Search

Your search keyword '"Cree, Ian"' showing total 17 results
Start Over Author "Cree, Ian" Language undetermined
17 results on '"Cree, Ian"'

1. Machine learning computational tools to assist the performance of systematic reviews: A mapping review

Author

Jimenez, Ramon, Cordova, Reynalda, Lee, Teresa, Rosillo, Nicolás, Cree, Ian, Gonzalez, Angel, and Ruiz, Blanca

Subjects
FOS: Computer and information sciences, Artificial intelligence, Artificial Intelligence and Robotics, Systematic mapping review, Epidemiology, Bioinformatics, Computer Sciences, Research Methods in Life Sciences, Life Sciences, Software development, Health Informatics, Systematic reviews, Evidence-based practice, Automatization, Bibliometrics, Machine learning, Physical Sciences and Mathematics, Medicine and Health Sciences, Systematic review, Humans, Mapping review, Software, Algorithms, Systematic Reviews as Topic
Abstract

Background Within evidence-based practice (EBP), systematic reviews (SR) are considered the highest level of evidence in that they summarize the best available research and describe the progress in a determined field. Due its methodology, SR require significant time and resources to be performed; they also require repetitive steps that may introduce biases and human errors. Machine learning (ML) algorithms therefore present a promising alternative and a potential game changer to speed up and automate the SR process. This review aims to map the current availability of computational tools that use ML techniques to assist in the performance of SR, and to support authors in the selection of the right software for the performance of evidence synthesis. Methods The mapping review was based on comprehensive searches in electronic databases and software repositories to obtain relevant literature and records, followed by screening for eligibility based on titles, abstracts, and full text by two reviewers. The data extraction consisted of listing and extracting the name and basic characteristics of the included tools, for example a tool’s applicability to the various SR stages, pricing options, open-source availability, and type of software. These tools were classified and graphically represented to facilitate the description of our findings. Results A total of 9653 studies and 585 records were obtained from the structured searches performed on selected bibliometric databases and software repositories respectively. After screening, a total of 119 descriptions from publications and records allowed us to identify 63 tools that assist the SR process using ML techniques. Conclusions This review provides a high-quality map of currently available ML software to assist the performance of SR. ML algorithms are arguably one of the best techniques at present for the automation of SR. The most promising tools were easily accessible and included a high number of user-friendly features permitting the automation of SR and other kinds of evidence synthesis reviews.

Published
2022
Full Text
View/download PDF

2. An introduction to the WHO 5th edition 2022 classification of testicular tumours

Author

Berney, Daniel M, Cree, Ian, Rao, Vishal, Moch, Holger, Srigley, John R, Tsuzuki, Toyonori, Amin, Mahul B, Comperat, Eva M, Hartmann, Arndt, Menon, Santosh, Netto, George J, Rubin, Mark A, Turajlic, Samra, Raspollini, Maria R, and Tickoo, Satish K

Subjects
Signalling & Oncogenes, Genome Integrity & Repair, Tumour Biology, Genetics & Genomics, Computational & Systems Biology
Abstract

The 5th edition of the World Health Organisation ‘blue book’ was recently published and includes a comprehensive update on testicular tumours. This builds upon the work of the 4th edition, retaining its structure, and main nomenclature, including the use of the term ‘germ cell neoplasia in situ’ (GCNIS) for the preinvasive lesion of most germ cell tumours and division from those not derived from GCNIS. While there have been important developments in understanding the molecular underpinnings of testicular cancer, this updated classification paradigm and approach remains rooted in morphology. Nomenclature changes include replacement of the term ‘Primitive neuroectodermal Tumour’ by ‘Embryonic Neuroectodermal Tumour’ based on the non-specificity of the former term and to separate these tumours clearly from Ewing sarcoma. Seminoma is placed in a germinoma family of tumours emphasising relation to those tumours at other sites. Criteria for the diagnosis of ‘teratoma with Somatic transformation’ have been modified to not include variable field size assessments. The word ‘carcinoid’ has been changed to ‘Neuroendocrine Tumour’ with most examples in the testis now classified as ‘Prepubertal Type Testicular Neuroendocrine Tumour’. For sex cord stromal tumours, the use of mitotic counts per high power field has been changed to per mm2 for malignancy assessments, and the new entities, ‘Signet Ring stromal Tumour’ and ‘Myoid Gonadal Stromal tumour’, are defined. Well-differentiated papillary mesothelial tumour has now been defined as tumour type with a favourable prognosis. Sertoliform Cystadenoma has been removed as an entity from testicular adnexal tumours and placed with Sertoli cell tumours.

Published
2022
Full Text
View/download PDF

3. WHO classification of tumours fifth edition: Evolving issues in the classification, diagnosis and prognostication of prostate cancer

Author

Kench, James G, Amin, Mahul B, Berney, Daniel M, Compérat, Eva M, Cree, Ian A, Gill, Anthony J, Hartmann, Arndt, Menon, Santosh, Moch, Holger, Netto, George J, Raspollini, Maria R, Rubin, Mark A, Tan, Puay Hoon, Tsuzuki, Toyonori, Turjalic, Samra, van der Kwast, Theo H, Zhou, Ming, Srigley, John R, University of Zurich, and Kench, James G

Subjects
2734 Pathology and Forensic Medicine, Signalling & Oncogenes, 10049 Institute of Pathology and Molecular Pathology, Genome Integrity & Repair, 610 Medicine & health, Tumour Biology, 2722 Histology, Genetics & Genomics, Computational & Systems Biology
Abstract

The 5th edition of the WHO Classification of Tumours of the Urinary and Male Genital Systems encompasses several updates to the classification and diagnosis of prostatic carcinoma as well as incorporating advancements in assessment of its prognosis, including recent grading modifications. Some of the salient aspects include: 1) recognition that PIN-like carcinoma is not synonymous with a pattern of ductal carcinoma but better classified as a subtype of acinar adenocarcinoma; 2) a specific section on treatment-related neuroendocrine prostatic carcinoma in view of the tight correlation between androgen deprivation therapy and the development of prostatic carcinoma with neuroendocrine morphology, and the emerging data on lineage plasticity; 3) a terminology change of basal cell carcinoma to “adenoid cystic (basal cell) cell carcinoma” given the presence of an underlying MYB::NFIB gene fusion in many cases; 4) discussion of the current issues in the grading of acinar adenocarcinoma and the prognostic significance of cribriform growth patterns; and 5) more detailed coverage of intraductal carcinoma of prostate (IDC-P) reflecting our increased knowledge of this entity, while recommending the descriptive term atypical intraductal proliferation (AIP) for lesions falling short of IDC-P but containing more atypia than typically seen in high-grade prostatic intraepithelial neoplasia (HGPIN). Lesions previously regarded as cribriform patterns of HGPIN are now included in the AIP category. This review discusses these developments, summarising the existing literature, as well as the emerging morphological and molecular data that underpins the classification and prognostication of prostatic carcinoma.

