Using deep learning to identify bladder cancers with FGFR-activating mutations from histology images.

Cancer Medicine
Constantine S VelmahosYing-Chun Lo

Abstract

In recent years, the fibroblast growth factor receptor (FGFR) pathway has been proven to be an important therapeutic target in bladder cancer. FGFR-targeted therapies are effective for patients with FGFR mutation, which can be discovered through genetic sequencing. However, genetic sequencing is not commonly performed at diagnosis, whereas a histologic assessment of the tumor is. We aim to computationally extract imaging biomarkers from existing tumor diagnostic slides in order to predict FGFR alterations in bladder cancer. This study analyzed genomic profiles and H&E-stained tumor diagnostic slides of bladder cancer cases from The Cancer Genome Atlas (n = 418 cases). A convolutional neural network (CNN) identified tumor-infiltrating lymphocytes (TIL). The percentage of the tissue containing TIL ("TIL percentage") was then used to predict FGFR activation status with a logistic regression model. This predictive model could proficiently identify patients with any type of FGFR gene aberration using the CNN-based TIL percentage (sensitivity = 0.89, specificity = 0.42, AUROC = 0.76). A similar model which focused on predicting patients with only FGFR2/FGFR3 mutation was also found to be highly sensitive, but also specific (sensitivi...Continue Reading

References

Jun 8, 2001·The American Journal of Pathology·C BillereyF Radvanyi
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Padmanee SharmaEiichi Sato
Jan 23, 2010·Nature Reviews. Cancer·Nicholas Turner, Richard Grose
Nov 5, 2010·Molecular Cancer Research : MCR·Ellen Margrethe HaugstenJørgen Wesche
May 10, 2013·Molecular Cancer Therapeutics·Kilian M GustPeter C Black
Sep 17, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Teresa HelstenRazelle Kurzrock
May 20, 2016·Cancer Immunology Research·Randy F SweisThomas F Gajewski
Sep 23, 2016·The New England Journal of Medicine·Robert L GrossmanLouis M Staudt
Sep 12, 2017·JCO Precision Oncology·Debyani ChakravartyNikolaus Schultz
May 31, 2018·Annals of Oncology : Official Journal of the European Society for Medical Oncology·H A HaenssleUNKNOWN Reader study level-I and level-II Groups
Oct 5, 2018·BMC Medicine·Clare Fiala, Eleftherios P Diamandis
Apr 14, 2019·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Titus J BrinkerUNKNOWN Collaborators
Jul 25, 2019·The New England Journal of Medicine·Yohann LoriotUNKNOWN BLC2001 Study Group
Dec 6, 2019·Therapeutic Advances in Medical Oncology·Chiara CasadeiUgo De Giorgi
Mar 4, 2020·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Erik A WilliamsMark C Mochel
Mar 26, 2021·Nature Cancer·Jakob Nikolas KatherTom Luedde

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