Browsing by Author "Lazar, Alexander J."

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    The Cancer Genomics Resource List 2014
    (CAP, 2015-08) Zutter, Mary M.; Bloom, Kenneth J.; Cheng, Liang; Hagemann, Ian S.; Kaufman, Jill H.; Krasinskas, Alyssa M.; Lazar, Alexander J.; Leonard, Debra G. B.; Lindeman, Neal I.; Moyer, Ann M.; Nikiforova, Marina N.; Nowak, Jan A.; Pfeifer, John D.; Sepulveda, Antonia R.; Willis, Joseph E.; Yohe, Sophia L.; Department of Pathology and Laboratory Medicine, IU School of Medicine
    Context.— Genomic sequencing for cancer is offered by commercial for-profit laboratories, independent laboratory networks, and laboratories in academic medical centers and integrated health networks. The variability among the tests has created a complex, confusing environment. Objective.— To address the complexity, the Personalized Health Care (PHC) Committee of the College of American Pathologists proposed the development of a cancer genomics resource list (CGRL). The goal of this resource was to assist the laboratory pathology and clinical oncology communities. Design.— The PHC Committee established a working group in 2012 to address this goal. The group consisted of site-specific experts in cancer genetic sequencing. The group identified current next-generation sequencing (NGS)–based cancer tests and compiled them into a usable resource. The genes were annotated by the working group. The annotation process drew on published knowledge, including public databases and the medical literature. Results.— The compiled list includes NGS panels offered by 19 laboratories or vendors, accompanied by annotations. The list has 611 different genes for which NGS-based mutation testing is offered. Surprisingly, of these 611 genes, 0 genes were listed in every panel, 43 genes were listed in 4 panels, and 54 genes were listed in 3 panels. In addition, tests for 393 genes were offered by only 1 or 2 institutions. Table 1 provides an example of gene mutations offered for breast cancer genomic testing with the annotation as it appears in the CGRL 2014. Conclusions.— The final product, referred to as the Cancer Genomics Resource List 2014, is available as supplemental digital content.
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    Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group
    (Nature Research, 2020-05-12) 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.; International Immuno-Oncology Biomarker Working Group; Pathology and Laboratory Medicine, School of Medicine
    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.
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    The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms
    (Springer Nature, 2022) Alaggio, Rita; Amador, Catalina; Anagnostopoulos, Ioannis; Attygalle, Ayoma D.; Araujo, Iguaracyra Barreto de Oliveira; Berti, Emilio; Bhagat, Govind; Borges, Anita Maria; Boyer, Daniel; Calaminici, Mariarita; Chadburn, Amy; Chan, John K. C.; Cheuk, Wah; Chng, Wee-Joo; Choi, John K.; Chuang, Shih-Sung; Coupland, Sarah E.; Czader, Magdalena; Dave, Sandeep S.; de Jong, Daphne; Du, Ming-Qing; Elenitoba-Johnson, Kojo S.; Ferry, Judith; Geyer, Julia; Gratzinger, Dita; Guitart, Joan; Gujral, Sumeet; Harris, Marian; Harrison, Christine J.; Hartmann, Sylvia; Hochhaus, Andreas; Jansen, Patty M.; Karube, Kennosuke; Kempf, Werner; Khoury, Joseph; Kimura, Hiroshi; Klapper, Wolfram; Kovach, Alexandra E.; Kumar, Shaji; Lazar, Alexander J.; Lazzi, Stefano; Leoncini, Lorenzo; Leung, Nelson; Leventaki, Vasiliki; Li, Xiao-Qiu; Lim, Megan S.; Liu, Wei-Ping; Louissai, Abnerm, Jr.; Marcogliese, Andrea; Medeiros, L. Jeffrey; Michal, Michael; Miranda, Roberto N.; Mitteldorf, Christina; Montes-Moreno, Santiago; Morice, William; Nardi, Valentina; Naresh, Kikkeri N.; Natkunam, Yasodha; Ng, Siok-Bian; Oschlies, Ilske; Ott, German; Parrens, Marie; Pulitzer, Melissa; Rajkumar, S. Vincent; Rawstron, Andrew C.; Rech, Karen; Rosenwald, Andreas; Said, Jonathan; Sarkozy, Clémentine; Sayed, Shahin; Saygin, Caner; Schuh, Anna; Sewell, William; Siebert, Reiner; Sohani, Aliyah R.; Tooze, Reuben; Traverse-Glehen, Alexandra; Vega, Francisco; Vergier, Beatrice; Wechalekar, Ashutosh D.; Wood, Brent; Xerri, Luc; Xiao, Wenbin; Pathology and Laboratory Medicine, School of Medicine
    We herein present an overview of the upcoming 5th edition of the World Health Organization Classification of Haematolymphoid Tumours focussing on lymphoid neoplasms. Myeloid and histiocytic neoplasms will be presented in a separate accompanying article. Besides listing the entities of the classification, we highlight and explain changes from the revised 4th edition. These include reorganization of entities by a hierarchical system as is adopted throughout the 5th edition of the WHO classification of tumours of all organ systems, modification of nomenclature for some entities, revision of diagnostic criteria or subtypes, deletion of certain entities, and introduction of new entities, as well as inclusion of tumour-like lesions, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms.