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Creating reproducible pharmacogenomic analysis pipelines.

Anthony Mammoliti1, Petr Smirnov1,2,3, Zhaleh Safikhani1,2,3

  • 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

Scientific Data
|September 5, 2019
PubMed
Summary
This summary is machine-generated.

Researchers developed reproducible pharmacogenomic workflows for breast cancer research using the Common Workflow Language. These standardized pipelines integrate multimodal data, enhancing data sharing and future cancer research.

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Area of Science:

  • Pharmacogenomics
  • Computational Biology
  • Bioinformatics

Background:

  • Reproducibility and data sharing are significant challenges in pharmacogenomics due to large, high-throughput multimodal datasets.
  • A lack of standardized, scalable, and flexible workflows hinders large-scale analyses in the field.

Purpose of the Study:

  • To develop standardized, reproducible, and scalable pharmacogenomic workflows for processing complex biological data.
  • To create portable data objects combining pharmacological and molecular profiles for breast cancer research.
  • To enhance data provenance and accessibility for the scientific community.

Main Methods:

  • Implementation of pharmacogenomic analysis pipelines using the Common Workflow Language (CWL).
  • Processing of two distinct breast cancer datasets, integrating multimodal data.
  • Packaging of processed data and workflows into portable data objects.

Main Results:

  • Successful development and application of CWL-based workflows for reproducible pharmacogenomic analysis.
  • Creation of integrated data objects containing both pharmacological and molecular profiles.
  • Shared data objects and workflows on Harvard Dataverse and Code Ocean with unique DOIs.

Conclusions:

  • The developed CWL workflows address key challenges in pharmacogenomic data analysis, promoting reproducibility and transparency.
  • Portable data objects and shared workflows facilitate future cancer research and data reuse.
  • The use of Digital Object Identifiers ensures data provenance and persistent accessibility.