Published
2022
Full Text
View/download PDF

5. Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Author

Amgad, Mohamed, Stovgaard, Elisabeth Specht, Balslev, Eva, Thagaard, Jeppe, Chen, Weijie, Dudgeon, Sarah, Sharma, Ashish, Kerner, Jennifer K., Denkert, Carsten, Yuan, Yinyin, AbdulJabbar, Khalid, Wienert, Stephan, Savas, Peter, Voorwerk, Leonie, Beck, Andrew H., Madabhushi, Anant, Hartman, Johan, Sebastian, Manu M., Horlings, Hugo M., Hudeček, Jan, Ciompi, Francesco, Moore, David A., Singh, Rajendra, Roblin, Elvire, Balancin, Marcelo Luiz, Mathieu, Marie-Christine, Lennerz, Jochen K., Kirtani, Pawan, Chen, I-Chun, Braybrooke, Jeremy P., Pruneri, Giancarlo, Demaria, Sandra, Adams, Sylvia, Schnitt, Stuart J., Lakhani, Sunil R., Rojo, Federico, Comerma, Laura, Badve, Sunil S., Khojasteh, Mehrnoush, Symmans, W. Fraser, Sotiriou, Christos, Gonzalez-Ericsson, Paula, Pogue-Geile, Katherine L., Kim, Rim S., Rimm, David L., Viale, Giuseppe, Hewitt, Stephen M., Bartlett, John M. S., Penault-Llorca, Frédérique, Goel, Shom, Lien, Huang-Chun, Loibl, Sibylle, Kos, Zuzana, Loi, Sherene, Hanna, Matthew G., Michiels, Stefan, Kok, Marleen, Nielsen, Torsten O., Lazar, Alexander J., Bago-Horvath, Zsuzsanna, Kooreman, Loes F. S., van der Laak, Jeroen A. W. M., Saltz, Joel, Gallas, Brandon D., Kurkure, Uday, Barnes, Michael, Salgado, Roberto, Cooper, Lee A. D., Hyytiäinen, Aini, Hida, Akira I., Thompson, Alastair, Lefevre, Alex, Gown, Allen, Lo, Amy, Sapino, Anna, Moreira, Andre, Richardson, Andrea, Vingiani, Andrea, Bellizzi, Andrew M., Tutt, Andrew, Guerrero-Zotano, Angel, Grigoriadis, Anita, Ehinger, Anna, Garrido-Castro, Anna C., Vincent-Salomon, Anne, Laenkholm, Anne-Vibeke, Cimino-Mathews, Ashley, Srinivasan, Ashok, Acs, Balazs, Singh, Baljit, Calhoun, Benjamin, Haibe-Kans, Benjamin, Solomon, Benjamin, Thapa, Bibhusal, Nelson, Brad H., Castaneda, Carlos, Ballesteroes-Merino, Carmen, Criscitiello, Carmen, Boeckx, Carolien, Colpaert, Cecile, Quinn, Cecily, Chennubhotla, Chakra S., Swanton, Charles, Solinas, Cinzia, Hiley, Crispin, Drubay, Damien, Bethmann, Daniel, Dillon, Deborah A., Larsimont, Denis, Sabanathan, Dhanusha, Peeters, Dieter, Zardavas, Dimitrios, Höflmayer, Doris, Johnson, Douglas B., Thompson, E. Aubrey, Brogi, Edi, Perez, Edith, ElGabry, Ehab A., Blackley, Elizabeth F., Reisenbichler, Emily, Bellolio, Enrique, Chmielik, Ewa, Gaire, Fabien, Andre, Fabrice, Lu, Fang-I, Azmoudeh-Ardalan, Farid, Gruosso, Forbius Tina, Peale, Franklin, Hirsch, Fred R., Klaushen, Frederick, Acosta-Haab, Gabriela, Farshid, Gelareh, van den Eynden, Gert, Curigliano, Giuseppe, Floris, Giuseppe, Broeckx, Glenn, Koeppen, Harmut, Haynes, Harry R., McArthur, Heather, Joensuu, Heikki, Olofsson, Helena, Cree, Ian, Nederlof, Iris, Frahm, Isabel, Brcic, Iva, Chan, Jack, Hall, Jacqueline A., Ziai, James, Brock, Jane, Wesseling, Jelle, Giltnane, Jennifer, Lemonnier, Jerome, Zha, Jiping, M. Ribeiro, Joana, Carter, Jodi M., Hainfellner, Johannes, Quesne, John Le, Juco, Jonathan W., Reis-Filho, Jorge, van den Berg, Jose, Sanchez, Joselyn, Sparano, Joseph, Cucherousset, Joël, Araya, Juan Carlos, Adam, Julien, Balko, Justin M., Saeger, Kai, Siziopikou, Kalliopi, Willard-Gallo, Karen, Sikorska, Karolina, Weber, Karsten, Steele, Keith E., Emancipator, Kenneth, El Bairi, Khalid, Blenman, Kim R. M., Allison, Kimberly H., van de Vijver, Koen K., Korski, Konstanty, Pusztai, Lajos, Buisseret, Laurence, Shi, Leming, Shi-wei, Liu, Molinero, Luciana, Estrada, M. Valeria, van Seijen, Maartje, Lacroix-Triki, Magali, Cheang, Maggie C. U., Bakir, Maise al, van de Vijver, Marc, Dieci, Maria Vittoria, Rebelatto, Marlon C., Piccart, Martine, Goetz, Matthew P., Preusser, Matthias, Sanders, Melinda E., Regan, Meredith M., Christie, Michael, Misialek, Michael, Ignatiadis, Michail, de Maaker, Michiel, van Bockstal, Mieke, Castillo, Miluska, Harbeck, Nadia, Tung, Nadine, Laudus, Nele, Sirtaine, Nicolas, Burchardi, Nicole, Ternes, Nils, Radosevic-Robin, Nina, Gluz, Oleg, Grimm, Oliver, Nuciforo, Paolo, Jank, Paul, Jelinic, Petar, Watson, Peter H., Francis, Prudence A., Russell, Prudence A., Pierce, Robert H., Hills, Robert, Leon-Ferre, Roberto, de Wind, Roland, Shui, Ruohong, Declercq, Sabine, Leung, Sam, Tabbarah, Sami, Souza, Sandra C., O’Toole, Sandra, Swain, Sandra, Willis, Scooter, Ely, Scott, Kim, Seong- Rim, Bedri, Shahinaz, Irshad, Sheeba, Liu, Shi-Wei, Hendry, Shona, Bianchi, Simonetta, Bragança, Sofia, Paik, Soonmyung, Fox, Stephen B., Luen, Stephen J., Naber, Stephen, Luz, Sua, Fineberg, Susan, Soler, Teresa, Gevaert, Thomas, d’Alfons, Timothy, John, Tom, Sugie, Tomohagu, Bossuyt, Veerle, Manem, Venkata, Cámaea, Vincente Peg, Tong, Weida, Yang, Wentao, Tran, William T., Wang, Yihong, Allory, Yves, Husain, Zaheed, Amgad, Mohamed [0000-0001-7599-6162], Sharma, Ashish [0000-0002-1011-6504], Savas, Peter [0000-0001-5999-428X], Hudeček, Jan [0000-0003-1071-5686], Braybrooke, Jeremy P. [0000-0003-1943-7360], Demaria, Sandra [0000-0003-4426-0499], Comerma, Laura [0000-0002-0249-4636], Badve, Sunil S. [0000-0001-8861-9980], Symmans, W. Fraser [0000-0002-1526-184X], Gonzalez-Ericsson, Paula [0000-0002-6292-6963], Rimm, David L. [0000-0001-5820-4397], Loi, Sherene [0000-0001-6137-9171], Hanna, Matthew G. [0000-0002-7536-1746], Lazar, Alexander J. [0000-0002-6395-4499], Bago-Horvath, Zsuzsanna [0000-0002-8555-7806], van der Laak, Jeroen A. W. M. [0000-0001-7982-0754], Gallas, Brandon D. [0000-0001-7332-1620], Kurkure, Uday [0000-0002-8273-7334], Cooper, Lee A. D. [0000-0002-3504-4965], and Apollo - University of Cambridge Repository

