducible analysis platform for pediatric brain tumors.
Contains genomic and clinical data from over 1000 pediatric brain tumors and 22 cell lines.
Identifies loss of the tumor suppressor gene TP53 as a significant marker of poor overall survival in specific brain tumors.
Transforms the approach to genomic research, providing a cloud-based, open-source framework to genomically characterize pediatric brain tumors.
Fuels accelerated collaborative innovation for children affected by brain tumors.
This collaborative model created by OpenPBTA allows for accelerated advancements in treatments for brain tumors, enabling better patient outcomes, and improved survival rates. OpenPBTA not only addresses the challenges associated with understanding pediatric brain tumors, but also the underlying principles of how genomic and medical research can be conducted collaboratively worldwide.
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Researchers from Children’s Hospital of Philadelphia (CHOP), Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Lab, Children’s Brain Tumor Network (CBTN), Pacific Pediatric Neuro-Oncology Consortium (PNOC), and more than 20 other institutions have partnered to create a first-of-its-kind, open source, reproducible analysis platform for pediatric brain tumors. With the help of thousands of genomically sequenced samples, researchers have used this platform to identify initial findings on genetic variants associated with poorer outcomes that could help guide future diagnostic and therapeutic advances.
Details of the platform and those initial findings were published online today by the journal Cellular Genomics.
Pediatric brain tumors are collectively the leading cause of cancer-related death in children in the United States. However, the severity of pediatric brain tumors varies greatly, with some having a nearly universal fatal prognosis, while others have relatively high long-term survival rates, although all brain tumors have a negative impact on these children and their families. at least up to a certain point. Limited access to tissue samples and patient-derived cell lines has been a major barrier to understanding the differences between pediatric brain tumors at the molecular level. That long-sought data could lead to better diagnostic techniques and possible targeted therapies that could treat these deadly tumors.
In 2011, CBTN and PNOC began extracting and preparing what has now become nearly 6,000 tumor samples with more than 68,000 subsamples. More than 1,000 of these tumors were sequenced to form the initial release of the Pediatric Brain Tumor Atlas (PTBA) in 2018, and the data was nevertheless made available so that researchers could study which variants might be driving certain types of brain tumors. With the help of the Alex’s Lemonade Stand Foundation Childhood Cancer Data Laboratory, the team of researchers was able to create an open source version of this atlas, the Open Pediatric Brain Tumor Atlas (OpenPBTA), to analyze this data.
OpenPBTA is accessible to anyone conducting research seeking new therapeutic targets or finding new ways to translate research into clinical practice. At the time of this study, OpenPBTA contained genomic and clinical data from more than 1000 pediatric brain tumors and 22 cell lines derived from CBTN and PNOC patients. OpenPBTA provides a real-time open framework to genomically characterize pediatric brain tumors. It is the first large-scale, collaborative, open analysis of genomic data and provides a cloud-based resource for researchers seeking more comprehensive data on pediatric brain tumors.
“While there have been many advocates for an open source model for scientific research, nothing like this existed for pediatric cancer,” said Jo Lynne Rokita, PhD, a bioinformatics supervising scientist who leads OpenPBTA at the Center for the Data Driven Discovery (D3B) at CHOP and one of the study’s corresponding authors. “We designed OpenPBTA so that anyone could access the data, contribute to its analysis, and/or use it in their own research.”
“Collaboration is key to accelerating the discovery of new cures. OpenPBTA made it possible for experts from around the world to come together and gain a deeper understanding of the leading cause of cancer-related death in children and young adults,” said Jay Scott. , co-executive director Director of Alex’s Lemonade Stand Foundation.
Jaclyn N. Taroni, PhD, another corresponding author of the study and director of the Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Laboratory, said, “With our successful launch of OpenPBTA, we hope the research community will adapt this model to other cancers. pediatric.”
OpenPBTA is already giving researchers more information about the potential drivers of pediatric brain tumors. In this study, the researchers found that loss of the tumor suppressor gene TP53 it is a significant marker of poor overall survival in fast-growing brain and spinal cord tumors called ependymomas and certain diffuse midline gliomas, and gene dysregulation has also been implicated in high-grade hypermutant gliomas.
“No one institution can achieve the solution of pediatric brain tumors. The OpenPBTA model of real-time co-collaboration supported by PNOC and CBTN has not only fueled new discoveries, but also innovative ways to perform the required science in the name of accelerated collaborative innovation. for children affected by brain tumors,” said Sabine Mueller MD, PhD, MAS, professor of neurology, neurosurgery and pediatrics at the University of California, San Francisco, and director of PNOC and co-executive chair of CBTN.
This study was supported by the Alex’s Lemonade Stand Foundation (ALSF) Childhood Cancer Data Laboratory, an ALSF Young Investigator Award, ALSF Catalyst Awards, a CCDL ALSF Postdoctoral Training Grant, Children’s Hospital of Philadelphia Division of Neurosurgery, the Government Australian, Department of Education, St. Anna Kinderkrebsforschung, Austria, Mildred Scheel Early Career Center Dresden P2, funded by German Cancer Aid and National Institutes of Health (NIH) Grants 3P30 CA016520-44S5, U2C HL138346-03, U24 CA220457-03, K12GM081259 , R03-CA23036 and NIH Contract No. HHSN261200800001E. This project was also funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024, Work Order No. 75N91020F00003. Additionally, this work was supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics of the National Cancer Institute.
https://www.sciencedaily.com/releases/2023/05/230531150122.htm
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