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Yaghoobi V, Martinez-Morilla S, Liu Y, Charette L, Rimm DL, Harigopal M. Advances in quantitative immunohistochemistry and their contribution to breast cancer. Expert Rev Mol Diagn 2020; 20:509-522. [PMID: 32178550 DOI: 10.1080/14737159.2020.1743178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Automated image analysis provides an objective, quantitative, and reproducible method of measurement of biomarkers. Image quantification is particularly well suited for the analysis of tissue microarrays which has played a major pivotal role in the rapid assessment of molecular biomarkers. Data acquired from grinding up bulk tissue samples miss spatial information regarding cellular localization; therefore, methods that allow for spatial cell phenotyping at high resolution have proven to be valuable in many biomarker discovery assays. Here, we focus our attention on breast cancer as an example of a tumor type that has benefited from quantitative biomarker studies using tissue microarray format.Areas covered: The history of immunofluorescence and immunohistochemistry and the current status of these techniques, including multiplexing technologies (spectral and non-spectral) and image analysis software will be addressed. Finally, we will turn our attention to studies that have provided proof-of-principle evidence that have been impacted from the use of these techniques.Expert opinion: Assessment of prognostic and predictive biomarkers on tissue sections and TMA using Quantitative immunohistochemistry is an important advancement in the investigation of biologic markers. The challenges in standardization of quantitative technologies for accurate assessment are required for adoption into routine clinical practice.
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Affiliation(s)
- Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lori Charette
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Malini Harigopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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Toffart AC, Asfari S, Mc Leer A, Reymond E, Jankowski A, Moro-Sibilot D, Stephanov O, Ghelfi J, Lantuejoul S, Ferretti GR. Percutaneous CT-guided biopsy of lytic bone lesions in patients clinically suspected of lung cancer: Diagnostic performances for pathological diagnosis and molecular testing. Lung Cancer 2020; 140:93-98. [PMID: 31901769 DOI: 10.1016/j.lungcan.2019.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/17/2023]
Abstract
OBJECTIVES Bone is a common location for lung cancer metastasis. Clinicians are often reluctant to biopsy bone metastases, as they are known to require a decalcification process that damages nucleic acids, which makes it incompatible with molecular testing. We performed this study to assess the diagnostic performance of histopathology and molecular testing of computed tomography (CT)-guided percutaneous bone biopsies of lytic bone lesions during the initial assessment or during the progression of lung cancer. MATERIALS AND METHODS This retrospective study included all patients suspected of having or known to have primary lung cancer and CT-guided percutaneous bone biopsies of lytic bone from January 2010 to June 2017. The main judgment criterion was the diagnostic performance of the pathological analysis. Secondary endpoints were the diagnostic performance of molecular testing and incidence of complications. RESULTS Fifty patients were included. The yield of CT-guided percutaneous bone biopsies for pathological analysis was 100 %, allowing for a diagnosis of certainty in all cases. The percentage of tumor cells in samples was higher than the 20 % threshold in 83.9 % of cases. The yield of molecular analysis was 94.6 %. A mutation was found in 60 % of cases; most frequently in KRAS (Kirsten rat sarcoma viral oncogene homolog) (28.6 %) and EGFR (epidermal growth factor receptor) (14.3 %). The complication rate was 2 %, i.e. a minor undrained pneumothorax. CONCLUSION CT-guided percutaneous biopsies of lytic bone is associated with a very low complication rate and high diagnostic performance for histopathology and mutation testing.
