Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology

Aims Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform inve...

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Veröffentlicht in:Brain pathology (Zurich, Switzerland) Switzerland), 2022-09, Vol.32 (5), p.e13050-n/a
Hauptverfasser: Cevik, Lokman, Landrove, Marilyn Vazquez, Aslan, Mehmet Tahir, Khammad, Vasilii, Garagorry Guerra, Francisco Jose, Cabello‐Izquierdo, Yolanda, Wang, Wesley, Zhao, Jing, Becker, Aline Paixao, Czeisler, Catherine, Rendeiro, Anne Costa, Véras, Lucas Luis Sousa, Zanon, Maicon Fernando, Reis, Rui Manuel, Matsushita, Marcus de Medeiros, Ozduman, Koray, Pamir, M. Necmettin, Ersen Danyeli, Ayca, Pearce, Thomas, Felicella, Michelle, Eschbacher, Jennifer, Arakaki, Naomi, Martinetto, Horacio, Parwani, Anil, Thomas, Diana L., Otero, José Javier
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container_issue 5
container_start_page e13050
container_title Brain pathology (Zurich, Switzerland)
container_volume 32
creator Cevik, Lokman
Landrove, Marilyn Vazquez
Aslan, Mehmet Tahir
Khammad, Vasilii
Garagorry Guerra, Francisco Jose
Cabello‐Izquierdo, Yolanda
Wang, Wesley
Zhao, Jing
Becker, Aline Paixao
Czeisler, Catherine
Rendeiro, Anne Costa
Véras, Lucas Luis Sousa
Zanon, Maicon Fernando
Reis, Rui Manuel
Matsushita, Marcus de Medeiros
Ozduman, Koray
Pamir, M. Necmettin
Ersen Danyeli, Ayca
Pearce, Thomas
Felicella, Michelle
Eschbacher, Jennifer
Arakaki, Naomi
Martinetto, Horacio
Parwani, Anil
Thomas, Diana L.
Otero, José Javier
description Aims Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. Methods We used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors. Results Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. Conclusions We posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation. Different clustering patterns with clinical, histologic, immunohistochemical, and molecular information on the brain cancer population simulation and information gain in the glioma simulation model for clinical decision‐making. Dimensionality reduction by principal component analysis is shown in A1–A4, and by t‐stochastic neighbor embedding in B1–B4, with the features delineated on the top of each graph. Each color represents a unique diagnosis in the WHO classification scheme. (A1 and B1) Dimensionality reduction with clinical features alone demonstrates only a few visible clusters. (A2 and B2) Incorporating clinical history with histology generates the commencement of clear layering in PCA and discrete clusters with t‐SNE. (A3 and B3) Inclusion of immunohistochemical data impro
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Necmettin ; Ersen Danyeli, Ayca ; Pearce, Thomas ; Felicella, Michelle ; Eschbacher, Jennifer ; Arakaki, Naomi ; Martinetto, Horacio ; Parwani, Anil ; Thomas, Diana L. ; Otero, José Javier</creator><creatorcontrib>Cevik, Lokman ; Landrove, Marilyn Vazquez ; Aslan, Mehmet Tahir ; Khammad, Vasilii ; Garagorry Guerra, Francisco Jose ; Cabello‐Izquierdo, Yolanda ; Wang, Wesley ; Zhao, Jing ; Becker, Aline Paixao ; Czeisler, Catherine ; Rendeiro, Anne Costa ; Véras, Lucas Luis Sousa ; Zanon, Maicon Fernando ; Reis, Rui Manuel ; Matsushita, Marcus de Medeiros ; Ozduman, Koray ; Pamir, M. Necmettin ; Ersen Danyeli, Ayca ; Pearce, Thomas ; Felicella, Michelle ; Eschbacher, Jennifer ; Arakaki, Naomi ; Martinetto, Horacio ; Parwani, Anil ; Thomas, Diana L. ; Otero, José Javier</creatorcontrib><description>Aims Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. Methods We used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&amp;E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors. Results Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. Conclusions We posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation. Different