Artificial intelligence for detection of microsatellite instability in colorectal cancer-a multicentric analysis of a pre-screening tool for clinical application

A Echle, N Ghaffari Laleh, P Quirke, H I Grabsch, H S Muti, O L Saldanha, S F Brockmoeller, P A van den Brandt, G G A Hutchins, S D Richman, K Horisberger, C Galata, M P Ebert, M Eckardt, M Boutros, D Horst, C Reissfelder, E Alwers, T J Brinker, R LangerJ C A Jenniskens, K Offermans, W Mueller, R Gray, S B Gruber, J K Greenson, G Rennert, J D Bonner, D Schmolze, J Chang-Claude, H Brenner, C Trautwein, P Boor, D Jaeger, N T Gaisa, M Hoffmeister, N P West, J N Kather*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

BACKGROUND: Microsatellite instability (MSI)/mismatch repair deficiency (dMMR) is a key genetic feature which should be tested in every patient with colorectal cancer (CRC) according to medical guidelines. Artificial intelligence (AI) methods can detect MSI/dMMR directly in routine pathology slides, but the test performance has not been systematically investigated with predefined test thresholds.

METHOD: We trained and validated AI-based MSI/dMMR detectors and evaluated predefined performance metrics using nine patient cohorts of 8343 patients across different countries and ethnicities.

RESULTS: Classifiers achieved clinical-grade performance, yielding an area under the receiver operating curve (AUROC) of up to 0.96 without using any manual annotations. Subsequently, we show that the AI system can be applied as a rule-out test: by using cohort-specific thresholds, on average 52.73% of tumors in each surgical cohort [total number of MSI/dMMR = 1020, microsatellite stable (MSS)/ proficient mismatch repair (pMMR) = 7323 patients] could be identified as MSS/pMMR with a fixed sensitivity at 95%. In an additional cohort of N = 1530 (MSI/dMMR = 211, MSS/pMMR = 1319) endoscopy biopsy samples, the system achieved an AUROC of 0.89, and the cohort-specific threshold ruled out 44.12% of tumors with a fixed sensitivity at 95%. As a more robust alternative to cohort-specific thresholds, we showed that with a fixed threshold of 0.25 for all the cohorts, we can rule-out 25.51% in surgical specimens and 6.10% in biopsies.

INTERPRETATION: When applied in a clinical setting, this means that the AI system can rule out MSI/dMMR in a quarter (with global thresholds) or half of all CRC patients (with local fine-tuning), thereby reducing cost and turnaround time for molecular profiling.

Original languageEnglish
Article number100400
Number of pages12
JournalESMO Open
Volume7
Issue number2
Early online date2 Mar 2022
DOIs
Publication statusPublished - Apr 2022

Keywords

  • Lynch syndrome
  • MODEL
  • PREDICTION
  • RISK
  • artificial intelligence
  • biomarker
  • colorectal cancer
  • deep learning
  • microsatellite instability

Fingerprint

Dive into the research topics of 'Artificial intelligence for detection of microsatellite instability in colorectal cancer-a multicentric analysis of a pre-screening tool for clinical application'. Together they form a unique fingerprint.

Cite this