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Affiliation(s)
- Anne-Claire Toffart
- Unité d'oncologie thoracique, Service de pneumologie, CS 10217, 38043 Grenoble, France; INSERM U 1209 IAB, la Tronche, 38700, France
| | - Stéphane Asfari
- Service de radiologie diagnostique et interventionnelle, CS 10217, 38043 Grenoble, France
| | - Anne Mc Leer
- INSERM U 1209 IAB, la Tronche, 38700, France; pathologie moléculaire, Institut de Biologie et de Pathologie, CS 10217, 38043 Grenoble, France
| | - Emilie Reymond
- Service de radiologie diagnostique et interventionnelle, CS 10217, 38043 Grenoble, France
| | - Adrien Jankowski
- Service de radiologie diagnostique et interventionnelle, CS 10217, 38043 Grenoble, France
| | - Denis Moro-Sibilot
- Unité d'oncologie thoracique, Service de pneumologie, CS 10217, 38043 Grenoble, France; INSERM U 1209 IAB, la Tronche, 38700, France
| | - Olivier Stephanov
- anatomopathologie, Institut de Biologie et de Pathologie, CS 10217, 38043 Grenoble, France
| | - Julien Ghelfi
- Service de radiologie diagnostique et interventionnelle, CS 10217, 38043 Grenoble, France
| | - Sylvie Lantuejoul
- Plateforme Anapath Recherche Synergie Lyon Cancer-Est, Département de Recherche Translationnelle et d'Innovations Centre de Lutte Contre le Cancer UNICANCER Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Gilbert R Ferretti
- INSERM U 1209 IAB, la Tronche, 38700, France; Service de radiologie diagnostique et interventionnelle, CS 10217, 38043 Grenoble, France.
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103
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Spencer RMSSB, de Camargo VP, Silva MLG, Pinto FFE, Costa FD, Cequeira WS, Munhoz RR, Mello CA, Schmerling RA, Filho WJD, Coelho TM, Ambrosio AVA, Leite ETT, Hanna SA, Nakagawa SA, Baptista AM, Pinheiro RN, de Oliveira JL, de Araújo MS, de Araujo RLC, Laporte GA, de Almeida Quadros C, de Oliveira AF, Lopes A. Brazilian consensus on the diagnosis and treatment of extremities soft tissue sarcomas. J Surg Oncol 2020; 121:743-758. [PMID: 31970785 DOI: 10.1002/jso.25847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Soft tissue sarcomas (STSs) are rare tumors and constitute only 1% of all tumors in adults. Indeed, due to their rarity, most cases in Brazil are not treated according to primary international guidelines. METHODS This consensus addresses the treatment of STSs in the extremities. It was made by workgroups from Brazilian Societies of Surgical Oncology, Orthopaedics, Clinical Oncology, Pathology, Radiology and Diagnostic Imaging, and Radiation Oncology. The workgroups based their arguments on the best level of evidence in the literature and recommendations were made according to diagnosis, staging, and treatment of STSs. A meeting was held with all the invited experts and the topics were presented individually with the definition of the degree of recommendation, based on the levels of evidence in the literature. RESULTS Risk factors and epidemiology were described as well as the pathological aspects and imaging. All recommendations are described with the degree of recommendation and levels of evidence. CONCLUSION Recommendations based on the best literature regional aspects were made to guide professionals who treat STS. Separate consensus on specific treatments for retroperitoneal, visceral, trunk, head and neck sarcomas, and gastrointestinal stromal tumor, are not contemplated into this consensus.
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Affiliation(s)
- Ranyell M S S B Spencer
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Veridiana P de Camargo
- Department of Directory, Brazilian Society of Clinical Surgical (BSCO), São Paulo, Brazil
| | - Maria L G Silva
- Department of Directory, Brazilian Society of Radiation Oncology (BSRO), São Paulo, Brazil
| | - Fabio F E Pinto
- Department of Directory, Brazilian Society of Orthopaedics and Traumatology (BSOT), São Paulo, Brazil
| | | | - Wagner S Cequeira
- AC Camargo Cancer Center, Department of Diagnosis and Imaging, São Paulo, Brazil
| | - Rodrigo R Munhoz
- Department of Directory, Brazilian Society of Clinical Surgical (BSCO), São Paulo, Brazil
| | - Celso A Mello
- Department of Directory, Brazilian Society of Clinical Surgical (BSCO), São Paulo, Brazil
| | - Rafael A Schmerling
- Department of Directory, Brazilian Society of Clinical Surgical (BSCO), São Paulo, Brazil
| | - Waldec J D Filho
- Department of Directory, Brazilian Society of Clinical Surgical (BSCO), São Paulo, Brazil
| | - Tharcisio M Coelho
- Department of Directory, Brazilian Society of Radiation Oncology (BSRO), São Paulo, Brazil
| | - Alexandre V A Ambrosio
- Department of Directory, Brazilian Society of Radiation Oncology (BSRO), São Paulo, Brazil
| | - Elton T T Leite
- Department of Directory, Brazilian Society of Radiation Oncology (BSRO), São Paulo, Brazil
| | - Samir A Hanna
- Department of Directory, Brazilian Society of Radiation Oncology (BSRO), São Paulo, Brazil
