Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning

Nature Medicine
Nicolas CoudrayAristotelis Tsirigos

Abstract

Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and subtype of lung tumors. Adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the most prevalent subtypes of lung cancer, and their distinction requires visual inspection by an experienced pathologist. In this study, we trained a deep convolutional neural network (inception v3) on whole-slide images obtained from The Cancer Genome Atlas to accurately and automatically classify them into LUAD, LUSC or normal lung tissue. The performance of our method is comparable to that of pathologists, with an average area under the curve (AUC) of 0.97. Our model was validated on independent datasets of frozen tissues, formalin-fixed paraffin-embedded tissues and biopsies. Furthermore, we trained the network to predict the ten most commonly mutated genes in LUAD. We found that six of them-STK11, EGFR, FAT1, SETBP1, KRAS and TP53-can be predicted from pathology images, with AUCs from 0.733 to 0.856 as measured on a held-out population. These findings suggest that deep-learning models can assist pathologists in the detection of cancer subtype or gene mutations. Our approach can be applied to any cancer type, and the co...Continue Reading

References

Dec 31, 1997·Science·R F BonnerL A Liotta
Sep 26, 2003·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Gabriella SozziUgo Pastorino
Jun 9, 2004·Trends in Cell Biology·Annette F BaasHans Clevers
Aug 18, 2004·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Román Pérez-SolerPhilip Bonomi
Apr 16, 2005·The American Journal of Surgical Pathology·Yasushi YatabeTetsuya Mitsudomi
Jun 24, 2008·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Hironori NinomiyaYuichi Ishikawa
Aug 30, 2008·British Journal of Cancer·L Makowski, D N Hayes
Mar 11, 2009·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Michael J DonovanDinah V Parums
Apr 16, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Jian YuMichael J Comb
Aug 13, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Scott J RodigLucian R Chirieac
Nov 26, 2010·The American Journal of Surgical Pathology·Jefferson TerryDiana N Ionescu
Jan 22, 2011·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·William D TravisDavid Yankelewitz
Feb 19, 2011·Journal of Biomedicine & Biotechnology·Akira Mogi, Hiroyuki Kuwano
Mar 25, 2011·Science Translational Medicine·Lecia V SequistJeffrey A Engelman
Jul 15, 2011·The American Journal of Surgical Pathology·Akihiko YoshidaHitoshi Tsuda
Sep 11, 2012·Nature·UNKNOWN Cancer Genome Atlas Research Network
Jun 1, 2013·Annals of Oncology : Official Journal of the European Society for Medical Oncology·S DeardenD Blowers
Jan 15, 2014·Virchows Archiv : an International Journal of Pathology·Erik ThunnissenMichael den Bakker
Aug 1, 2014·Nature·UNKNOWN Cancer Genome Atlas Research Network
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Sep 29, 2015·IEEE Transactions on Medical Imaging·Fuyong XingLin Yang
Feb 11, 2016·IEEE Transactions on Medical Imaging·Korsuk SirinukunwattanaNasir M Rajpoot
Mar 10, 2016·IEEE Transactions on Medical Imaging·Marios AnthimopoulosStavroula Mougiakakou
May 14, 2016·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Simone Bsp TerraJennifer M Boland
Sep 23, 2016·The New England Journal of Medicine·Robert L GrossmanLouis M Staudt
Nov 9, 2016·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Xin LuoGuanghua Xiao
Nov 30, 2016·JAMA : the Journal of the American Medical Association·Varun GulshanDale R Webster
Dec 4, 2016·Cancer Research·Sarah ChiangStuart J Schnitt
Mar 17, 2017·Annual Review of Biomedical Engineering·Dinggang ShenHeung-Il Suk
Jun 7, 2017·Journal of Pathology Informatics·Esther Abels, Liron Pantanowitz
Aug 15, 2017·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Nasser HannaGregory Masters

❮ Previous
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Citations

Jan 3, 2019·Journal of Pathology and Translational Medicine·Hye Yoon ChangTae-Yeong Kwak
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
Apr 17, 2019·JCO Clinical Cancer Informatics·Andrew JanowczykAnant Madabhushi
Mar 28, 2019·PLoS Computational Biology·Andrea BizzegoCesare Furlanello
Feb 26, 2019·Histopathology·Andrew D JonesHooman H Rashidi
May 28, 2019·Nature Methods·Erick MoenDavid Van Valen
Jul 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Benjamin R KingstonWarren C W Chan
Sep 7, 2019·Journal of the American Society of Nephrology : JASN·Brandon GinleyPinaki Sarder
Sep 10, 2019·International Journal of Laboratory Hematology·Haneen T SalahShahrukh K Hashmi
Aug 30, 2019·The Journal of Pathology·Balazs Acs, Johan Hartman
Aug 25, 2019·Molecular Psychiatry·Karl GrenierPhedias Diamandis
Oct 12, 2019·American Journal of Clinical Dermatology·Emanuelle M RizkYvonne M Saenger
Feb 15, 2020·International Journal of Computer Assisted Radiology and Surgery·Xilei DaiChubin Ou
Apr 12, 2020·Cancer Communications·Yahui JiangYan Sun
Jul 16, 2019·NPJ Digital Medicine·Shihab SarwarPhedias Diamandis
Jan 30, 2020·The Journal of Pathology·Ralf Huss, Sarah E Coupland
May 2, 2020·Brain : a Journal of Neurology·Shangran QiuVijaya B Kolachalama
Jan 25, 2020·Journal of the National Cancer Institute·Shirin BajajIman Osman
May 5, 2020·Journal of the American Medical Informatics Association : JAMIA·Kun-Hsing YuIsaac S Kohane
Mar 7, 2020·Cancer Science·Hideyuki Shimizu, Keiichi I Nakayama
Apr 5, 2020·Cytopathology : Official Journal of the British Society for Clinical Cytology·Daniel GonzalezLiron Pantanowitz
Jun 25, 2020·The Analyst·Shuxia GuoThomas Bocklitz
Jan 3, 2020·International Journal of Molecular Medicine·Masuko Katoh, Masaru Katoh
Jun 20, 2020·Clinical Pharmacology and Therapeutics·Sebastien Benzekry
Jun 28, 2020·Diseases of the Esophagus : Official Journal of the International Society for Diseases of the Esophagus·Naser DavarzaniHeike I Grabsch
May 31, 2020·Occupational and Environmental Medicine·Xiaohua WangJiantao Pu
Aug 22, 2020·Yearbook of Medical Informatics·Ashley C GriffinArlene E Chung
Aug 26, 2020·Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG·Heinz KutznerTitus J Brinker
Aug 29, 2020·Emerging Topics in Life Sciences·Olivier Elemento

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Methods Mentioned

BETA
biopsies
surgical resection
biopsy
laser-capture microdissection

Software Mentioned

openslide
GoogleNet
Tensorflow
sklearn
Genome Analyzer II
Inception
RMSProp69

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