Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Apr:5:479-486.
doi: 10.1200/CCI.20.00179.

BloodPAC Data Commons for Liquid Biopsy Data

Robert L Grossman  1   2 , Jonathan R Dry  3 , Sean E Hanlon  4 , Donald J Johann  5 , Anand Kolatkar  6 , Jerry S H Lee  7 , Christopher Meyer  1 , Lea Salvatore  2 , Walt Wells  1   8 , Lauren Leiman  9
Affiliations

BloodPAC Data Commons for Liquid Biopsy Data

Robert L Grossman et al. JCO Clin Cancer Inform. 2021 Apr.

Abstract

Purpose: The Blood Profiling Atlas in Cancer (BloodPAC) Data Commons (BPDC) is being developed and is operated by the public-private BloodPAC Consortium to support the liquid biopsy community. It is an interoperable data commons with the ultimate aim of serving as a recognized source of valid scientific evidence for liquid biopsy assays for industry, academia, and standards and regulatory stakeholders.

Methods: The BPDC is implemented using the open source Gen3 data commons platform (https://gen3.org). In particular, the BPDC Data Exploration Portal, BPDC Data Submission Portal, the BPDC Workspace Hub, and the BloodPAC application programming interface (API) were all automatically generated from the BloodPAC Data Model using the Gen3 data commons platform. BPDC uses Gen3's implementation of the data commons framework services so that it can interoperate through secure, compliant APIs with other data commons using data commons framework service, such as National Cancer Institute's Cancer Research Data Commons.

Results: The BPDC contains 57 studies and projects spanning more than 4,100 cases. This amounts to 5,700 aliquots (blood plasma, serum, or a contrived sample) that have been subjected to a liquid biopsy assay, quantified, and then contributed by members of the BloodPAC Consortium. In all, there are more than 31,000 files in the commons as of December 2020. We describe the BPDC, the data it manages, the process that the BloodPAC Consortium used to develop it, and some of the applications that have been developed using its API.

Conclusion: The BPDC has been the data platform used by BloodPAC during the past 4 years to manage the data for the consortium and to provide workspaces for its working groups.

PubMed Disclaimer

Conflict of interest statement

Robert L. GrossmanStock and Other Ownership Interests: Tempus, HealthSeqResearch Funding: Abbvie Jonathan R. DryEmployment: Tempus, AstraZenecaStock and Other Ownership Interests: AstraZeneca, Tempus Anand KolatkarStock and Other Ownership Interests: Epic SciencesPatents, Royalties, Other Intellectual Property: HD-SCA technology was developed by myself and members of my team while at The Scripps Research Institute, which has subsequently licensed the technology to Epic Sciences for exclusive commercial development Jerry S. H. LeeConsulting or Advisory Role: AtlasXomics Inc Lauren LeimanStock and Other Ownership Interests: Exact Sciences, Illumina, InVitae, Starr Surgical, LillyNo other potential conflicts of interest were reported.

Figures

FIG 1.
FIG 1.
The BloodPAC Data Commons data model. BloodPAC, Blood Profiling Atlas in Cancer; UAMS, University of Arkansas Medical Sciences; USC, University of Southern California.
FIG 2.
FIG 2.
The BloodPAC Data Commons portal. BloodPAC, Blood Profiling Atlas in Cancer.
FIG 3.
FIG 3.
The figure shows how applications can be built over the BloodPAC Data Commons API. The heatmap and plots described for application 3 can be seen at the top right of this image highlighted by the dashed rectangle. BloodPAC, Blood Profiling Atlas in Cancer; MTDE, minimum technical data elements; UAMS, University of Arkansas Medical Sciences; USC, University of Southern California.
See this image and copyright information in PMC

References

    1. Aggarwal C Rolfo CD Oxnard GR, et al. : Strategies for the successful implementation of plasma-based NSCLC genotyping in clinical practice. Nat Rev Clin Oncol 18:56-62, 2021 - PubMed
    1. Grossman RL: Data lakes, clouds, and commons: A review of platforms for analyzing and sharing genomic data. Trends Genet 35:223-234, 2019 - PMC - PubMed
    1. Grossman RL Abel B Angiuoli S, et al. : Collaborating to compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium. Clin Pharmacol Ther 101:589-592, 2017 - PMC - PubMed
    1. Febbo PG Martin A-M Scher HI, et al. : Minimum technical data elements for liquid biopsy data submitted to public databases. Clin Pharmacol Ther 107:730-734, 2020 - PMC - PubMed
    1. Godsey JH Silvestro A Barrett JC, et al. : Generic protocols for the analytical validation of next-generation sequencing-based ctDNA assays: A joint consensus recommendation of the BloodPAC's analytical variables working group. Clin Chem 66:1156-1166, 2020 - PMC - PubMed

Publication types