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Assessing consistency across functional screening datasets in cancer cells.

Ling Cai1,2,3, Hongyu Liu1, John D Minna3,4,5,6

  • 1Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA.

Bioinformatics (Oxford, England)
|June 3, 2021
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Summary

This study introduces a new method to assess the consistency of cancer cell line screening data, revealing poor concordance in many datasets. A web tool, the Functional Data Consistency Explorer (FDCE), is now available for global data consistency analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • High-throughput screening in cancer cell lines is crucial for identifying therapeutic agents and targets.
  • Previous consistency assessments were limited, examining only two datasets and selected features, potentially overlooking global data concordance issues.

Purpose of the Study:

  • To develop and present novel measures for assessing the global consistency of functional genomics and compound screening data in cancer cell lines.
  • To create an accessible web application for users to explore and visualize data consistency.

Main Methods:

  • Assembled nine compound screening datasets and three functional genomics datasets.
  • Derived direct and indirect measures of data consistency, including associations with copy number-adjusted gene expression data.
  • Integrated consistency measures into an interactive web application, the Functional Data Consistency Explorer (FDCE).

Main Results:

  • Identified significant inconsistencies across multiple cancer cell line screening datasets.
  • Developed a comprehensive approach to assess global data consistency beyond selected features.
  • The Functional Data Consistency Explorer (FDCE) enables interactive querying and visualization of feature-specific data consistency.

Conclusions:

  • Existing cancer cell line screening data exhibit considerable inconsistencies, impacting the reliability of therapeutic agent and target identification.
  • The developed functional data consistency measures and the FDCE web tool provide a valuable resource for researchers to evaluate data reliability.
  • Promotes more rigorous assessment of high-throughput screening data for improved translational research in cancer therapy.