clustering patterns with clinical, histologic, immunohistochemical, and molecular information on the brain cancer population simulation and information gain in the glioma simulation model for clinical decision‐making. Dimensionality reduction by principal component analysis is shown in A1–A4, and by t‐stochastic neighbor embedding in B1–B4, with the features delineated on the top of each graph. Each color represents a unique diagnosis in the WHO classification scheme. (A1 and B1) Dimensionality reduction with clinical features alone demonstrates only a few visible clusters. (A2 and B2) Incorporating clinical history with histology generates the commencement of clear layering in PCA and discrete clusters with t‐SNE. (A3 and B3) Inclusion of immunohistochemical data improves the capacity of discerning clusters. (A4 and B4) The additional molecular features does not significantly improve the clustering. (C) Individual information gains with all clinical, histologic, immunohistochemical, and molecular features in the glioma simulation model. Age, site, and Ki67 are the features that have the most amount of necessary information for the diagnosis. (D) Information gains with clinical, histologic, immunohistochemical, and molecular information. Histology provides most of the necessary information for the diagnosis. Combining the clinical data with histology and immunohistochemistry provides more than 95% of the necessary information, whereas adding molecular data provides minimal information gain. (E) IDH1/2‐mutated tumors were subsetted, and the mutual information of the features on the X‐axis was quantified as % information on the Y‐axis. The conditional information function call was called on data the 1p19q status.</description><identifier>ISSN: 1015-6305</identifier><identifier>EISSN: 1750-3639</identifier><identifier>DOI: 10.1111/bpa.13050</identifier><identifier>PMID: 35014126</identifier><language>eng</language><publisher>Switzerland: John Wiley &amp; Sons, Inc</publisher><subject>1p/19q codeletion ; Analysis ; Biomarkers ; Brain cancer ; Brain tumors ; Care and treatment ; Central nervous system ; cIMPACT ; Diagnosis ; Diagnostic equipment (Medical) ; Diagnostic systems ; Digital imaging ; Feature extraction ; Fluorescence in situ hybridization ; Glioma ; Gliomas ; Health care ; Image analysis ; Image processing ; Image segmentation ; Information theory ; Investment strategy ; machine learning ; Medical imaging ; Mutants ; Neuropathology ; Olig2 protein ; p53 Protein ; Patients ; Prediction models ; Simulation models ; Strategic planning ; Tumor proteins ; Tumors ; Workflow</subject><ispartof>Brain pathology (Zurich, Switzerland), 2022-09, Vol.32 (5), p.e13050-n/a</ispartof><rights>2022 The Authors. Brain Pathology published by John Wiley &amp; Sons Ltd on behalf of International Society of Neuropathology.</rights><rights>COPYRIGHT 2022 John Wiley &amp; Sons, Inc.</rights><rights>2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the "License"). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4710-5f1f63e533f62015f2c28f43cdad8e9ce16dcc7137c51f4c1673a7452cbcdefb3</citedby><cites>FETCH-LOGICAL-c4710-5f1f63e533f62015f2c28f43cdad8e9ce16dcc7137c51f4c1673a7452cbcdefb3</cites><orcidid>0000-0002-9639-7940 ; 0000-0003-0680-4520 ; 0000-0001-8015-9916 ; 0000-0002-8695-810X ; 0000-0001-7904-9015</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9425010/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9425010/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1411,11541,27901,27902,45550,45551,46027,46451,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35014126$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Cevik, Lokman</creatorcontrib><creatorcontrib>Landrove, Marilyn