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540 results on '"Pfeifer, John D."'

4. Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes

Author

Wang, Ya-Ting, Zaitsev, Konstantin, Lu, Qun, Li, Shan, Schaiff, W. Timothy, Kim, Ki-Wook, Droit, Lindsay, Wilen, Craig B., Desai, Chandni, Balce, Dale R., Orchard, Robert C., Orvedahl, Anthony, Park, Sunmin, Kreamalmeyer, Darren, Handley, Scott A., Pfeifer, John D., Baldridge, Megan T., Artyomov, Maxim N., Stallings, Christina L., and Virgin, Herbert W.

Published
2020
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7. Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine

Author

Compton, Carolyn C., Robb, James A., Anderson, Matthew W., Berry, Anna B., Birdsong, George G., Bloom, Kenneth J., Branton, Philip A., Crothers, Jessica W., Cushman-Vokoun, Allison M., Hicks, David G., Khoury, Joseph D., Laser, Jordan, Marshall, Carrie B., Misialek, Michael J., Natale, Kristen E., Nowak, Jan Anthony, Olson, Damon, Pfeifer, John D., Schade, Andrew, Vance, Gail H., Walk, Eric E., and Yohe, Sophia Louise

Subjects
United States. National Cancer Institute, Precision medicine, Evidence-based medicine, Medical practice, Medical research, Medical care quality, Breast cancer, Medical societies, Health, College of American Pathologists
Abstract

* Biospecimens acquired during routine medical practice are the primary sources of molecular information about patients and their diseases that underlies precision medicine and translational research. In cancer care, molecular analysis of biospecimens is especially common because it often determines treatment choices and may be used to monitor therapy in real time. However, patient specimens are collected, handled, and processed according to routine clinical procedures during which they are subjected to factors that may alter their molecular quality and composition. Such artefactual alteration may skew data from molecular analyses, render analysis data uninterpretable, or even preclude analysis altogether if the integrity of a specimen is severely compromised. As a result, patient care and safety may be affected, and medical research dependent on patient samples may be compromised. Despite these issues, there is currently no requirement to control or record preanalytical variables in clinical practice with the single exception of breast cancer tissue handled according to the guideline jointly developed by the American Society of Clinical Oncology and College of American Pathologists (CAP) and enforced through the CAP Laboratory Accreditation Program. Recognizing the importance of molecular data derived from patient specimens, the CAP Personalized Healthcare Committee established the Preanalytics for Precision Medicine Project Team to develop a basic set of evidence-based recommendations for key preanalytics for tissue and blood specimens. If used for biospecimens from patients, these preanalytical recommendations would ensure the fitness of those specimens for molecular analysis and help to assure the quality and reliability of the analysis data. (Arch Pathol Lab Med. 2019;143:1346-1363; doi: 10.5858/arpa.2019-0009-SA), OVERVIEW: THE CRITICAL ROLE OF PREANALYTICS IN THE MOLECULAR ANALYSIS OF PATIENT BIOSPECIMENS Biospecimens acquired during routine medical practice are the primary sources of the molecular information about patients and [...]

Published
2019
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14. Author Correction: Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes

Author

Wang, Ya-Ting, Zaitsev, Konstantin, Lu, Qun, Li, Shan, Schaiff, W. Timothy, Kim, Ki-Wook, Droit, Lindsay, Wilen, Craig B., Desai, Chandni, Balce, Dale R., Orchard, Robert C., Orvedahl, Anthony, Park, Sunmin, Kreamalmeyer, Darren, Handley, Scott A., Pfeifer, John D., Baldridge, Megan T., Artyomov, Maxim N., Stallings, Christina L., and Virgin, Herbert W.