| | - Sueli A Nakagawa
- Department of Directory, Brazilian Society of Orthopaedics and Traumatology (BSOT), São Paulo, Brazil
| | - Andre M Baptista
- Department of Directory, Brazilian Society of Orthopaedics and Traumatology (BSOT), São Paulo, Brazil
| | - Rodrigo N Pinheiro
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Jadivan L de Oliveira
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Marcelo Sá de Araújo
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Raphael L C de Araujo
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Gustavo A Laporte
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | | | - Alexandre F de Oliveira
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
| | - Ademar Lopes
- Department of Directory, Brazilian Society of Surgical Oncology (BSSO), Rio de Janeiro, Brazil
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104
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Cummings M, King H, Hurst J, Tanner G, Khazin L, Thompson P, Gray A, Gahir N, Cartlidge C, Farooq Z, Raveendran K, Allen K, Rotimi O, Orsi NM. Decreasing formalin concentration improves quality of DNA extracted from formalin-fixed paraffin-embedded tissue specimens without compromising tissue morphology or immunohistochemical staining. J Clin Pathol 2020; 73:514-518. [PMID: 31919142 DOI: 10.1136/jclinpath-2019-206368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/03/2022]
Abstract
Genomic technologies are increasingly used clinically for both diagnosis and guiding cancer therapy. However, formalin fixation can compromise DNA quality. This study aimed to optimise tissue fixation using normal colon, liver and uterus (n=8 each) by varying neutral buffered formalin (NBF) concentration (1%-5% w/v) and fixation time (24-48 hours). Fixation using 4% NBF improved DNA quality (assessed by qPCR) compared with routine (4% unbuffered formal saline-fixed) specimens (p<0.01). Further improvements were achieved by reducing NBF concentration (p<0.00001), whereas fixation time had no effect (p=0.110). No adverse effects were detected by histopathological or QuPath morphometric analysis. Immunohistochemistry for multicytokeratin and α-smooth muscle actin revealed no changes in staining specificity or intensity in any tissue other than on liver multicytokeratin staining intensity, where the effect of fixation time was more significant (p=0.0004) than NBF concentration (p=0.048). Thus, reducing NBF concentration can maximise DNA quality without compromising tissue morphology or standard histopathological analyses.
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Affiliation(s)
- Michele Cummings
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Henry King
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - James Hurst
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Georgette Tanner
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Leah Khazin
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Phillip Thompson
- Department of Histopathology, St. James's University Hospital, Leeds, UK
| | - Allan Gray
- Department of Histopathology, St. James's University Hospital, Leeds, UK
| | - Narinder Gahir
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Caroline Cartlidge
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Zara Farooq
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Keyura Raveendran
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
| | - Katie Allen
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK.,Department of Histopathology, St. James's University Hospital, Leeds, UK
| | - Olorunda Rotimi
- Department of Histopathology, St. James's University Hospital, Leeds, UK
| | - Nicolas M Orsi
- Women's Health Research Group, Pathology & Data Analytics, Leeds Institute of Medical Research at St. James's, University of Leeds, Wellcome Trust Brenner Building, Leeds, UK
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105
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Lantuejoul S, Sound-Tsao M, Cooper WA, Girard N, Hirsch FR, Roden AC, Lopez-Rios F, Jain D, Chou TY, Motoi N, Kerr KM, Yatabe Y, Brambilla E, Longshore J, Papotti M, Sholl LM, Thunnissen E, Rekhtman N, Borczuk A, Bubendorf L, Minami Y, Beasley MB, Botling J, Chen G, Chung JH, Dacic S, Hwang D, Lin D, Moreira A, Nicholson AG, Noguchi M, Pelosi G, Poleri C, Travis W, Yoshida A, Daigneault JB, Wistuba II, Mino-Kenudson M. PD-L1 Testing for Lung Cancer in 2019: Perspective From the IASLC Pathology Committee. J Thorac Oncol 2019; 15:499-519. [PMID: 31870882 DOI: 10.1016/j.jtho.2019.12.107] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/29/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