Vazquez</creatorcontrib><creatorcontrib>Aslan, Mehmet Tahir</creatorcontrib><creatorcontrib>Khammad, Vasilii</creatorcontrib><creatorcontrib>Garagorry Guerra, Francisco Jose</creatorcontrib><creatorcontrib>Cabello‐Izquierdo, Yolanda</creatorcontrib><creatorcontrib>Wang, Wesley</creatorcontrib><creatorcontrib>Zhao, Jing</creatorcontrib><creatorcontrib>Becker, Aline Paixao</creatorcontrib><creatorcontrib>Czeisler, Catherine</creatorcontrib><creatorcontrib>Rendeiro, Anne Costa</creatorcontrib><creatorcontrib>Véras, Lucas Luis Sousa</creatorcontrib><creatorcontrib>Zanon, Maicon Fernando</creatorcontrib><creatorcontrib>Reis, Rui Manuel</creatorcontrib><creatorcontrib>Matsushita, Marcus de Medeiros</creatorcontrib><creatorcontrib>Ozduman, Koray</creatorcontrib><creatorcontrib>Pamir, M. Necmettin</creatorcontrib><creatorcontrib>Ersen Danyeli, Ayca</creatorcontrib><creatorcontrib>Pearce, Thomas</creatorcontrib><creatorcontrib>Felicella, Michelle</creatorcontrib><creatorcontrib>Eschbacher, Jennifer</creatorcontrib><creatorcontrib>Arakaki, Naomi</creatorcontrib><creatorcontrib>Martinetto, Horacio</creatorcontrib><creatorcontrib>Parwani, Anil</creatorcontrib><creatorcontrib>Thomas, Diana L.</creatorcontrib><creatorcontrib>Otero, José Javier</creatorcontrib><title>Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology</title><title>Brain pathology (Zurich, Switzerland)</title><addtitle>Brain Pathol</addtitle><description>Aims Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. Methods We used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&amp;E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors. Results Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. Conclusions We posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation. Different clustering patterns with clinical, histologic, immunohistochemical, and molecular information on the brain cancer population simulation and information gain in the glioma simulation model for clinical decision‐making. Dimensionality reduction by principal component analysis is shown in A1–A4, and by t‐stochastic neighbor embedding in B1–B4, with the features delineated on the top of each graph. Each color represents a unique diagnosis in the WHO classification scheme. (A1 and B1) Dimensionality reduction with clinical features alone demonstrates only a few visible clusters. (A2 and B2) Incorporating clinical history with histology generates the commencement of clear layering in PCA and discrete clusters with t‐SNE. (A3 and B3) Inclusion of immunohistochemical data improves the capacity of discerning clusters. (A4 and B4) The additional molecular features does not significantly improve the clustering. (C) Individual information gains with all clinical, histologic, immunohistochemical, and molecular features in the glioma simulation model. Age, site, and Ki67 are the features that have the most amount of necessary information for the diagnosis. (D) Information gains with clinical, histologic, immunohistochemical, and molecular information. Histology provides most of the necessary information for the diagnosis. Combining the clinical data with histology and immunohistochemistry provides more than 95% of the necessary information, whereas adding molecular data provides minimal information gain. (E) IDH1/2‐mutated tumors were subsetted, and the mutual information of the features on the X‐axis was quantified as % information on the Y‐axis. The conditional information function call was called on data the 1p19q status.