Subjects
631/67/580, 692/4028/67/1857, 631/67/2321, 692/53/2422, review-article, Review Article, 631/67/1347
Abstract

Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.

Published
2020

6. The path to a better biomarker: application of a risk management framework for the implementation of PD-L1 and TILs as immuno-oncology biomarkers in breast cancer clinical trials and daily practice

Author

Gonzalez-Ericsson, Paula, Stovgaard, Elisabeth, Sua, Luz, Reisenbichler, Emily, Kos, Zuzana, Carter, Jodi, Michiels, Stefan, Le Quesne, John, Nielsen, Torsten, Laenkholm, Anne-Vibeke, Fox, Stephen, Adam, Julien, Bartlett, John MS, Rimm, David, Quinn, Cecily, Peeters, Dieter, Dieci, Maria, Vincent-Salomon, Anne, Cree, Ian, Hida, Akira, Balko, Justin, Haynes, Harry, Frahm, Isabel, Acosta-Haab, Gabriela, Balancin, Marcelo, Bellolio, Enrique, Yang, Wentao, Kirtani, Pawan, Sugie, Tomoharu, Ehinger, Anna, Castaneda, Carlos, Kok, Marleen, McArthur, Heather, Siziopikou, Kalliopi, Badve, Sunil, Fineberg, Susan, Gown, Allen, Viale, Giuseppe, Schnitt, Stuart, Pruneri, Giancarlo, Penault-Llorca, Frédérique, Hewitt, Stephen, Thompson, E Aubrey, Allison, Kimberly, Symmans, William, Bellizzi, Andrew, Brogi, Edi, Moore, David, Larsimont, Denis, Dillon, Deborah, Lazar, Alexander, Lien, Huangchun, Goetz, Matthew, Broeckx, Glenn, El Bairi, Khalid, Harbeck, Nadia, Cimino-Mathews, Ashley, Sotiriou, Christos, Adams, Sylvia, Liu, Shi-Wei, Loibl, Sibylle, Chen, I-Chun, Lakhani, Sunil, Juco, Jonathan, Denkert, Carsten, Blackley, Elizabeth, Demaria, Sandra, Leon-Ferre, Roberto, Gluz, Oleg, Zardavas, Dimitrios, Emancipator, Kenneth, Ely, Scott, Loi, Sherene, Salgado, Roberto, Sanders, Melinda, Gonzalez‐Ericsson, Paula, Lænkholm, Anne‐Vibeke, Vincent‐Salomon, Anne, Acosta‐Haab, Gabriela, Penault‐Llorca, Frederique, Cimino‐Mathews, Ashley, Liu, Shi‐wei, Chen, I‐Chun, Leon‐Ferre, Roberto, Int Immuno-Oncology Biomarker Work, Service de biostatistique et d'épidémiologie (SBE), Direction de la recherche clinique [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), University of Leicester, Department of Pathology, Odense University Hospital, Universita degli Studi di Padova, Pharmacogenomics Unit [Paris], Department of Genetics [Paris], Institut Curie [Paris]-Institut Curie [Paris], Vanderbilt University Medical Center [Nashville], Vanderbilt University [Nashville], Helsingborg Hospital, Ctr Biomol Struct & Org, University of Maryland [College Park], University of Maryland System-University of Maryland System, The Netherlands Cancer Institute, Division of Pathology and Laboratory Medicine, Università degli Studi di Milano [Milano] (UNIMI)-European Institute of Oncology [Milan] (ESMO), European Institute of Oncology [Milan] (ESMO), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Innovation North - Faculty of Information and Technology, Leeds Metropolitan University, Institut Jules Bordet [Bruxelles], Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), The University of Texas M.D. Anderson Cancer Center [Houston], Université Mohamed 1 Oujda MAROC, Frauenklinik, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), German Breast Group, University of Southern Queensland (USQ), Charité, Institute of Pathology, Translational Tumorpathology Unit, West German Study Group, Breast International Group [Brussels, Belgium] (BIG aisbl), Breast Cancer Translational Research Laboratory, Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), Oncostat (U1018 (Équipe 2)), Institut Gustave Roussy (IGR)-Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Università degli Studi di Padova = University of Padua (Unipd), Università degli Studi di Milano = University of Milan (UNIMI)-European Institute of Oncology [Milan] (ESMO), and German Breast Group (GBG)