The recent development of immune checkpoint inhibitors (ICIs) has led to promising advances in the treatment of patients with NSCLC and SCLC with advanced or metastatic disease. Most ICIs target programmed cell death protein 1 (PD-1) or programmed death ligand 1 (PD-L1) axis with the aim of restoring antitumor immunity. Multiple clinical trials for ICIs have evaluated a predictive value of PD-L1 protein expression in tumor cells and tumor-infiltrating immune cells (ICs) by immunohistochemistry (IHC), for which different assays with specific IHC platforms were applied. Of those, some PD-L1 IHC assays have been validated for the prescription of the corresponding agent for first- or second-line treatment. However, not all laboratories are equipped with the dedicated platforms, and many laboratories have set up in-house or laboratory-developed tests that are more affordable than the generally expensive clinical trial-validated assays. Although PD-L1 IHC test is now deployed in most pathology laboratories, its appropriate implementation and interpretation are critical as a predictive biomarker and can be challenging owing to the multiple antibody clones and platforms or assays available and given the typically small size of samples provided. Because many articles have been published since the issue of the IASLC Atlas of PD-L1 Immunohistochemistry Testing in Lung Cancer, this review by the IASLC Pathology Committee provides updates on the indications of ICIs for lung cancer in 2019 and discusses important considerations on preanalytical, analytical, and postanalytical aspects of PD-L1 IHC testing, including specimen type, validation of assays, external quality assurance, and training.
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Affiliation(s)
- Sylvie Lantuejoul
- Centre Léon Bérard Unicancer, Lyon, France; Université Grenoble Alpes, Grenoble, France
| | - Ming Sound-Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Nicolas Girard
- Institut Curie, Paris, and Université Claude Bernard, Lyon, France
| | - Fred R Hirsch
- Center for Thoracic Oncology, The Tisch Cancer Institute, New York, New York; Ichan School of Medicine, Mount Sinai Health System, New York, New York
| | | | | | - Deepali Jain
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | - Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | | | | | | | | | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | | | | | - Lukas Bubendorf
- Institute of Pathology, University of Basel, Basel, Switzerland
| | - Yuko Minami
- Ibarakihigashi National Hospital, Tokai, Japan
| | - Mary Beth Beasley
- Ichan School of Medicine, Mount Sinai Health System, New York, New York
| | | | - Gang Chen
- Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jin-Haeng Chung
- Seoul National University Bundang Hospital, Seoul, South Korea
| | - Sanja Dacic
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - David Hwang
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Dongmei Lin
- Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Andre Moreira
- New York University School of Medicine, New York, New York
| | - Andrew G Nicholson
- Royal Brompton and Harefield NHS Foundation Trust, London, and National Heart and Lung Institute, Imperial College, United Kingdom
| | | | | | - Claudia Poleri
- Office of Pathology Consultants, Buenos Aires, Argentina
| | - William Travis
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Mari Mino-Kenudson
- Department of Pathology, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
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106
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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107
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Pavlakis N, Cooper C, John T, Kao S, Klebe S, Lee CK, Leong T, Millward M, O'Byrne K, Russell PA, Solomon B, Cooper WA, Fox S. Australian consensus statement for best practice ROS1 testing in advanced non-small cell lung cancer. Pathology 2019; 51:673-680. [PMID: 31668406 DOI: 10.1016/j.pathol.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/24/2022]
Abstract
Lung cancer is the most commonly diagnosed malignancy and the leading cause of death from cancer globally. Diagnosis of advanced non-small cell lung cancer (NSCLC) is associated with 5-year relative survival of 3.2%. ROS proto-oncogene 1 (ROS1) is an oncogenic driver of NSCLC occurring in up to 2% of cases and commonly associated with younger age and a history of never or light smoking. Results of an early trial with the tyrosine kinase inhibitor (TKI) crizotinib that inhibits tumours that harbour ROS1 rearrangements have shown an objective response rate (ORR) of 72% (95% CI 58-83%), median progression free survival (PFS) of 19.3 months (95% CI 15.2-39.1 months) and median overall survival (OS) of 51.4 months (95% CI 29.3 months to not reached). Therefore, with the availability of highly effective ROS1-targeted TKI therapy, upfront molecular testing for ROS1 status alongside EGFR and ALK testing is recommended for all patients with NSCLC. We review the tissue requirements for ROS1 testing by immunohistochemistry (IHC) and fluorescent in situ hybridisation (FISH) and we present a testing algorithm for advanced NSCLC and consider how the future of pathology testing for ROS1 may evolve.