</description><subject>1p/19q codeletion</subject><subject>Analysis</subject><subject>Biomarkers</subject><subject>Brain cancer</subject><subject>Brain tumors</subject><subject>Care and treatment</subject><subject>Central nervous system</subject><subject>cIMPACT</subject><subject>Diagnosis</subject><subject>Diagnostic equipment (Medical)</subject><subject>Diagnostic systems</subject><subject>Digital imaging</subject><subject>Feature extraction</subject><subject>Fluorescence in situ hybridization</subject><subject>Glioma</subject><subject>Gliomas</subject><subject>Health care</subject><subject>Image analysis</subject><subject>Image processing</subject><subject>Image segmentation</subject><subject>Information theory</subject><subject>Investment strategy</subject><subject>machine learning</subject><subject>Medical imaging</subject><subject>Mutants</subject><subject>Neuropathology</subject><subject>Olig2 protein</subject><subject>p53 Protein</subject><subject>Patients</subject><subject>Prediction models</subject><subject>Simulation models</subject><subject>Strategic planning</subject><subject>Tumor proteins</subject><subject>Tumors</subject><subject>Workflow</subject><issn>1015-6305</issn><issn>1750-3639</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>BENPR</sourceid><recordid>eNp1kUuPFCEURonROA9d-AcMiRtnUTO8aTYm7cTHJJPoQteEpqCakYISqqbT_17GHsdHIhsgnBzuvR8ALzA6x21dbCZzjini6BE4xpKjjgqqHrczwrwT7eEInNR6gxBWQvGn4IhyhBkm4hjoq-RzGc0ccoLz1uWyh2aaSjZ26yqcMwxju906OMSQRwP7YIaU6xws3OXyzce8qzAkWJcyBGsiTG4peTLzNsc87J-BJ97E6p7f76fg6_t3Xy4_dtefPlxdrq87yyRGHffYC-o4pV6QVrUnlqw8o7Y3_cop67DorZWYSsuxZxYLSY1knNiN7Z3f0FPw5uCdls3oeuvSXEzUUwmjKXudTdB_v6Sw1UO-1YqRNgzUBK_vBSV_X1yd9RiqdTGa5PJSNRF4pRBXmDX01T_oTV5Kau1pIpGUUiG1-k0NJjod2pjbv_ZOqteSIYa5lKRRZwfKllxrcf6hZIz0Xbi6hat_htvYl3_2-ED-SrMBFwdgF6Lb_9-k335eH5Q_AJl2r9Y</recordid><startdate>202209</startdate><enddate>202209</enddate><creator>Cevik, Lokman</creator><creator>Landrove, Marilyn Vazquez</creator><creator>Aslan, Mehmet Tahir</creator><creator>Khammad, Vasilii</creator><creator>Garagorry Guerra, Francisco Jose</creator><creator>Cabello‐Izquierdo, Yolanda</creator><creator>Wang, Wesley</creator><creator>Zhao, Jing</creator><creator>Becker, Aline Paixao</creator><creator>Czeisler, Catherine</creator><creator>Rendeiro, Anne Costa</creator><creator>Véras, Lucas Luis Sousa</creator><creator>Zanon, Maicon Fernando</creator><creator>Reis, Rui Manuel</creator><creator>Matsushita, Marcus de Medeiros</creator><creator>Ozduman, Koray</creator><creator>Pamir, M. Necmettin</creator><creator>Ersen Danyeli, Ayca</creator><creator>Pearce, Thomas</creator><creator>Felicella, Michelle</creator><creator>Eschbacher, Jennifer</creator><creator>Arakaki, Naomi</creator><creator>Martinetto, Horacio</creator><creator>Parwani, Anil</creator><creator>Thomas, Diana L.</creator><creator>Otero, José Javier</creator><general>John Wiley &amp; Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>M7S</scope><scope>P5Z</scope><scope>P62</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-9639-7940</orcidid><orcidid>https://orcid.org/0000-0003-0680-4520</orcidid><orcidid>https://orcid.org/0000-0001-8015-9916</orcidid><orcidid>https://orcid.org/0000-0002-8695-810X</orcidid><orcidid>https://orcid.org/0000-0001-7904-9015</orcidid></search><sort><creationdate>202209</creationdate><title>Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology</title><author>Cevik, Lokman ; Landrove, Marilyn Vazquez ; Aslan, Mehmet Tahir ; Khammad, Vasilii ; Garagorry Guerra, Francisco Jose ; Cabello‐Izquierdo, Yolanda ; Wang, Wesley ; Zhao, Jing ; Becker, Aline Paixao ; Czeisler, Catherine ; Rendeiro, Anne Costa ; Véras, Lucas Luis Sousa ; Zanon, Maicon Fernando ; Reis, Rui Manuel ; Matsushita, Marcus de Medeiros ; Ozduman, Koray ; Pamir, M. Necmettin ; Ersen Danyeli, Ayca ; Pearce, Thomas ; Felicella, Michelle ; Eschbacher, Jennifer ; Arakaki, Naomi ; Martinetto, Horacio ; Parwani, Anil ; Thomas, Diana L. ; Otero, José Javier</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4710-5f1f63e533f62015f2c28f43cdad8e9ce16dcc7137c51f4c1673a7452cbcdefb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>1p/19q