Published
2021
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34. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows

Author

Rosenbaum, Jason N., primary, Berry, Anna B., additional, Church, Alanna J., additional, Crooks, Kristy, additional, Gagan, Jeffrey R., additional, López-Terrada, Dolores, additional, Pfeifer, John D., additional, Rennert, Hanna, additional, Schrijver, Iris, additional, Snow, Anthony N., additional, Wu, David, additional, and Ewalt, Mark D., additional

Published
2021
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37. Clinical next-generation sequencing in patients with non–small cell lung cancer

Author

Hagemann, Ian S., Devarakonda, Siddhartha, Lockwood, Christina M., Spencer, David H., Guebert, Kalin, Bredemeyer, Andrew J., Al-Kateb, Hussam, Nguyen, TuDung T., Duncavage, Eric J., Cottrell, Catherine E., Kulkarni, Shashikant, Nagarajan, Rakesh, Seibert, Karen, Baggstrom, Maria, Waqar, Saiama N., Pfeifer, John D., Morgensztern, Daniel, and Govindan, Ramaswamy

Published
2015
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39. A novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth

Author

Koch Institute for Integrative Cancer Research at MIT, Liu, Ta-Chiang, VanBuskirk, Kelley, Ali, Syed A, Kelly, M Paul, Holtz, Lori R, Yilmaz, Omer H, Sadiq, Kamran, Iqbal, Najeeha, Amadi, Beatrice, Syed, Sana, Ahmed, Tahmeed, Moore, Sean, Ndao, I Malick, Isaacs, Michael H, Pfeifer, John D, Atlas, Hannah, Tarr, Phillip I, Denno, Donna M, Moskaluk, Christopher A, Koch Institute for Integrative Cancer Research at MIT, Liu, Ta-Chiang, VanBuskirk, Kelley, Ali, Syed A, Kelly, M Paul, Holtz, Lori R, Yilmaz, Omer H, Sadiq, Kamran, Iqbal, Najeeha, Amadi, Beatrice, Syed, Sana, Ahmed, Tahmeed, Moore, Sean, Ndao, I Malick, Isaacs, Michael H, Pfeifer, John D, Atlas, Hannah, Tarr, Phillip I, Denno, Donna M, and Moskaluk, Christopher A

Abstract

© 2020 Liu et al. Background A major limitation to understanding the etiopathogenesis of environmental enteric dysfunction (EED) is the lack of a comprehensive, reproducible histologic framework for characteriz-ing the small bowel lesions. We hypothesized that the development of such a system will identify unique histology features for EED, and that some features might correlate with clinical severity. Methods Duodenal endoscopic biopsies from two cohorts where EED is prevalent (Pakistan, Zambia) and North American children with and without gluten sensitive enteropathy (GSE) were pro-cessed for routine hematoxylin & eosin (H&E) staining, and scanned to produce whole slide images (WSIs) which we shared among study pathologists via a secure web browser-based platform. A semi-quantitative scoring index composed of 11 parameters encompassing tis-sue injury and response patterns commonly observed in routine clinical practice was con-structed by three gastrointestinal pathologists, with input from EED experts. The pathologists then read the WSIs using the EED histology index, and inter-observer reliability was assessed. The histology index was further used to identify within-and between-child variations as well as features common across and unique to each cohort, and those that cor-related with host phenotype. Results Eight of the 11 histologic scoring parameters showed useful degrees of variation. The over-all concordance across all parameters was 96% weighted agreement, kappa 0.70, and Gwet’s AC 0.93. Zambian and Pakistani tissues shared some histologic features with GSE, but most features were distinct, particularly abundance of intraepithelial lymphocytes in the Pakistani cohort, and marked villous destruction and loss of secretory cell lineages in the Zambian cohort. Conclusions We propose the first EED histology index for interpreting duodenal biopsies. This index should be useful in future clinical and translational studies of this widespread, poorly under-stood, a

Published
2021

43. Odontoblast TRPC5 channels signal cold pain in teeth

Author

Bernal, Laura, primary, Sotelo-Hitschfeld, Pamela, additional, König, Christine, additional, Sinica, Viktor, additional, Wyatt, Amanda, additional, Winter, Zoltan, additional, Hein, Alexander, additional, Touska, Filip, additional, Reinhardt, Susanne, additional, Tragl, Aaron, additional, Kusuda, Ricardo, additional, Wartenberg, Philipp, additional, Sclaroff, Allen, additional, Pfeifer, John D., additional, Ectors, Fabien, additional, Dahl, Andreas, additional, Freichel, Marc, additional, Vlachova, Viktorie, additional, Brauchi, Sebastian, additional, Roza, Carolina, additional, Boehm, Ulrich, additional, Clapham, David E., additional, Lennerz, Jochen K., additional, and Zimmermann, Katharina, additional

