BloodPAC Data Commons (Liquid-Biopsy Data Commons)

The community data commons for liquid biopsy, operated by the BloodPAC Consortium (Blood Profiling Atlas in Cancer), a public-private partnership formed to accelerate and standardize blood-based cancer testing. It aggregates and harmonizes roughly 35 terabytes of data across about 75 studies and 14 cancer types, spanning circulating tumor DNA (ctDNA), circulating tumor cells, exosome and protein assays, and the matched clinical context such as diagnosis, treatment history, and outcomes. BloodPAC also defines the minimal technical, clinical, and patient data elements that liquid-biopsy datasets should carry, which makes this a reference point for how MRD and treatment-monitoring data are structured and reported. The commons runs on the open-source Gen3 platform at data.bloodpac.org. An open-access tier is freely available; controlled studies require a BloodPAC data access agreement. Described by Grossman et al., JCO Clinical Cancer Informatics, 2021.

Category
Genomics & Bioinformatics
Provider
BloodPAC Consortium (Blood Profiling Atlas in Cancer)
License
Per-study; open-access tier free, controlled tiers require a BloodPAC data access agreement
DOI
10.1200/CCI.20.00179
Hosted on
bucket data.bloodpac.org
Access
Access requires credentials issued by the data provider.
Source
https://www.bloodpac.org/data-commons
Data structure and loading code

Fields

project_idstring (program-project, i.e. the contri
subject / casestring (de-identified participant)
primary_diagnosis / cancer_typestring (1 of 14 cancer types)
sample / assay typestring (ctDNA | CTC | exosome | protein)
clinical contextBloodPAC dictionary: ~22 clinical-contex
data_file (GUID)string (object_id resolved to a signed U

Load the data

# api archive: no mount, credentialed Gen3 commons. Authenticate with your API key, then explore.
# pip install gen3
from gen3.auth import Gen3Auth
from gen3.submission import Gen3Submission
auth = Gen3Auth(refresh_file="~/.gen3/bloodpac-credentials.json")  # download from data.bloodpac.org profile
sub = Gen3Submission("https://data.bloodpac.org", auth)
print(sub.get_programs())  # then drill into projects/studies

Written for a Scigantic notebook, where /mnt/archive is the mounted dataset.

Analyze this dataset without downloading it

On Scigantic, BloodPAC Data Commons (Liquid-Biopsy Data Commons) opens in a hosted JupyterLab notebook with the data already mounted, so you can read files where they are stored instead of copying them first. Each notebook includes an AI assistant that can see the mounted files and write and run analysis code. Open the dataset page to launch a notebook, or browse the full catalog.

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