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Affiliation(s)
- Nick Pavlakis
- Royal North Shore Hospital, St Leonards, and Sydney University, Camperdown, NSW, Australia.
| | - Caroline Cooper
- Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, Qld, Australia
| | - Thomas John
- Olivia Newton-John Cancer Research Institute, Heidelberg, Vic, Australia
| | - Steven Kao
- Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Sonja Klebe
- SA Pathology, and Flinders University at Flinders Medical Centre, Bedford Park, SA, Australia
| | | | | | | | - Ken O'Byrne
- Princess Alexandra Hospital, Woolloongabba, Qld, Australia
| | - Prudence A Russell
- St Vincent's Hospital, University of Melbourne, Melbourne, Vic, Australia
| | | | - Wendy A Cooper
- Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia; School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Stephen Fox
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
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108
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Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, Wu Z, Gao H, Cai X, Ruan G, Zhu T, Xu C, Lou S, Yu X, Gillet L, Blattmann P, Saba K, Fankhauser CD, Schmid MB, Rutishauser D, Ljubicic J, Christiansen A, Fritz C, Rupp NJ, Poyet C, Rushing E, Weller M, Roth P, Haralambieva E, Hofer S, Chen C, Jochum W, Gao X, Teng X, Chen L, Zhong Q, Wild PJ, Aebersold R, Guo T. High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Mol Oncol 2019; 13:2305-2328. [PMID: 31495056 PMCID: PMC6822243 DOI: 10.1002/1878-0261.12570] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/09/2019] [Accepted: 09/03/2019] [Indexed: 11/06/2022] Open
Abstract
Formalin‐fixed, paraffin‐embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT)‐SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B‐cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh‐frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.
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Affiliation(s)
- Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Bo Wang
- Department of Pathology, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Yi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zhicheng Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Guan Ruan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiansheng Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chao Xu
- College of Mathematics and Informatics, Digital Fujian Institute of Big Data Security Technology, Fujian Normal University, Fuzhou, China
| | - Sai Lou
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiaoyan Yu
- Department of Pathology, The Second Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Karim Saba
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | | | - Michael B Schmid
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Jelena Ljubicic
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Ailsa Christiansen
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Christine Fritz
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Cedric Poyet
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | - Elisabeth Rushing
- Department of Neuropathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Patrick Roth
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Eugenia Haralambieva
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Silvia Hofer
- Division of Medical Oncology, Lucerne Cantonal Hospital and Cancer Center, Switzerland
| | | | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, Switzerland
| | - Xiaofei Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland.,Children's Medical Research Institute, University of Sydney, Australia
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland.,Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Faculty of Science, University of Zurich, Switzerland
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
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109
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McFadden WC, Walsh H, Richter F, Soudant C, Bryce CH, Hof PR, Fowkes M, Crary JF, McKenzie AT. Perfusion fixation in brain banking: a systematic review. Acta Neuropathol Commun 2019; 7:146. [PMID: 31488214 PMCID: PMC6728946 DOI: 10.1186/s40478-019-0799-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023] Open
Abstract
Background Perfusing fixatives through the cerebrovascular system is the gold standard approach in animals to prepare brain tissue for spatial biomolecular profiling, circuit tracing, and ultrastructural studies such as connectomics. Translating these discoveries to humans requires examination of postmortem autopsy brain tissue. Yet banked brain tissue is routinely prepared using immersion fixation, which is a significant barrier to optimal preservation of tissue architecture. The challenges involved in adopting perfusion fixation in brain banks and the extent to which it improves histology quality are not well defined. Methodology We searched four databases to identify studies that have performed perfusion fixation in human brain tissue and screened the references of the eligible studies to identify further studies. From the included studies, we extracted data about the methods that they used, as well as any data comparing perfusion fixation to immersion fixation. The protocol was preregistered at the Open Science Framework: https://osf.io/cv3ys/. Results We screened 4489 abstracts, 214 full-text publications, and identified 35 studies that met our inclusion criteria, which collectively reported on the perfusion fixation of 558 human brains. We identified a wide variety of approaches to perfusion fixation, including perfusion fixation of the brain in situ and ex situ, perfusion fixation through different sets of blood vessels, and perfusion fixation with different washout solutions, fixatives, perfusion pressures, and postfixation tissue processing methods. Through a qualitative synthesis of data comparing the outcomes of perfusion and immersion fixation, we found moderate confidence evidence showing that perfusion fixation results in equal or greater subjective histology quality compared to immersion fixation of relatively large volumes of brain tissue, in an equal or shorter amount of time. Conclusions This manuscript serves as a resource for investigators interested in building upon the methods and results of previous research in designing their own perfusion fixation studies in human brains or other large animal brains. We also suggest several future research directions, such as comparing the in situ and ex situ approaches to perfusion fixation, studying the efficacy of different washout solutions, and elucidating the types of brain donors in which perfusion fixation is likely to result in higher fixation quality than immersion fixation. Electronic supplementary material The online version of this article (10.1186/s40478-019-0799-y) contains supplementary material, which is available to authorized users.