Subjects
0301 basic medicine, Oncology, PD-L1, medicine.medical_specialty, [SDV]Life Sciences [q-bio], [SDV.CAN]Life Sciences [q-bio]/Cancer, Triple Negative Breast Neoplasms, Pembrolizumab, biomarker risk-management, B7-H1 Antigen, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, breast cancer, Lymphocytes, Tumor-Infiltrating, Atezolizumab, Internal medicine, Biomarkers, Tumor, Medicine, Humans, TILs, Triple-negative breast cancer, Tumor marker, Cancer immunology, Risk Management, business.industry, Médecine pathologie humaine, Sciences bio-médicales et agricoles, immunotherapy, medicine.disease, 3. Good health, Clinical trial, Cancérologie, 030104 developmental biology, 030220 oncology & carcinogenesis, Human medicine, Nivolumab, business
Abstract

Immune checkpoint inhibitor therapies targeting PD-1/PD-L1 are now standard of care in oncology across several hematologic and solid tumor types, including triple negative breast cancer (TNBC). Patients with metastatic or locally advanced TNBC with PD-L1 expression on immune cells occupying ≥1% of tumor area demonstrated survival benefit with the addition of atezolizumab to nab-paclitaxel. However, concerns regarding variability between immunohistochemical PD-L1 assay performance and inter-reader reproducibility have been raised. High tumor-infiltrating lymphocytes (TILs) have also been associated with response to PD-1/PD-L1 inhibitors in patients with breast cancer. TILs can be easily assessed on hematoxylin and eosin stained slides and have shown reliable inter-reader reproducibility. As an established prognostic factor in early stage TNBC, TILs are soon anticipated to be reported in daily practice in many pathology laboratories worldwide. Since TILs and PD-L1 are parts of an immunological spectrum in breast cancer, we propose the systematic implementation of combined PD-L1 and TIL analyses as a more comprehensive immune-oncological biomarker for patient selection for PD-1/PD-L1 inhibition-based therapy in patients with breast cancer. Although practical and regulatory considerations differ by jurisdiction, the pathology community has the responsibility to patients to implement assays that lead to optimal patient selection. We propose herewith a risk-management framework that may help mitigate the risks of suboptimal patient selection for immuno-therapeutic approaches in clinical trials and daily practice based on combined TILs/PD-L1 assessment in breast cancer. This article is protected by copyright. All rights reserved., info:eu-repo/semantics/published

Published
2020
Full Text
View/download PDF

7. Additional file 1: of Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study

Author

Vaughn, Cecily, Costa, José, Feilotter, Harriet, Petraroli, Rosella, Varun Bagai, Rachiglio, Anna, Marino, Federica, Tops, Bastiaan, Kurth, Henriette, Sakai, Kazuko, Mafficini, Andrea, Bastien, Roy, Reiman, Anne, Corre, Delphine Le, Boag, Alexander, Crocker, Susan, Bihl, Michel, Hirschmann, Astrid, Scarpa, Aldo, Machado, José, Blons, Hélène, Sheils, Orla, Bramlett, Kelli, Ligtenberg, Marjolijn, Cree, Ian, Normanno, Nicola, Nishio, Kazuto, and Laurent-Puig, Pierre

Abstract

Table S1. RT-PCR Targets within the Ion AmpliSeq™ Lung Fusion Research Panel. A list of all targets in the multiplex PCR studied – including targeted fusions (genes and exons), expression control genes, and 3′and 5′regions. Table S2. ALK Clinical Samples. Table depicting details on all ALK clinical research samples analyzed in the study. Table S3. ROS1 and RET clinical samples. Table depicting details on all ROS1 and RET clinical research samples analyzed in the study. (DOCX 57 kb)

Published
2018
Full Text
View/download PDF

8. Multi institutional evaluation of a high sensitive NGS assay for liquid biopsy mutation detection in lung cancer

Author

Vollbrecht, Claudia, Costa, Jose Luis, Weren, Robbert, Rachiglio, Anna Maria, Mafficini, Andrea, Kurth, Henriette, Reiman, Anne, Didelot, Audrey, Boag, Alexander, Nishio, Kazuto, Feilotter, Harriet, Laurent-Puig, Pierre, Sheils, Orla, Scarpa, Aldo, Majolijn Ligtenberg, Cree, Ian A., Machado, Jose Carlos, Normanno, Nicola, and Hummel, Michael

Published
2017
Full Text
View/download PDF

9. Additional file 1: Table S1. of Validation of an NGS mutation detection panel for melanoma

Author

Reiman, Anne, Kikuchi, Hugh, Scocchia, Daniela, Smith, Peter, Tsang, Yee, Snead, David, and Cree, Ian

Subjects
endocrine system diseases, neoplasms, digestive system diseases
Abstract

Complete mutation hotspot list included in Custom Ampliseq gene panel for melanoma, including common driver mutations in BRAF, NRAS, KRAS, MEK, GNAQ, and GNA11. (DOCX 125 kb)

Published
2017
Full Text
View/download PDF

10. Multi institutional evaluation of a new NGS assay for mutation detection from cfDNA in lung cancer

Author

Costa, Jose Luis, Weren, Robbert, Rachiglio, Anna Maria, Mafficini, Andrea, Kurth, Henriette, Reiman, Anne, Didelot, Audrey, Boag, Alexander, Vollbrecht, Claudia, Nishino, Kazuto, Pfeilotter, Harriet E., Laurent-Puig, Pierre, Sheils, Orla, Scarpa, Aldo, Ligtenberg, Marjolijn, Cree, Ian A., Hummel, Michael, Machado, Jose Crlos, and Normanno, Nicola

Published
2017
Full Text
View/download PDF

11. Additional file 1: Table S1. of Chronic tarsal conjunctivitis

Author

Cook, Nicholas, Fizza Mushtaq, Leitner, Christina, Ilchyshyn, Andrew, Smith, George, and Cree, Ian

Subjects
body regions, macromolecular substances
Abstract

Clinical features of 55 patients with Chronic Tarsal Conjunctivitis. Inflammation was graded empirically on a scale fromâ +â (mild) to +++ (severe). (DOCX 24Â kb)

Published
2016
Full Text
View/download PDF

13. Abnormalities of the transforming growth factor-beta pathway in ocular melanoma

Author

Myatt, Nyree, Bhattacharya, Shom Shanker, and Cree, Ian A.

