Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning.

Gut
Korsuk SirinukunwattanaS:CORT consortium

Abstract

Complex phenotypes captured on histological slides represent the biological processes at play in individual cancers, but the link to underlying molecular classification has not been clarified or systematised. In colorectal cancer (CRC), histological grading is a poor predictor of disease progression, and consensus molecular subtypes (CMSs) cannot be distinguished without gene expression profiling. We hypothesise that image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data and to resolve unclassifiable or heterogeneous cases. In this study, we present an image-based approach to predict CRC CMS from standard H&E sections using deep learning. Training and evaluation of a neural network were performed using a total of n=1206 tissue sections with comprehensive multi-omic data from three independent datasets (training on FOCUS trial, n=278 patients; test on rectal cancer biopsies, GRAMPIAN cohort, n=144 patients; and The Cancer Genome Atlas (TCGA), n=430 patients). Ground truth CMS calls were ascertained by matching random forest and single sample predictions from CMS classifier. Image-based CMS (imCMS) accurately classified slides in unseen datasets from TCGA (n=43...Continue Reading

References

Jun 28, 2000·Cancer·P Kleihues, L H Sobin
Mar 24, 2007·Nature Reviews. Drug Discovery·Mark R TrusheimFrank L Douglas
Apr 3, 2009·The New England Journal of Medicine·Eric Van CutsemPhilippe Rougier
Apr 12, 2011·The Oncologist·Susanna B ParkMatthew C Kiernan
Aug 28, 2014·Molecular Oncology·Manuel Salto-TellezPeter W Hamilton
Feb 24, 2015·Nature Genetics·Claudio IsellaEnzo Medico
Oct 13, 2015·Nature Medicine·Justin GuinneySabine Tejpar
May 7, 2016·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Philip D DunneSandra Van Schaeybroeck
Jul 18, 2016·Medical Image Analysis·Anant Madabhushi, George Lee
Dec 7, 2016·Nature Reviews. Clinical Oncology·Cornelis J A PuntLouis Vermeulen
Jan 5, 2017·Nature Reviews. Cancer·Rodrigo DienstmannJosep Tabernero
Feb 6, 2017·Bioinformatics·Vlad PopoviciFred Bosman
Nov 9, 2017·Nature Reviews. Clinical Oncology·Ibiayi Dagogo-Jack, Alice T Shaw
Dec 14, 2017·Gut·Mark LawlerUNKNOWN Bowel Cancer UK Critical Research Gaps in Colorectal Cancer Initiative
Oct 3, 2018·Histopathology·Manuel Salto-TellezPeter Hamilton
Mar 20, 2019·Nature Reviews. Gastroenterology & Hepatology·Karuna GaneshLuis A Diaz

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Citations

Nov 19, 2020·British Journal of Cancer·Amelie EchleJakob Nikolas Kather
Jan 11, 2021·Current Opinion in Genetics & Development·Tamsin Rm LannaganOwen J Sansom
Feb 19, 2021·Computational and Structural Biotechnology Journal·M P HumphriesM Salto-Tellez
May 11, 2021·World Journal of Gastroenterology : WJG·Jia-Sheng CaoXiu-Jun Cai
Jun 8, 2021·World Journal of Gastroenterology : WJG·Soma KobayashiVincent W Yang
Jun 18, 2021·World Journal of Gastroenterology : WJG·Hiroshi Yoshida, Tomoharu Kiyuna
Jul 16, 2021·NPJ Genomic Medicine·Peter W EideAnita Sveen
Jul 25, 2021·British Journal of Cancer·Alexandra M ZaborowskiLydia Lynch
Jun 3, 2021·Journal of the National Cancer Institute·Sanne Ten HoornLouis Vermeulen
Aug 15, 2021·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Sara KuntzTitus J Brinker
Sep 4, 2021·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Huu-Giao NguyenInti Zlobec

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Methods Mentioned

BETA
biopsies
light microscopy
biopsy
surgical resection
surgical resections

Software Mentioned

imCMS
FOCUS
GRAMPIAN

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