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110
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Haile S, Corbett RD, Bilobram S, Bye MH, Kirk H, Pandoh P, Trinh E, MacLeod T, McDonald H, Bala M, Miller D, Novik K, Coope RJ, Moore RA, Zhao Y, Mungall AJ, Ma Y, Holt RA, Jones SJ, Marra MA. Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples. Nucleic Acids Res 2019; 47:e12. [PMID: 30418619 PMCID: PMC6344851 DOI: 10.1093/nar/gky1142] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/06/2018] [Indexed: 01/01/2023] Open
Abstract
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome. Here, we show that a major proportion of such chimeric reads align to both the ‘Watson’ and ‘Crick’ strands of the reference genome. We refer to these as strand-split artifact reads (SSARs). This study provides a conceptual framework for the mechanistic basis of the genesis of SSARs and other chimeric artifacts along with supporting experimental evidence, which have led to approaches to reduce the levels of such artifacts. We demonstrate that one of these approaches, involving S1 nuclease-mediated removal of single-stranded fragments and overhangs, also reduces sequence bias, base error rates, and false positive detection of copy number and single nucleotide variants. Finally, we describe an analytical approach for quantifying SSARs from NGS data.
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Affiliation(s)
- Simon Haile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Steve Bilobram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Morgan H Bye
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Eva Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Tina MacLeod
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Helen McDonald
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Miruna Bala
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Diane Miller
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Karen Novik
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robin J Coope
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Rob A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Steven J Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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111
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Compton CC, Robb JA, Anderson MW, Berry AB, Birdsong GG, Bloom KJ, Branton PA, Crothers JW, Cushman-Vokoun AM, Hicks DG, Khoury JD, Laser J, Marshall CB, Misialek MJ, Natale KE, Nowak JA, Olson D, Pfeifer JD, Schade A, Vance GH, Walk EE, Yohe SL. Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine. Arch Pathol Lab Med 2019; 143:1346-1363. [PMID: 31329478 DOI: 10.5858/arpa.2019-0009-sa] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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.
