Whole slide imaging and analysis for biomarker evaluation in digital pathology

X. Moles Lopez, O. Debeir, I. Salmon and C. Decaestecker 1 DIAPATH, Center for Microscopy and Molecular Imaging, Universite Libre de Bruxelles, Rue Adrienne Bolland 8, B6041 Gosselies, Belgium 2 Laboratories of Image, Signal processing and Acoustics, Brussels School of Engineering, Universite Libre de Bruxelles, 50, av. Franklin Roosevelt, B-1050 Brussels, Belgium 3 Department of Pathology, Erasme Hospital, Universite Libre de Bruxelles, Route de Lennik 808, B-1070 Brussels, Belgium

[1]  Shaimaa Al-Janabi,et al.  Digital pathology: current status and future perspectives , 2012, Histopathology.

[2]  T. V. van Gulik,et al.  Accurate Quantitation of Ki67-positive Proliferating Hepatocytes in Rabbit Liver by a Multicolor Immunohistochemical (IHC) Approach Analyzed with Automated Tissue and Cell Segmentation Software , 2013, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[3]  Yves-Rémi Van Eycke,et al.  Registration of whole immunohistochemical slide images: an efficient way to characterize biomarker colocalization , 2015, J. Am. Medical Informatics Assoc..

[4]  A. Ruifrok,et al.  Quantification of histochemical staining by color deconvolution. , 2001, Analytical and quantitative cytology and histology.

[5]  Jeroen van der Laak,et al.  Parametric mapping of immunohistochemically stained tissue sections; a method to quantify the colocalization of tumor markers , 2011, Cellular Oncology.

[6]  Isabelle Salmon,et al.  An Automated Blur Detection Method for Histological Whole Slide Imaging , 2013, PloS one.

[7]  Joachim M. Buhmann,et al.  Computational Pathology: Challenges and Promises for Tissue Analysis , 2015, Comput. Medical Imaging Graph..

[8]  Bas Hulsken,et al.  Real-time deformable registration of multi-modal whole slides for digital pathology , 2011, Comput. Medical Imaging Graph..

[9]  C. Loos.  Multiple Immunoenzyme Staining: Methods and Visualizations for the Observation With Spectral Imaging , 2008 .

[10]  Miyuki Saito,et al.  Frequent co-localization of Cox-2 and laminin-5 gamma2 chain at the invasive front of early-stage lung adenocarcinomas. , 2002, The American journal of pathology.

[11]  G. Metzger,et al.  Development of Multigene Expression Signature Maps at the Protein Level from Digitized Immunohistochemistry Slides , 2012, PloS one.

[12]  Jane Fridlyand,et al.  Considerations for the successful co-development of targeted cancer therapies and companion diagnostics , 2013, Nature Reviews Drug Discovery.

[13]  Matthias Dehmer,et al.  Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers , 2013, PloS one.

[14]  Sunil R Lakhani,et al.  Cytokeratin 5/6 in normal human breast: lack of evidence for a stem cell phenotype , 2004, The Journal of pathology.

[15]  Jason A Papin,et al.  Simple: A Sequential Immunoperoxidase Labeling and Erasing Method , 2009, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[16]  Fabio A. González,et al.  Visual pattern mining in histology image collections using bag of features , 2011, Artif. Intell. Medicine.

[17]  Jean-Pierre Timmermans,et al.  Triple Immunofluorescence Staining with Antibodies Raised in the Same Species to Study the Complex Innervation Pattern of Intrapulmonary Chemoreceptors , 2002, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[18]  C Decaestecker,et al.  Epithelial expression of FHL2 is negatively associated with metastasis-free and overall survival in colorectal cancer , 2013, British Journal of Cancer.

[19]  Hans-Peter Kriegel,et al.  A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise , 1996, KDD.

[20]  Isabelle Salmon,et al.  A Simplified Approach for the Molecular Classification of Glioblastomas , 2012, PloS one.

[21]  Marco Saerens,et al.  Clustering methods applied in the detection of Ki67 hot‐spots in whole tumor slide images: An efficient way to characterize heterogeneous tissue‐based biomarkers , 2012, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[22]  M. Hayat.  Microscopy, Immunohistochemistry, and Antigen Retrieval Methods: For Light and Electron Microscopy , 2002 .

[23]  Isabelle Salmon,et al.  TIMP-4 and CD63: new prognostic biomarkers in human astrocytomas , 2010, Modern Pathology.

