Digital counting of tissue cells for molecular analysis: the QuANTUM pipeline

Vincenzo L'Imperio; Giorgio Cazzaniga; Mauro Mannino; Davide Seminati; Francesco Mascadri; Joranda Ceku; Gabriele Casati; Francesca Bono; Catarina Eloy; Elena Guerini Rocco; Chiara Frascarelli; Matteo Fassan; Umberto Malapelle; Fabio Pagni

doi:10.1007/s00428-024-03794-9

Digital counting of tissue cells for molecular analysis: the QuANTUM pipeline

Virchows Arch. 2024 Mar 26. doi: 10.1007/s00428-024-03794-9. Online ahead of print.

Authors

Vincenzo L'Imperio¹, Giorgio Cazzaniga², Mauro Mannino², Davide Seminati², Francesco Mascadri², Joranda Ceku², Gabriele Casati², Francesca Bono², Catarina Eloy^{3

4}, Elena Guerini Rocco^{5

6}, Chiara Frascarelli^{5

6}, Matteo Fassan^{7

8}, Umberto Malapelle⁹, Fabio Pagni²

Affiliations

¹ Department of Medicine and Surgery, Pathology, IRCCS Fondazione San Gerardo Dei Tintori, University of Milano-Bicocca, Milan, Italy. vincenzo.limperio@unimib.it.
² Department of Medicine and Surgery, Pathology, IRCCS Fondazione San Gerardo Dei Tintori, University of Milano-Bicocca, Milan, Italy.
³ Pathology Laboratory, Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.
⁴ Pathology Department, Medical Faculty of University of Porto, Porto, Portugal.
⁵ Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy.
⁶ Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
⁷ Surgical Pathology and Cytopathology Unit, Department of Medicine, DIMED, University of Padua, Padua, Italy.
⁸ Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy.
⁹ Department of Public Health, University of Naples Federico II, Naples, Italy.

PMID: 38532196
DOI: 10.1007/s00428-024-03794-9

Abstract

The estimation of tumor cellular fraction (TCF) is a crucial step in predictive molecular pathology, representing an entry adequacy criterion also in the next-generation sequencing (NGS) era. However, heterogeneity of quantification practices and inter-pathologist variability hamper the robustness of its evaluation, stressing the need for more reliable results. Here, 121 routine histological samples from non-small cell lung cancer (NSCLC) cases with complete NGS profiling were used to evaluate TCF interobserver variability among three different pathologists (pTCF), developing a computational tool (cTCF) and assessing its reliability vs ground truth (GT) tumor cellularity and potential impact on the final molecular results. Inter-pathologist reproducibility was fair to good, with overall Wk ranging between 0.46 and 0.83 (avg. 0.59). The obtained cTCF was comparable to the GT (p = 0.129, 0.502, and 0.130 for surgical, biopsies, and cell block, respectively) and demonstrated good reliability if elaborated by different pathologists (Wk = 0.9). Overall cTCF was lower as compared to pTCF (30 ± 10 vs 52 ± 19, p < 0.001), with more cases < 20% (17, 14%, p = 0.690), but none containing < 100 cells for the algorithm. Similarities were noted between tumor area estimation and pTCF (36 ± 29, p < 0.001), partly explaining variability in the human assessment of tumor cellularity. Finally, the cTCF allowed a reduction of the copy number variations (CNVs) called (27 vs 29, - 6.9%) with an increase of effective CNVs detection (13 vs 7, + 85.7%), some with potential clinical impact previously undetected with pTCF. An automated computational pipeline (Qupath Analysis of Nuclei from Tumor to Uniform Molecular tests, QuANTUM) has been created and is freely available as a QuPath extension. The computational method used in this study has the potential to improve efficacy and reliability of TCF estimation in NSCLC, with demonstrated impact on the final molecular results.

Keywords: Computational pathology; Molecular pathology; NGS; Non-small cell lung cancer; Tumor cellular fraction.

Abstract

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