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Affiliation(s)
- Carolyn C Compton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - James A Robb
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Matthew W Anderson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Anna B Berry
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - George G Birdsong
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kenneth J Bloom
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Philip A Branton
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jessica W Crothers
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Allison M Cushman-Vokoun
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - David G Hicks
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Joseph D Khoury
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jordan Laser
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Carrie B Marshall
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Michael J Misialek
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Kristen E Natale
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Jan Anthony Nowak
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Damon Olson
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - John D Pfeifer
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Andrew Schade
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Gail H Vance
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Eric E Walk
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
| | - Sophia Louise Yohe
- From School of Life Sciences, Arizona State University and Mayo Clinic School of Medicine, Scottsdale (Dr Compton); Consulting Pathologist, Boca Raton, Florida (Dr Robb); Versiti Diagnostic Laboratories, Milwaukee, Wisconsin (Dr Anderson); Molecular Pathology and Genomics, Swedish Cancer Institute, Seattle, Washington (Dr Berry); Anatomic Pathology, Grady Health System, Atlanta, Georgia (Dr Birdsong); Advanced Genomic Services, Ambry Genetics, Aliso Viejo, California (Dr Bloom); Gynecologic & Breast Pathology, Joint Pathology Center, Silver Spring, Maryland (Dr Branton); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Crothers); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Cushman-Vokoun); IHC-ISH Laboratory and Breast Subspecialty Service, University of Rochester Medical Center, Rochester, New York (Dr Hicks); the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Khoury); the Department of Pathology and Laboratory Medicine, Northwell Health, New Hyde Park, New York (Dr Laser); the Department of Pathology, University of Colorado, Aurora (Dr Marshall); the Department of Pathology, Newton-Wellesley Hospital, Newton, Massachusetts (Dr Misialek); the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland (Dr Natale); the Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York (Dr Nowak); he Department of Pathology, Children's Hospitals and Clinics, Minneapolis, Minnesota (Dr Olson); the Department of Pathology, Washington University School of Medicine, St. Louis, Missouri (Dr Pfeifer); Lilly Research Labs, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana (Dr Schade); he Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (Dr Vance); Medical & Scientific Affairs, Roche Tissue Diagnostics, Tucson, Arizona (Dr Walk); and Special Hematology MMC, University of Minnesota Medical Center, Minneapolis (Dr Yohe)
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Mombaerts I, Ramberg I, Coupland SE, Heegaard S. Diagnosis of orbital mass lesions: clinical, radiological, and pathological recommendations. Surv Ophthalmol 2019; 64:741-756. [PMID: 31276737 DOI: 10.1016/j.survophthal.2019.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023]
Abstract
The orbit can harbor mass lesions of various cellular origins. The symptoms vary considerably according to the nature, location, and extent of the disease and include common signs of proptosis, globe displacement, eyelid swelling, and restricted eye motility. Although radiological imaging tools are improving, with each imaging pattern having its own differential diagnosis, orbital mass lesions often pose a diagnostic challenge. To provide an accurate, specific, and sufficiently comprehensive diagnosis, to optimize clinical management and estimate prognosis, pathological examination of a tissue biopsy is essential. Diagnostic orbital tissue biopsy is obtained through a minimally invasive orbitotomy procedure or, in selected cases, fine needle aspiration. The outcome of successful biopsy, however, is centered on its representativeness, processing, and interpretation. Owing to the often small volume of the orbital biopsies, artifacts in the specimens should be limited by careful peroperative tissue handling, fixation, processing, and storage. Some orbital lesions can be characterized on the basis of cytomorphology alone, whereas others need ancillary molecular testing to render the most reliable diagnosis of therapeutic, prognostic, and predictive value. Herein, we review the diagnostic algorithm for orbital mass lesions, using clinical, radiological, and pathological recommendations, and discuss the methods and potential pitfalls in orbital tissue biopsy acquisition and analysis.
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Affiliation(s)
- Ilse Mombaerts
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium.
| | - Ingvild Ramberg
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sarah E Coupland
- Department of Cellular and Molecular Pathology, University of Liverpool, Liverpool, UK; Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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113
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Impact of delayed and prolonged fixation on the evaluation of immunohistochemical staining on lung carcinoma resection specimen. Virchows Arch 2019; 475:191-199. [PMID: 31264038 PMCID: PMC6647403 DOI: 10.1007/s00428-019-02595-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 11/23/2022]
Abstract
Pre-analytical factors, such as fixation time, influence morphology of diagnostic and predictive immunohistochemical staining, which are increasingly used in the evaluation of lung cancer. Our aim was to investigate if variations in fixation time influence the outcome of immunohistochemical staining in lung cancer. From lung resections, specimen with tumor size bigger than 4 cm, 10 samples were obtained: 2 were put through the standard fixation protocol, 5 through the delayed, and 3 through the prolonged fixation protocol. After paraffin embedding, tissue microarrays (TMAs) were made. They were stained with 20 antibodies and scored for quality and intensity of staining. Samples with delay in fixation showed loss of TMA cores on glass slides and deterioration of tissue quality leading to reduction in the expression of CK 7, Keratin MNF116, CAM 5.2, CK 5/6, TTF-1, C-MET, Napsin A, D2-40, and PD-L1. Prolonged fixation had no influence on the performance of immunohistochemical stains. Delay of fixation negatively affects the expression of different immunohistochemical markers, influencing diagnostic (cytokeratins) and predictive (PD-L1) testing. These results emphasize the need for adequate fixation of resection specimen.
