Evidence map›Paper›PMID 37652006›Full record

ArticleCancer cell2023

Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study.

Sophia J Wagner, Daniel Reisenbüchler, Nicholas P West, Jan Moritz Niehues, Jiefu Zhu, Sebastian Foersch, Gregory Patrick Veldhuizen, Philip Quirke, Heike I Grabsch, Piet A van den Brandt and 39 more

Open access · hybridAbstract readMulticenter Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Cancer cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 171 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
171citing papers in PubMed, 4 pooled it
52.0field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

171 citing papers in PubMed, 4 syntheses or guidelines pooled it, 226 citations in OpenAlex.

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111 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

49 authors at 20 institutions in 9 countries.

Sophia J WagnerHelmholtz Munich - German Research Center for Environment and Health, Munich, Germany; School of Computation, Information and Technology, Technical University of Munich, Munich, Germany; Else Kroener Fresenius Center for Digital Health (EFFZ), Technical University Dresden, Dresden, Germany.
Daniel ReisenbüchlerHelmholtz Munich - German Research Center for Environment and Health, Munich, Germany.
Nicholas P WestInstitute of Pathology, University Medical Center Mainz, Mainz, Germany.
Jan Moritz NiehuesElse Kroener Fresenius Center for Digital Health (EFFZ), Technical University Dresden, Dresden, Germany.
Jiefu ZhuElse Kroener Fresenius Center for Digital Health (EFFZ), Technical University Dresden, Dresden, Germany.
Sebastian FoerschInstitute of Pathology, University Medical Center Mainz, Mainz, Germany.
Gregory Patrick VeldhuizenElse Kroener Fresenius Center for Digital Health (EFFZ), Technical University Dresden, Dresden, Germany.
Philip QuirkeDivision of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
Heike I GrabschDivision of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK; Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center+, Maastricht, the Netherlands.
Piet A van den BrandtDepartment of Epidemiology, Maastricht University Medical Center+, Maastricht, the Netherlands.
Gordon G A HutchinsDivision of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
Susan D RichmanDivision of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
Tanwei YuanDivision of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Rupert LangerInstitute of Pathology und Molecular Pathology, Johannes Kepler University Hospital Linz, Linz, Österreich.
Josien C A JenniskensDepartment of Epidemiology, Maastricht University Medical Center+, Maastricht, the Netherlands.
Kelly OffermansDepartment of Epidemiology, Maastricht University Medical Center+, Maastricht, the Netherlands.
Wolfram MuellerGemeinschaftspraxis Pathologie, Starnberg, Germany.
Richard GrayNuffield Department of Population Health, University of Oxford, Oxford, UK.
Stephen B GruberCenter for Precision Medicine and Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA.
Joel K GreensonDepartment of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
Gad RennertDepartment of Community Medicine & Epidemiology, Lady Davis Carmel Medical Center, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel; Steve and Cindy Rasmussen Institute for Genomic Medicine, Lady Davis Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel.
Joseph D BonnerDepartment of Community Medicine & Epidemiology, Lady Davis Carmel Medical Center, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
Daniel SchmolzeCenter for Precision Medicine and Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA.
Jitendra JonnagaddalaSchool of Population Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
Nicholas J HawkinsSchool of Medical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
Robyn L WardSchool of Medical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
Dion MortonUniversity Hospital Birmingham, Birmingham, UK.
Matthew SeymourSt James's University Hospital, Leeds, UK.
Laura MagillUniversity of Birmingham Clinical Trials Unit, Birmingham, UK.
Marta NowakDepartment of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
Jennifer HayGlasgow Tissue Research Facility, University of Glasgow, Queen Elizabeth University Hospital, Glasgow, UK.
Viktor H KoelzerDepartment of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Oncology, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK.
David N ChurchNuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
TransSCOT consortium
Christian MatekHelmholtz Munich - German Research Center for Environment and Health, Munich, Germany; Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nuremberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC), University Hospital Erlangen, FAU Erlangen-Nuremberg, Erlangen, Germany.
Carol GeppertInstitute of Pathology, University Hospital Erlangen, FAU Erlangen-Nuremberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC), University Hospital Erlangen, FAU Erlangen-Nuremberg, Erlangen, Germany.
Chaolong PengMedical School, Jianggang Shan University, Jiangxi, China.
Cheng ZhiDepartment of Pathology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
Xiaoming OuyangDepartment of Pathology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
Jacqueline A JamesPrecision Medicine Centre of Excellence, Health Sciences Building, The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK; Regional Molecular Diagnostic Service, Belfast Health and Social Care Trust, Belfast, UK; The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
Maurice B LoughreyThe Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK; Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK; Centre for Public Health, Queen's University Belfast, Belfast, UK.
Manuel Salto-TellezPrecision Medicine Centre of Excellence, Health Sciences Building, The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK; Regional Molecular Diagnostic Service, Belfast Health and Social Care Trust, Belfast, UK; Integrated Pathology Unit, Institute for Cancer Research and Royal Marsden Hospital, London, UK.
Hermann BrennerDivision of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Michael HoffmeisterDivision of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Daniel TruhnDepartment of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany.
Julia A SchnabelHelmholtz Munich - German Research Center for Environment and Health, Munich, Germany; School of Computation, Information and Technology, Technical University of Munich, Munich, Germany; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK.
Melanie BoxbergInstitute of Pathology, Technical University Munich, Munich, Germany; Institute of Pathology Munich-North, Munich, Germany.
Tingying PengHelmholtz Munich - German Research Center for Environment and Health, Munich, Germany. Electronic address: tingying.peng@helmholtz-munich.de.
Jakob Nikolas KatherElse Kroener Fresenius Center for Digital Health (EFFZ), Technical University Dresden, Dresden, Germany; Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK; Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg. Electronic address: jakob_nikolas.kather@tu-dresden.de.
Helmholtz Zentrum München · DEGerman Cancer Research Center · DEMaastricht University · NLQueen's University Belfast · GBUniversity of Leeds · GBFresenius (Germany) · DEJohannes Gutenberg University Mainz · DESecond Affiliated Hospital of Guangzhou Medical University · CNUniversity of Oxford · GBCity Of Hope National Medical Center · USJinggangshan University · CNTechnical University of Munich · DETechnion – Israel Institute of Technology · ILUniversity of Zurich · CHUNSW Sydney · AUBelfast Health and Social Care Trust · GBCancer Research UK Clinical Trials Unit · GBCenter for Environmental Health · USCity of Hope · USComprehensive Cancer Center Erlangen · DE