Published
2021
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44. Odontoblast TRPC5 channels signal cold pain in teeth

Author

Bernal, Laura, Sotelo-Hitschfeld, Pamela, König, Christine, Sinica, Viktor, Wyatt, Amanda, Winter, Zoltan, Hein, Alexander, Touska, Filip, Reinhardt, Susanne, Tragl, Aaron, Kusuda, Ricardo, Wartenberg, Philipp, Sclaroff, Allen, Pfeifer, John D., Ectors, Fabien, Dahl, Andreas, Freichel, Marc, Vlachova, Viktorie, Brauchi, Sebastian, Roza, Carolina, Boehm, Ulrich, Clapham, David E., Lennerz, Jochen K., and Zimmermann, Katharina

Subjects
stomatognathic diseases, stomatognathic system, SciAdv r-articles, Neurophysiology, ddc:610, Research Articles, Research Article, Signal Transduction
Abstract

The odontoblast, with processes beyond the dentin-enamel boundary, is the initial site of TRPC5 cold transduction in teeth., Teeth are composed of many tissues, covered by an inflexible and obdurate enamel. Unlike most other tissues, teeth become extremely cold sensitive when inflamed. The mechanisms of this cold sensation are not understood. Here, we clarify the molecular and cellular components of the dental cold sensing system and show that sensory transduction of cold stimuli in teeth requires odontoblasts. TRPC5 is a cold sensor in healthy teeth and, with TRPA1, is sufficient for cold sensing. The odontoblast appears as the direct site of TRPC5 cold transduction and provides a mechanism for prolonged cold sensing via TRPC5’s relative sensitivity to intracellular calcium and lack of desensitization. Our data provide concrete functional evidence that equipping odontoblasts with the cold-sensor TRPC5 expands traditional odontoblast functions and renders it a previously unknown integral cellular component of the dental cold sensing system.

Published
2020

50. Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics.

Author

Pfeifer, John D, Loberg, Robert, Lofton-Day, Catherine, and Zehnbauer, Barbara A

Subjects
*COLON tumors, *PILOT projects, *SEQUENCE analysis, *GENETIC mutation, *RESEARCH funding
Abstract

Objectives: Diversity of laboratory-developed tests (LDTs) using next-generation sequencing (NGS) raises concerns about their accuracy for selection of targeted therapies. A working group developed a pilot study of traceable reference samples to measure NGS LDT performance among a cohort of clinical laboratories.Methods: Human cell lines were engineered via CRISPR/Cas9 and prepared as formalin-fixed, paraffin-embedded cell pellets ("wet" samples) to assess the entire NGS test cycle. In silico mutagenized NGS sequence files ("dry" samples) were used to assess the bioinformatics component of the NGS test cycle. Single and multinucleotide variants (n = 36) of KRAS and NRAS were tested at 5% or 15% variant allele fraction to determine eligibility for therapy with the EGFR inhibitor panitumumab in the setting of metastatic colorectal cancer.Results: Twenty-one (21/21) laboratories tested wet samples; 19 of 21 analyzed dry samples. Of the laboratories that tested both the wet and dry samples, 7 (37%) of 19 laboratories correctly reported all variants, 3 (16%) of 19 had fewer than five errors, and 9 (47%) of 19 had five or more errors. Most errors were false negatives.Conclusions: Genetically engineered cell lines and mutagenized sequence files are complementary reference samples for evaluating NGS test performance among clinical laboratories using LDTs. Variable accuracy in detection of genetic variants among some LDTs may identify different patient populations for targeted therapy. [ABSTRACT FROM AUTHOR]

Published
2022
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