Pediatric Genomic Data Inventory: A Valuable Resource of Pediatric Cancer Projects

Circos plot from PGDI banner
Pamela C. Birriel, Ph.D. and Jaime M. Guidry Auvil, Ph.D.

Each year, more than 200,000 children and adolescents under the age of 20 are diagnosed with cancer worldwide1. Although the cancer mortality rate has declined, cancer remains an important cause of child mortality with an estimated 80,000 cancer-related deaths worldwide in children over the age of one1-3. Cancer is a genetic disease in that pediatric malignancies of the same name can differ in an older adult population, thereby requiring potentially unique therapeutic strategies. The Office of Cancer Genomics (OCG) at the National Cancer Institute (NCI) is committed to advancing the understanding of the biology, as well as improving therapeutic mortality and morbidity, of childhood cancers through its highly-successful Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. The pediatric research community has benefitted from programs like TARGET that provide access to well-curated molecular, genomic, and clinical data from large numbers of children and young adults, alongside the computational resources to analyze it.

To fuel new discoveries and treatments specific to the field of pediatric oncology, OCG developed a dynamic resource called the Pediatric Genomic Data Inventory (PGDI) to allow investigators to more easily locate genomic datasets being generated globally. PGDI is a new open-access resource for identifying and locating genomic datasets that can be used to further the understanding of childhood cancers and develop better treatment protocols for sick children. This resource lists ongoing and completed molecular characterization projects of pediatric cancer cohorts from the United States and other countries, along with some basic details and reference metadata.

The newly-launched PGDI is an evolving catalog that will be continually updated as new information is deposited by the research community and is only valuable if people contribute. Researchers are urged to participate and submit information about any pediatric molecular characterization cohort(s) and/or project(s) by becoming a ‘PGDI Data Contributor’. The success of this resource requires ongoing participation by investigators around the world, and feedback is both welcomed and encouraged.

The PGDI Contributor Application registers a secure submitter account (Figure 1). Detailed login instructions are then emailed to the applicant once a secure account has been created by an OCG site administrator.

PGDI Contributor Application

Figure 1: PGDI Contributor Application.

Once an account is secured, data contributors can log-in and add content to the PGDI by completing the online form registering a new pediatric cancer project. Contributors have the option to submit information via an interactive online form or by uploading a tab-delimited file (Figure 2). Contributors can edit their submitted information at any time using either method.

PGDI Template

Figure 2: Tab-delimited Template File Provided for Adding PGDI Content.

When adding content for PGDI, whatever available detailed information should be included for the following categories: genomic project information; disease descriptors; patient case information; sequencing available (e.g. whole exome, whole genome, DNA panel, transcriptome); additional molecular data types available; and project contact information. Instructions for Contributors provide further detailed instructions on how to register a new pediatric cancer sequencing project.

Submitted information is sent to a PGDI moderator within NCI to review for completeness and formatting prior to posting.

The OCG website provides the ability to view, sort, and search through the interactive inventory through the PGDI Display in a customized way. Individuals can view the default display categories, select up to 10 categories among cancer types and data (Figure 3) to create a custom view, and/or download the complete tab-delimited inventory.

PGDI Display

Figure 3: Table Column Options Available for the PGDI Display.

PGDI, the investigator-driven community resource, will continue to grow with data as data generation and participant interaction expand. For more details about PGDI and/or for help accessing and submitting data, please contact the NCI OCG at: ocg@mail.nih.gov.

References

  1. International Agency for Research on Cancer. International Childhood Cancer Day 2018. World Health Organization, 2018. Retrieved from https://www.iarc.fr/featured-news/media-centre-iarc-news-international-c...   
  2. National Cancer Institute. Cancer in Children and Adolescents. National Institutes of Health, 2017. Retrieved from https://www.cancer.gov/types/childhood-cancers/child-adolescent-cancers-fact-sheet
  3. National Cancer Institute. Childhood Cancers. National Institutes of Health, 2017. Retrieved from https://www.cancer.gov/types/childhood-cancers
Last updated: November 30, 2018