Funding

Integration of epidemiology, pathology, immunology and outcomes in colorectal cancerR01CA263318 · NCI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI STEPHEN B GRUBER · 2022 to 2026
$3.4M
Cancer Research UK 27963Cancer Research UK C26642/A27963Cancer Research UK C551/A8283Cancer Research UK C6716/A13941Cancer Research UK C6716/A9894Department of HealthDepartment of Health 14/140/84Medical Research CouncilMedical Research Council G0601705NCI NIH HHS R01 CA263318
6 · The paper itself

Abstract

Deep learning (DL) can accelerate the prediction of prognostic biomarkers from routine pathology slides in colorectal cancer (CRC). However, current approaches rely on convolutional neural networks (CNNs) and have mostly been validated on small patient cohorts. Here, we develop a new transformer-based pipeline for end-to-end biomarker prediction from pathology slides by combining a pre-trained transformer encoder with a transformer network for patch aggregation. Our transformer-based approach substantially improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training and evaluating on a large multicenter cohort of over 13,000 patients from 16 colorectal cancer cohorts, we achieve a sensitivity of 0.99 with a negative predictive value of over 0.99 for prediction of microsatellite instability (MSI) on surgical resection specimens. We demonstrate that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem.

Indexed as

AlgorithmsColorectal NeoplasmsBiomarkersBiopsyHumansMicrosatellite InstabilityBiomarkersartificial intelligencebiomarkercolorectal cancerdeep learningmicrosatellite instabilitymultiple instance learningtransformer

Identifiers

PMID37652006
PMCPMC10507381
OpenAlexW4386303561

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.