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Appropriate Statistical Methods to Assess Cross-study Diagnostic 23-Gene Expression Profile Test Performance for

Matthew S Goldberg1,2, Clay J Cockerell3, Jason H Rogers1

  • 1Castle Biosciences, Inc., Friendswood, TX.

The American Journal of Dermatopathology
|August 14, 2024
PubMed
Summary

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Standardizing calculation methods for the 23-gene expression profile (23-GEP) test is crucial for comparing diagnostic accuracy in cutaneous melanocytic neoplasms. Recalculating data revealed no significant differences between studies when using a unified approach.

Area of Science:

  • Dermatology
  • Molecular Diagnostics
  • Oncology

Background:

  • Comparing diagnostic accuracy of molecular tests for challenging skin tumors is difficult due to varying calculation methods.
  • A recent study reported lower accuracy for the 23-gene expression profile (23-GEP) test due to a unique method of handling indeterminate results.

Purpose of the Study:

  • To re-evaluate the accuracy of the 23-GEP test by standardizing its calculation methods.
  • To enable direct comparison of the 23-GEP test's performance across different studies.

Main Methods:

  • The accuracy metrics from Boothby-Shoemaker et al. were recalculated using the same methodology as previous studies.
  • Balanced cohorts were resampled to account for enrollment imbalances in benign versus malignant cases across studies.

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  • Sensitivity, specificity, positive predictive value, and negative predictive value were calculated and compared.

    • Main Results:

    • Corrected analysis of the Boothby-Shoemaker et al. data yielded a sensitivity of 92.1% and specificity of 94.4%.
    • No statistically significant differences in accuracy metrics (sensitivity, specificity, PPV, NPV) were found when comparing previous studies with the recalculated data using a unified approach.
    • The ranges for 23-GEP sensitivity were 90.4%-96.3%, specificity 87.3%-96.2%, PPV 88.5%-96.1%, and NPV 91.1%-96.3% across studies.

    Conclusions:

    • The 23-GEP test demonstrates consistent accuracy across studies when standardized calculation methods are applied.
    • Methodological standardization is essential for reliable cross-study comparisons of diagnostic test performance.
    • Consistent application of calculation methods ensures accurate assessment of molecular diagnostic tools for cutaneous melanocytic neoplasms.