Subjects
Loss of heterozygosity, Transforming growth factor beta, p27, Eye, Melanoma, SMAD
Abstract

8 páginas, 4 figuras, 2 tablas.-- et al., The majority of ocular melanomas occur in the uveal tract. Chemotherapy is generally ineffective and large tumours requiring enucleation have a greater than 50% mortality at 5 years. Monosomy for chromosome 3 is common in uveal melanoma and it is known that there is loss of responsiveness to transforming growth factor beta (TGFβ) in melanoma cell lines. Since the gene for TGFβ receptor II (TGFβR2) is located on chromosome 3p22, this study investigates the possibility that the TGFβ pathway, and TGFβR2 in particular, might be involved in the pathogenesis of this rare eye tumour. To this end, the expression of molecules in the pathway has been examined by immunocytochemistry (TGFβ, TGFβR2, SMAD2, SMAD3, SMAD4, and p27), backed up by a cell culture assay of TGFβ-mediated growth suppression, RT-PCR for SMAD4, and loss of heterozygosity (LOH) on 3p22. There was LOH at 3p22 in 6/19 tumours and loss of TGFβR2 expression in 10/27 tumours. Immunohistochemistry for SMADs 2, 3, and 4 showed potential loss of signal transduction in 14/27 tumours. The results indicate abnormality of the TGFβ pathway in 61% of tumours for which unequivocal results were obtained and suggest that abrogation of control of melanocyte growth by the TGFβ pathway may be important in the formation of uveal melanoma., This research was supported by the Guide Dogs for the Blind Association.

Published
2000

14. Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Author

Amgad, Mohamed, Stovgaard, Elisabeth Specht, Balslev, Eva, Thagaard, Jeppe, Chen, Weijie, Dudgeon, Sarah, Sharma, Ashish, Kerner, Jennifer K., Denkert, Carsten, Yuan, Yinyin, AbdulJabbar, Khalid, Wienert, Stephan, Savas, Peter, Voorwerk, Leonie, Beck, Andrew H., Madabhushi, Anant, Hartman, Johan, Sebastian, Manu M., Horlings, Hugo M., Hudeček, Jan, Ciompi, Francesco, Moore, David A., Singh, Rajendra, Roblin, Elvire, Balancin, Marcelo Luiz, Mathieu, Marie-Christine, Lennerz, Jochen K., Kirtani, Pawan, Chen, I-Chun, Braybrooke, Jeremy P., Pruneri, Giancarlo, Demaria, Sandra, Adams, Sylvia, Schnitt, Stuart J., Lakhani, Sunil R., Rojo, Federico, Comerma, Laura, Badve, Sunil S., Khojasteh, Mehrnoush, Symmans, W. Fraser, Sotiriou, Christos, Gonzalez-Ericsson, Paula, Pogue-Geile, Katherine L., Kim, Rim S., Rimm, David L., Viale, Giuseppe, Hewitt, Stephen M., Bartlett, John M. S., Penault-Llorca, Frédérique, Goel, Shom, Lien, Huang-Chun, Loibl, Sibylle, Kos, Zuzana, Loi, Sherene, Hanna, Matthew G., Michiels, Stefan, Kok, Marleen, Nielsen, Torsten O., Lazar, Alexander J., Bago-Horvath, Zsuzsanna, Kooreman, Loes F. S., Van Der Laak, Jeroen A. W. M., Saltz, Joel, Gallas, Brandon D., Kurkure, Uday, Barnes, Michael, Salgado, Roberto, Cooper, Lee A. D., Hyytiäinen, Aini, Hida, Akira I., Thompson, Alastair, Lefevre, Alex, Gown, Allen, Lo, Amy, Sapino, Anna, Moreira, Andre, Richardson, Andrea, Vingiani, Andrea, Bellizzi, Andrew M., Tutt, Andrew, Guerrero-Zotano, Angel, Grigoriadis, Anita, Ehinger, Anna, Garrido-Castro, Anna