codeletion</topic><topic>Analysis</topic><topic>Biomarkers</topic><topic>Brain cancer</topic><topic>Brain tumors</topic><topic>Care and treatment</topic><topic>Central nervous system</topic><topic>cIMPACT</topic><topic>Diagnosis</topic><topic>Diagnostic equipment (Medical)</topic><topic>Diagnostic systems</topic><topic>Digital imaging</topic><topic>Feature extraction</topic><topic>Fluorescence in situ hybridization</topic><topic>Glioma</topic><topic>Gliomas</topic><topic>Health care</topic><topic>Image analysis</topic><topic>Image processing</topic><topic>Image segmentation</topic><topic>Information theory</topic><topic>Investment strategy</topic><topic>machine learning</topic><topic>Medical imaging</topic><topic>Mutants</topic><topic>Neuropathology</topic><topic>Olig2 protein</topic><topic>p53 Protein</topic><topic>Patients</topic><topic>Prediction models</topic><topic>Simulation models</topic><topic>Strategic planning</topic><topic>Tumor proteins</topic><topic>Tumors</topic><topic>Workflow</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cevik, Lokman</creatorcontrib><creatorcontrib>Landrove, Marilyn Vazquez</creatorcontrib><creatorcontrib>Aslan, Mehmet Tahir</creatorcontrib><creatorcontrib>Khammad, Vasilii</creatorcontrib><creatorcontrib>Garagorry Guerra, Francisco Jose</creatorcontrib><creatorcontrib>Cabello‐Izquierdo, Yolanda</creatorcontrib><creatorcontrib>Wang, Wesley</creatorcontrib><creatorcontrib>Zhao, Jing</creatorcontrib><creatorcontrib>Becker, Aline Paixao</creatorcontrib><creatorcontrib>Czeisler, Catherine</creatorcontrib><creatorcontrib>Rendeiro, Anne Costa</creatorcontrib><creatorcontrib>Véras, Lucas Luis Sousa</creatorcontrib><creatorcontrib>Zanon, Maicon Fernando</creatorcontrib><creatorcontrib>Reis, Rui Manuel</creatorcontrib><creatorcontrib>Matsushita, Marcus de Medeiros</creatorcontrib><creatorcontrib>Ozduman, Koray</creatorcontrib><creatorcontrib>Pamir, M. Necmettin</creatorcontrib><creatorcontrib>Ersen Danyeli, Ayca</creatorcontrib><creatorcontrib>Pearce, Thomas</creatorcontrib><creatorcontrib>Felicella, Michelle</creatorcontrib><creatorcontrib>Eschbacher, Jennifer</creatorcontrib><creatorcontrib>Arakaki, Naomi</creatorcontrib><creatorcontrib>Martinetto, Horacio</creatorcontrib><creatorcontrib>Parwani, Anil</creatorcontrib><creatorcontrib>Thomas, Diana L.</creatorcontrib><creatorcontrib>Otero, José Javier</creatorcontrib><collection>Wiley Open Access</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>ProQuest Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science &amp; Engineering Database (Proquest)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies &amp; Aerospace Database‎ (1962 - current)</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>ProQuest Engineering Collection</collection><collection>Biological Sciences</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>ProQuest Engineering Database</collection><collection>ProQuest advanced technologies &amp; aerospace journals</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering collection</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Brain pathology (Zurich, Switzerland)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cevik, Lokman</au><au>Landrove, Marilyn Vazquez</au><au>Aslan, Mehmet Tahir</au><au>Khammad, Vasilii</au><au>Garagorry Guerra, Francisco Jose</au><au>Cabello‐Izquierdo, Yolanda</au><au>Wang, Wesley</au><au>Zhao, Jing</au><au>Becker, Aline Paixao</au><au>Czeisler, Catherine</au><au>Rendeiro, Anne Costa</au><au>Véras, Lucas Luis Sousa</au><au>Zanon, Maicon Fernando</au><au>Reis, Rui Manuel</au><au>Matsushita, Marcus de Medeiros</au><au>Ozduman, Koray</au><au>Pamir, M. Necmettin</au><au>Ersen Danyeli, Ayca</au><au>Pearce, Thomas</au><au>Felicella, Michelle</au><au>Eschbacher, Jennifer</au><au>Arakaki, Naomi</au><au>Martinetto, Horacio</au><au>Parwani, Anil</au><au>Thomas, Diana L.