Automated tumor analysis for molecular profiling in lung cancer

Oncotarget
Peter W HamiltonManuel Salto-Tellez

Abstract

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and s...Continue Reading

References

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Citations

Jun 14, 2017·Cancer Cytopathology·Matthew G Hanna, Liron Pantanowitz
Oct 3, 2018·Histopathology·Manuel Salto-TellezPeter Hamilton
Feb 16, 2019·The Journal of Pathology. Clinical Research·Robert PellUNKNOWN UK National Cancer Research Institute (NCRI) Cellular-Molecular Pathology (CM-Path) quality assurance working group
Oct 22, 2019·Frontiers in Medicine·Ahmed SeragPeter Hamilton
Jan 19, 2016·Laboratory Investigation; a Journal of Technical Methods and Pathology·Jacob S SarneckiPei-Hsun Wu
Aug 25, 2017·Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission·B F Boyce
Aug 9, 2020·Journal of Clinical Pathology·Irene GulloFernando Schmitt
Dec 14, 2016·Histopathology·Jon Griffin, Darren Treanor
May 7, 2019·Acta Cytologica·Derek B Allison, Christopher J VandenBussche

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Datasets Mentioned

BETA
NIB13-0079

Methods Mentioned

BETA
PCR
nucleic acid extraction
feature extraction

Software Mentioned

OncotypeDX
Aperio
TumorMap
Mammaprint
Prolaris
Oncotype
TissueMark
PathXL

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