C., Vincent-Salomon, Anne, Laenkholm, Anne-Vibeke, Cimino-Mathews, Ashley, Srinivasan, Ashok, Acs, Balazs, Singh, Baljit, Calhoun, Benjamin, Haibe-Kans, Benjamin, Solomon, Benjamin, Thapa, Bibhusal, Nelson, Brad H., Castaneda, Carlos, Ballesteroes-Merino, Carmen, Criscitiello, Carmen, Boeckx, Carolien, Colpaert, Cecile, Quinn, Cecily, Chennubhotla, Chakra S., Swanton, Charles, Solinas, Cinzia, Hiley, Crispin, Drubay, Damien, Bethmann, Daniel, Dillon, Deborah A., Larsimont, Denis, Sabanathan, Dhanusha, Peeters, Dieter, Zardavas, Dimitrios, Höflmayer, Doris, Johnson, Douglas B., Thompson, E. Aubrey, Brogi, Edi, Perez, Edith, ElGabry, Ehab A., Blackley, Elizabeth F., Reisenbichler, Emily, Bellolio, Enrique, Chmielik, Ewa, Gaire, Fabien, Andre, Fabrice, Lu, Fang-I, Azmoudeh-Ardalan, Farid, Gruosso, Forbius Tina, Peale, Franklin, Hirsch, Fred R., Klaushen, Frederick, Acosta-Haab, Gabriela, Farshid, Gelareh, Van Den Eynden, Gert, Curigliano, Giuseppe, Floris, Giuseppe, Broeckx, Glenn, Koeppen, Harmut, Haynes, Harry R., McArthur, Heather, Joensuu, Heikki, Olofsson, Helena, Cree, Ian, Nederlof, Iris, Frahm, Isabel, Brcic, Iva, Chan, Jack, Hall, Jacqueline A., Ziai, James, Brock, Jane, Wesseling, Jelle, Giltnane, Jennifer, Lemonnier, Jerome, Zha, Jiping, M. Ribeiro, Joana, Carter, Jodi M., Hainfellner, Johannes, Quesne, John Le, Juco, Jonathan W., Reis-Filho, Jorge, Van Den Berg, Jose, Sanchez, Joselyn, Sparano, Joseph, Cucherousset, Joël, Araya, Juan Carlos, Adam, Julien, Balko, Justin M., Saeger, Kai, Siziopikou, Kalliopi, Willard-Gallo, Karen, Sikorska, Karolina, Weber, Karsten, Steele, Keith E., Emancipator, Kenneth, El Bairi, Khalid, Blenman, Kim R. M., Allison, Kimberly H., Van De Vijver, Koen K., Korski, Konstanty, Pusztai, Lajos, Buisseret, Laurence, Shi, Leming, Shi-Wei, Liu, Molinero, Luciana, Estrada, M. Valeria, Van Seijen, Maartje, Lacroix-Triki, Magali, Cheang, Maggie C. U., Bakir, Maise Al, Van De Vijver, Marc, Dieci, Maria Vittoria, Rebelatto, Marlon C., Piccart, Martine, Goetz, Matthew P., Preusser, Matthias, Sanders, Melinda E., Regan, Meredith M., Christie, Michael, Misialek, Michael, Ignatiadis, Michail, De Maaker, Michiel, Van Bockstal, Mieke, Castillo, Miluska, Harbeck, Nadia, Tung, Nadine, Laudus, Nele, Sirtaine, Nicolas, Burchardi, Nicole, Ternes, Nils, Radosevic-Robin, Nina, Gluz, Oleg, Grimm, Oliver, Nuciforo, Paolo, Jank, Paul, Jelinic, Petar, Watson, Peter H., Francis, Prudence A., Russell, Prudence A., Pierce, Robert H., Hills, Robert, Leon-Ferre, Roberto, De Wind, Roland, Shui, Ruohong, Declercq, Sabine, Leung, Sam, Tabbarah, Sami, Souza, Sandra C., O’Toole, Sandra, Swain, Sandra, Willis, Scooter, Ely, Scott, Kim, Seong- Rim, Bedri, Shahinaz, Irshad, Sheeba, Liu, Shi-Wei, Hendry, Shona, Bianchi, Simonetta, Bragança, Sofia, Paik, Soonmyung, Fox, Stephen B., Luen, Stephen J., Naber, Stephen, Luz, Sua, Fineberg, Susan, Soler, Teresa, Gevaert, Thomas, D’Alfons, Timothy, John, Tom, Sugie, Tomohagu, Bossuyt, Veerle, Manem, Venkata, Cámaea, Vincente Peg, Tong, Weida, Yang, Wentao, Tran, William T., Wang, Yihong, Allory, Yves, and Husain, Zaheed

