Developing and using a data commons for understanding the molecular characteristics of germ cell tumors

Bo Ci, Shin Yi Lin, Bo Yao, Danni Luo, Lin Xu, Mark Krailo, Matthew J. Murray, James F Amatruda, A. Lindsay Frazier, Yang Xie

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Germ cell tumors (GCTs) are a rare disease, but they account for 15% of all malignancies diagnosed during adolescence. The biological mechanisms underpinning their development are only starting to be explored. Current GCT treatment may be associated with significant toxicity. Therefore, there is an urgent need to understand the molecular basis of GCT and identify biomarkers to tailor the therapy for individual patients. However, this research is severely hamstrung by the rarity of GCTs in individual hospitals/institutes. A publicly available genomic data commons with GCT datasets compiled from different institutes/studies would be a valuable resource to facilitate such research. In this study, we first reviewed publicly available web portals containing GCT genomics data, focusing on comparing data availability, data access, and analysis tools, and the limitations of using these resources for GCT molecular studies. Next, we specifically designed a GCT data commons with a web portal, GCT Explorer, to assist the research community to store, manage, search, share, and analyze data. The goal of this work is to facilitate GCT molecular basis exploration and translational research.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages263-275
Number of pages13
DOIs
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
Volume2195
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Data commons
  • Data standards
  • Germ cell tumor

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Ci, B., Lin, S. Y., Yao, B., Luo, D., Xu, L., Krailo, M., Murray, M. J., Amatruda, J. F., Frazier, A. L., & Xie, Y. (2021). Developing and using a data commons for understanding the molecular characteristics of germ cell tumors. In Methods in Molecular Biology (pp. 263-275). (Methods in Molecular Biology; Vol. 2195). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-0860-9_17