[24]  Nektarios A. Valous,et al.  Semantic Focusing Allows Fully Automated Single-Layer Slide Scanning of Cervical Cytology Slides , 2013, PloS one.

[25]  Raphaël Marée,et al.  A rich internet application for remote visualization and collaborative annotation of digital slides in histology and cytology , 2013, Diagnostic Pathology.

[26]  C. Scopa,et al.  Expression of cell cycle inhibitors p21, p27, p14 and p16 in gliomas. Correlation with classic prognostic factors and patients' outcome , 2008, Neuropathology : official journal of the Japanese Society of Neuropathology.

[27]  Stephen T. C. Wong,et al.  The knowledge-integrated network biomarkers discovery for major adverse cardiac events. , 2008, Journal of proteome research.

[28]  Hermann Herbst,et al.  Common Adult Stem Cells in the Human Breast Give Rise to Glandular and Myoepithelial Cell Lineages: A New Cell Biological Concept , 2002, Laboratory Investigation.

[29]  Natasa Przulj,et al.  Biological function through network topology: a survey of the human diseasome , 2012, Briefings in functional genomics.

[30]  Anthony Rhodes,et al.  American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[31]  R. Bast,et al.  American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. , 2007, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[32]  Samir Kumar-Singh,et al.  Antibody Elution Method for Multiple Immunohistochemistry on Primary Antibodies Raised in the Same Species and of the Same Subtype , 2009, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[33]  O. Debeir,et al.  Matrix metalloproteinase‐9 interplays with the IGFBP2–IGFII complex to promote cell growth and motility in astrocytomas , 2008, Glia.

[34]  Isabelle Salmon,et al.  Requirements for the valid quantification of immunostains on tissue microarray materials using image analysis , 2009, Proteomics.

[35]  G. Petris,et al.  Objective Quantification of the Ki67 Proliferative Index in Neuroendocrine Tumors of the Gastroenteropancreatic System: A Comparison of Digital Image Analysis With Manual Methods , 2013 .

[36]  M. Raffeld,et al.  Multiple antigen immunostaining procedures. , 2010, Methods in molecular biology.

[37]  Robert N. Muller,et al.  Design and evaluation of a 6-mer amyloid-beta protein derived phage display library for molecular targeting of amyloid plaques in Alzheimer's disease: Comparison with two cyclic heptapeptides derived from a randomized phage display library , 2011, Peptides.

[38]  S Wolfsberger,et al.  Ki67 index in intracranial ependymoma: a promising histopathological candidate biomarker , 2008, Histopathology.

[39]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[40]  John M S Bartlett,et al.  Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. , 2014, Archives of pathology & laboratory medicine.

[41]  A. Scarpa,et al.  TNM staging of midgut and hindgut (neuro) endocrine tumors: a consensus proposal including a grading system , 2007, Virchows Archiv.

[42]  Sabrina Oliveira,et al.  Recent advances in molecular imaging biomarkers in cancer: application of bench to bedside technologies. , 2010, Drug discovery today.

[43]  Jinha M. Park,et al.  Diagnostic Evaluation of HER-2 as a Molecular Target: An Assessment of Accuracy and Reproducibility of Laboratory Testing in Large, Prospective, Randomized Clinical Trials , 2005, Clinical Cancer Research.

[44]  Isabelle Salmon,et al.  KI-67 hot-spots detection on glioblastoma tissue sections , 2010, 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[45]  F. Cordelières,et al.  A guided tour into subcellular colocalization analysis in light microscopy , 2006, Journal of microscopy.

[46]  Max A. Viergever,et al.  elastix: A Toolbox for Intensity-Based Medical Image Registration , 2010, IEEE Transactions on Medical Imaging.

[47]  H. Müller-Hermelink,et al.  Tissue array technology for testing interlaboratory and interobserver reproducibility of immunohistochemical estrogen receptor analysis in a large multicenter trial. , 2002, American journal of clinical pathology.

[48]  A. Richardson,et al.  Interobserver concordance in implementing the 2010 ASCO/CAP recommendations for reporting ER in breast carcinomas: a demonstration of the difficulties of consistently reporting low levels of ER expression by manual quantification. , 2013, American journal of clinical pathology.

[49]  N. Morgan,et al.  Expression of endoplasmic reticulum stress markers in the islets of patients with type 1 diabetes , 2012, Diabetologia.

[50]  Ruijun Tian.  Exploring intercellular signaling by proteomic approaches , 2014, Proteomics.