Subjects
631/67/580, 692/4028/67/1857, 631/67/2321, 692/53/2422, review-article, Review Article, 631/67/1347, humanities, 3. Good health
Abstract

Funder: U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI), Funder: National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University., Funder: Susan G Komen Foundation (CCR CCR18547966) and a Young Investigator Grant from the Breast Cancer Alliance., Funder: The Canadian Cancer Society, Funder: Breast Cancer Research Foundation (BCRF), Grant No. 17-194, Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.

15. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Author

Kos, Zuzana, Roblin, Elvire, Kim, Rim S., Michiels, Stefan, Gallas, Brandon D., Chen, Weijie, Van De Vijver, Koen K., Goel, Shom, Adams, Sylvia, Demaria, Sandra, Viale, Giuseppe, Nielsen, Torsten O., Badve, Sunil S., Symmans, W. Fraser, Sotiriou, Christos, Rimm, David L., Hewitt, Stephen, Denkert, Carsten, Loibl, Sibylle, Luen, Stephen J., Bartlett, John M. S., Savas, Peter, Pruneri, Giancarlo, Dillon, Deborah A., Cheang, Maggie Chon U., Tutt, Andrew, Hall, Jacqueline A., Kok, Marleen, Horlings, Hugo M., Madabhushi, Anant, Van Der Laak, Jeroen, Ciompi, Francesco, Laenkholm, Anne-Vibeke, Bellolio, Enrique, Gruosso, Tina, Fox, Stephen B., Araya, Juan Carlos, Floris, Giuseppe, Hudeček, Jan, Voorwerk, Leonie, Beck, Andrew H., Kerner, Jen, Larsimont, Denis, Declercq, Sabine, Van Den Eynden, Gert, Pusztai, Lajos, Ehinger, Anna, Yang, Wentao, AbdulJabbar, Khalid, Yuan, Yinyin, Singh, Rajendra, Hiley, Crispin, Bakir, Maise Al, Lazar, Alexander J., Naber, Stephen, Wienert, Stephan, Castillo, Miluska, Curigliano, Giuseppe, Dieci, Maria-Vittoria, André, Fabrice, Swanton, Charles, Reis-Filho, Jorge, Sparano, Joseph, Balslev, Eva, Chen, I-Chun, Stovgaard, Elisabeth Ida Specht, Pogue-Geile, Katherine, Blenman, Kim R. M., Penault-Llorca, Frédérique, Schnitt, Stuart, Lakhani, Sunil R., Vincent-Salomon, Anne, Rojo, Federico, Braybrooke, Jeremy P., Hanna, Matthew G., Soler-Monsó, M. Teresa, Bethmann, Daniel, Castaneda, Carlos A., Willard-Gallo, Karen, Sharma, Ashish, Lien, Huang-Chun, Fineberg, Susan, Thagaard, Jeppe, Comerma, Laura, Gonzalez-Ericsson, Paula, Brogi, Edi, Loi, Sherene, Saltz, Joel, Klaushen, Frederick, Cooper, Lee, Amgad, Mohamed, Moore, David A., Salgado, Roberto, Hyytiäinen, Aini, Hida, Akira I., Thompson, Alastair, Lefevre, Alex, Gown, Allen, Lo, Amy, Sapino, Anna, Moreira, Andre M., Richardson, Andrea, Vingiani, Andrea, Bellizzi, Andrew M., Guerrero, Angel, Grigoriadis, Anita, Garrido-Castro, Ana C., Cimino-Mathews, Ashley, Srinivasan, Ashok, Acs, Balazs, Singh, Baljit, Calhoun, Benjamin, Haibe-Kans, Benjamin, Solomon, Benjamin, Thapa, Bibhusal, Nelson, Brad H., Ballesteroes-Merino, Carmen, Criscitiello, Carmen, Boeckx, Carolien, Colpaert, Cecile, Quinn, Cecily, Chennubhotla, Chakra S., Solinas, Cinzia, Drubay, Damien, Sabanathan, Dhanusha, Peeters, Dieter, Zardavas, Dimitrios, Höflmayer, Doris, Johnson, Douglas B., Thompson, E. Aubrey, Perez, Edith, ElGabry, Ehab A., Blackley, Elizabeth F., Reisenbichler, Emily, Chmielik, Ewa, Gaire, Fabien, Lu, Fang-I, Azmoudeh-Ardalan, Farid, Peale, Franklin, Hirsch, Fred R., Acosta-Haab, Gabriela, Farshid, Gelareh, Broeckx, Glenn, Koeppen, Harmut, Haynes, Harry R., McArthur, Heather, Joensuu, Heikki, Olofsson, Helena, Cree, Ian, Nederlof, Iris, Frahm, Isabel, Brcic, Iva, Chan, Jack, Ziai, James, Brock, Jane, Weseling, Jelle, Giltnane, Jennifer, Lemonnier, Jerome, Zha, Jiping, Ribeiro, Joana, Lennerz, Jochen K., Carter, Jodi M., Hartman, Johan, Hainfellner, Johannes, Le Quesne, John, Juco, Jonathan W., Van Den Berg, Jose, Sanchez, Joselyn, Cucherousset, Joël, Adam, Julien, Balko, Justin M., Saeger, Kai, Siziopikou, Kalliopi, Sikorska, Karolina, Weber, Karsten, Steele, Keith E., Emancipator, Kenneth, El Bairi, Khalid, Allison, Kimberly H., Korski, Konstanty, Buisseret, Laurence, Shi, Leming, Kooreman, Loes F. S., Molinero, Luciana, Estrada, M. Valeria, Van Seijen, Maartje, Lacroix-Triki, Magali, Sebastian, Manu M., Balancin, Marcelo L., Mathieu, Marie-Christine, Van De Vijver, Mark, Rebelatto, Marlon C., Piccart, Martine, Goetz, Matthew P., Preusser, Matthias, Khojasteh, Mehrnoush, Sanders, Melinda E., Regan, Meredith M., Barnes, Michael, Christie, Michael, Misialek, Michael, Ignatiadis, Michail, De Maaker, Michiel, Van Bockstal, Mieke, Harbeck, Nadia, Tung, Nadine, Laudus, Nele, Sirtaine, Nicolas, Burchardi, Nicole, Ternes, Nils, Radosevic-Robin, Nina, Gluz, Oleg, Grimm, Oliver, Nuciforo, Paolo, Jank, Paul, Kirtani, Pawan, Watson, Peter H., Jelinic, Peter, Francis, Prudence A., Russell, Prudence A., Pierce, Robert H., Hills, Robert, Leon-Ferre, Roberto, De Wind, Roland, Shui, Ruohong, Leung, Samuel, Tabbarah, Sami, Souza, Sandra C., O’Toole, Sandra, Swain, Sandra, Dudgeon, Sarah, Willis, Scooter, Ely, Scott, Bedri, Shahinaz, Irshad, Sheeba, Liu, Shiwei, Hendry, Shona, Bianchi, Simonetta, Bragança, Sofia, Paik, Soonmyung, Luz, Sua, Gevaert, Thomas, D’Alfons, Timothy, John, Tom, Sugie, Tomohagu, Kurkure, Uday, Bossuyt, Veerle, Manem, Venkata, Cámaea, Vincente Peg, Tong, Weida, Tran, William T., Wang, Yihong, Allory, Yves, Husain, Zaheed, and Bago-Horvath, Zsuzsanna

Subjects
692/53/2422, article, 3. Good health, 631/67/580/1884
Abstract

Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls.

16. Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Author

Hudeček, Jan, Voorwerk, Leonie, Van Seijen, Maartje, Nederlof, Iris, De Maaker, Michiel, Van Den Berg, Jose, Van De Vijver, Koen K., Sikorska, Karolina, Adams, Sylvia, Demaria, Sandra, Viale, Giuseppe, Nielsen, Torsten O., Badve, Sunil S., Michiels, Stefan, Symmans, William Fraser, Sotiriou, Christos, Rimm, David L., Hewitt, Stephen M., Denkert, Carsten, Loibl, Sibylle, Loi, Sherene, Bartlett, John M. S., Pruneri, Giancarlo, Dillon, Deborah A., Cheang, Maggie C. U., Tutt, Andrew, Hall, Jacqueline A., Kos, Zuzana, Salgado, Roberto, Kok, Marleen, Horlings, Hugo M., Hyytiäinen, Aini, Hida, Akira I., Thompson, Alastair, Lefevre, Alex, Lazar, Alexander J., Gown, Allen, Lo, Amy, Sapino, Anna, Madabhushi, Anant, Moreira, Andre, Richardson, Andrea, Vingiani, Andrea, Beck, Andrew H., Bellizzi, Andrew M., Guerrero, Angel, Grigoriadis, Anita, Ehinger, Anna, Garrido-Castro, Ana, Vincent-Salomon, Anne, Laenkholm, Anne-Vibeke, Sharma, Ashish, Cimino-Mathews, Ashley, Srinivasan, Ashok, Acs, Balazs, Singh, Baljit, Calhoun, Benjamin, Haibe-Kans, Benjamin, Solomon, Benjamin, Thapa, Bibhusal, Nelson, Brad H., Gallas, Brandon D., Castaneda, Carlos, Ballesteros-Merino, Carmen, Criscitiello, Carmen, Boeckx, Carolien, Colpaert, Cecile, Quinn, Cecily, Chennubhotla, Chakra S., Swanton, Charles, Solinas, Cinzia, Hiley, Crispin, Drubay, Damien, Bethmann, Daniel, Moore, David A., Larsimont, Denis, Sabanathan, Dhanusha, Peeters, Dieter, Zardavas, Dimitrios, Höflmayer, Doris, Johnson, Douglas B., Thompson, E. Aubrey, Brogi, Edi, Perez, Edith, ElGabry, Ehab A., Stovgaard, Elisabeth Specht, Blackley, Elizabeth F., Roblin, Elvire, Reisenbichler, Emily, Bellolio, Enrique, Balslev, Eva, Chmielik, Ewa, Gaire, Fabien, Andre, Fabrice, Lu, Fang-I, Azmoudeh-Ardalan, Farid, Rojo, Federico, Gruosso, Tina, Ciompi, Francesco, Peale, Franklin, Hirsch, Fred R., Klauschen, Frederick, Penault-Llorca, Frédérique, Acosta Haab, Gabriela, Farshid, Gelareh, Van Den Eynden, Gert, Curigliano, Giuseppe, Floris, Giuseppe, Broeckx, Glenn, Gonzalez-Ericsson, Koeppen, Harmut, Haynes, Harry R., McArthur, Heather, Joensuu, Heikki, Olofsson, Helena, Lien, Huang-Chun, Chen, I-Chun, Cree, Ian, Frahm, Isabel, Brcic, Iva, Chan, Jack, Ziai, James, Brock, Jane, Wesseling, Jelle, Giltnane, Jennifer, Kerner, Jennifer K., Thagaard, Jeppe, Braybrooke, Jeremy P., Van Der Laak, Jeroen A. W. M., Lemonnier, Jerome, Zha, Jiping, Ribeiro, Joana, Lennerz, Jochen K., Carter, Jodi M., Saltz, Joel, Hartman, Johan, Hainfellner, Johannes, Quesne, John Le, Juco, Jonathon W., Reis-Filho, Jorge, Sanchez, Joselyn, Sparano, Joseph, Cucherousset, Joël, Araya, Juan Carlos, Adam, Julien, Balko, Justin M., Saeger, Kai, Siziopikou, Kalliopi, Willard-Gallo, Karen, Weber, Karsten, Pogue-Geile, Katherine L., Steele, Keith E., Emancipator, Kenneth, AbdulJabbar, Khalid, El Bairi, Khalid, Blenman, Kim R. M., Allison, Kimberly H., Korski, Konstanty, Pusztai, Lajos, Comerma, Laura, Buisseret, Laurence, Cooper, Lee A. D., Shi, Leming, Kooreman, Loes F. S., Molinero, Luciana, Estrada, M. Valeria, Lacroix-Triki, Magali, Al Bakir, Maise, Sebastian, Manu M., Van De Vijver, Marc, Balancin, Marcelo Luiz, Dieci, Maria Vittoria, Mathieu, Marie-Christine, Rebelatto, Marlon C., Piccart, Martine, Hanna, Matthew G., Goetz, Matthew P., Preusser, Matthias, Khojasteh, Mehrnoush, Sanders, Melinda E., Regan, Meredith M., Barnes, Michael, Christie, Michael, Misialek, Michael, Ignatiadis, Michail, Van Bockstal, Mieke, Castillo, Miluska, Amgad, Mohamed, Harbeck, Nadia, Tung, Nadine, Laudus, Nele, Sirtaine, Nicolas, Burchardi, Nicole, Ternes, Nils, Radosevic-Robin, Nina, Gluz, Oleg, Grimm, Oliver, Nuciforo, Paolo, Jank, Paul, Gonzalez-Ericsson, Paula, Kirtani, Pawan, Jelinic, Petar, Watson, Peter H., Savas, Peter, Francis, Prudence A., Russell, Prudence A., Singh, Rajendra, Kim, Rim S., Pierce, Robert H., Hills, Robert, Leon-Ferre, Roberto, De Wind, Roland, Shui, Ruohong, De Clercq, Sabine, Leung, Sam, Tabbarah, Sami, Souza, Sandra C., O’Toole, Sandra, Swain, Sandra, Dudgeon, Sarah, Willis, Scooter, Ely, Scott, Kim, Seong-Rim, Bedri, Shahinaz, Irshad, Sheeba, Liu, Shi-Wei, Goel, Shom, Hendry, Shona, Bianchi, Simonetta, Bragança, Sofia, Paik, Soonmyung, Wienert, Stephan, Fox, Stephen B., Luen, Stephen J., Naber, Stephen, Schnitt, Stuart J., Sua, Luz F., Lakhani, Sunil R., Fineberg, Susan, Soler, Teresa, Gevaert, Thomas, D’Alfonso, Timothy, John, Tom, Sugie, Tomohagu, Kurkure, Uday, Bossuyt, Veerle, Manem, Venkata, Cámara, Vincente Peg, Tong, Weida, Chen, Weijie, Yang, Wentao, Tran, William T., Wang, Yihong, Yuan, Yinyin, Allory, Yves, Husain, Zaheed, and Bago-Horvath, Zsuzsanna

Subjects
692/53, review-article, Review Article, 631/67/1347, 692/4028/67/580, 631/67/1857, 3. Good health
Abstract

Funder: Breast Cancer Research Foundation (BCRF); doi: https://doi.org/10.13039/100001006, Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting.

17. Response to the Comments from the Groupe Francophone de Cytogénétique Hématologique (GFCH) on the 5th edition of the World Health Organization classification of haematolymphoid tumors

Author

Reiner Siebert, Anna Schuh, German Ott, Ian A. Cree, Ming-Qing Du, Judith Ferry, Andreas Hochhaus, Kikkeri N. Naresh, Eric Solary, Joseph D. Khoury, Siebert, Reiner [0000-0001-7433-3703], Schuh, Anna [0000-0002-3938-8490], Cree, Ian A [0000-0001-5007-9456], Du, Ming-Qing [0000-0002-1017-5045], Hochhaus, Andreas [0000-0003-0626-0834], Naresh, Kikkeri N [0000-0003-3807-3638], Solary, Eric [0000-0002-8629-1341], Khoury, Joseph D [0000-0003-2621-3584], and Apollo - University of Cambridge Repository

Subjects
Chromosome Aberrations, Cancer Research, Oncology, Neoplasms, Cytogenetic Analysis, Humans, Hematology
Published
2023

Catalog

Books, media, physical & digital resources
See catalog results