</au><au>Otero, José Javier</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology</atitle><jtitle>Brain pathology (Zurich, Switzerland)</jtitle><addtitle>Brain Pathol</addtitle><date>2022-09</date><risdate>2022</risdate><volume>32</volume><issue>5</issue><spage>e13050</spage><epage>n/a</epage><pages>e13050-n/a</pages><issn>1015-6305</issn><eissn>1750-3639</eissn><abstract>Aims Resource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. Methods We used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&amp;E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors. Results Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. Conclusions We posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation. Different clustering patterns with clinical, histologic, immunohistochemical, and molecular information on the brain cancer population simulation and information gain in the glioma simulation model for clinical decision‐making. Dimensionality reduction by principal component analysis is shown in A1–A4, and by t‐stochastic neighbor embedding in B1–B4, with the features delineated on the top of each graph. Each color represents a unique diagnosis in the WHO classification scheme. (A1 and B1) Dimensionality reduction with clinical features alone demonstrates only a few visible clusters. (A2 and B2) Incorporating clinical history with histology generates the commencement of clear layering in PCA and discrete clusters with t‐SNE. (A3 and B3) Inclusion of immunohistochemical data improves the capacity of discerning clusters. (A4 and B4) The additional molecular features does not significantly improve the clustering. (C) Individual information gains with all clinical, histologic, immunohistochemical, and molecular features in the glioma simulation model. Age, site, and Ki67 are the features that have the most amount of necessary information for the diagnosis. (D) Information gains with clinical, histologic, immunohistochemical, and molecular information. Histology provides most of the necessary information for the diagnosis. Combining the clinical data with histology and immunohistochemistry provides more than 95% of the necessary information, whereas adding molecular data provides minimal information gain. (E) IDH1/2‐mutated tumors were subsetted, and the mutual information of the features on the X‐axis was quantified as % information on the Y‐axis. The conditional information function call was called on data the 1p19q status.</abstract><cop>Switzerland</cop><pub>John Wiley &amp; Sons, Inc</pub><pmid>35014126</pmid><doi>10.1111/bpa.13050</doi><tpages>17</tpages><orcidid>https://orcid.org/0000-0002-9639-7940</orcidid><orcidid>https://orcid.org/0000-0003-0680-4520</orcidid><orcidid>https://orcid.org/0000-0001-8015-9916</orcidid><orcidid>https://orcid.org/0000-0002-8695-810X</orcidid><orcidid>https://orcid.org/0000-0001-7904-9015</orcidid><oa>free_for_read</oa></addata></record>
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subjects 1p/19q codeletion
Analysis
Biomarkers
Brain cancer
Brain tumors
Care and treatment
Central nervous system
cIMPACT
Diagnosis
Diagnostic equipment (Medical)
Diagnostic systems
Digital imaging
Feature extraction
Fluorescence in situ hybridization
Glioma
Gliomas
Health care
Image analysis
Image processing
Image segmentation
Information theory
Investment strategy
machine learning
Medical imaging
Mutants
Neuropathology
Olig2 protein
p53 Protein
Patients
Prediction models
Simulation models
Strategic planning
Tumor proteins
Tumors
Workflow
title Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology
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