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114
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Asefy Z, Hoseinnejhad S, Dolati S, Ceferov Z, Hasanzadeh A, Azergun R, Nouri M. miR-515-5p and Notch1 as New Diagnostic Markers of Hepatocellular Carcinoma. AVICENNA JOURNAL OF MEDICAL BIOCHEMISTRY 2019. [DOI: 10.34172/ajmb.2019.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background: Modifications of miRNA expression have been related to various types of cancers including hepatocellular carcinoma (HCC). miRNAs directly act as repressors of gene expression, as they reside in fragile sites, as well as cancer-related genomic regions. Notch signaling is a conserved evolutionary pathway that controls cell functions. The dysregulation of this pathway leads to different diseases such as cancer. Objectives: This study aimed to investigate the role of miR-515-5p and Notch1 as new diagnostic markers in HCC. Methods: Forty formalin fixed paraffin embedded (FFPE) autopsy blocks and 40 FFPE normal liver tissues were selected from the archives of the pathology of Imam Reza hospital, Tabriz, Iran. Real-time polymerase chain reaction (PCR) was used for gene expression. Immune histochemistry method was used for detecting notch1 in normal and cancer FFPE tissues. Hematoxylin and eosin staining was also used for the diagnosis of normal and cancerous tissues. Results: miR-515-5P showed higher expression in the cancer group compared to the normal group (4.7 fold). Hematoxylin and eosin staining of HCC tissues showed significant color intensity than that of normal tissues. Immune histochemistry results revealed significant Ag-Ab reaction in the cancer group. In this study, we analyzed miRNA gene expression and notch 1 level in HCC patients. miRNA dysregulation has been found in a large variety of HCCs. Hepatocarcinogenesis was associated with the expression level of miR-515-5p with carcinogenesis. Moreover, notch1 was a key protein in liver cell fate and a progressive molecule in HCC. Conclusion: Our study demonstrated the main role of miR-515-5p in the pathogenesis of HCC. Likewise, it disclosed the expression of these genes could be utilized in HCC prognosis.
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Affiliation(s)
- Zahra Asefy
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Medicine Faculty (Biochemistry, Immunology, Microbiology Departments), Tabriz University of Medical Sciences, Tabriz, Iran
- Maragheh University of Medical Sciences, Maragheh, Iran
| | - Sirus Hoseinnejhad
- Department of Biochemistry, Baku State University, Baku, Azerbaijan
- Maragheh University of Medical Sciences, Maragheh, Iran
| | - Sanam Dolati
- Medicine Faculty (Biochemistry, Immunology, Microbiology Departments), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zaker Ceferov
- Department of Biochemistry, Baku State University, Baku, Azerbaijan
| | | | - Robab Azergun
- Maragheh University of Medical Sciences, Maragheh, Iran
| | - Mohammad Nouri
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Medicine Faculty (Biochemistry, Immunology, Microbiology Departments), Tabriz University of Medical Sciences, Tabriz, Iran
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115
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Avoiding non-contributive molecular results in cancer samples: proposal of a score-based approach for sample choice. Pathology 2019; 51:524-528. [PMID: 31227255 DOI: 10.1016/j.pathol.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 03/05/2019] [Accepted: 03/17/2019] [Indexed: 01/22/2023]
Abstract
Mutational analyses have become crucial for therapeutic choices in patients with advanced lung cancer, colorectal cancer and melanoma. Short turnaround times for molecular analyses are necessary to match the patient's therapeutic management. Non-contributive molecular analyses may increase the delay in reaching a relevant mutational status. We attempted to identify criteria in samples associated with non-contributive molecular results to better anticipate them and select samples with contributive analyses. We compared several criteria such as cancer type, sample type, organ of origin and percentage of tumour cells between samples with non-contributive or contributive EGFR, KRAS, NRAS and BRAF mutation analyses. Among two sets of 3367 and 554 tumour samples analysed in 2015-2017 and 2018, respectively, 11.7% and 15.7% of sample analyses were non-contributive for at least one oncogene. Lung cancer and melanoma cancer subtypes [odds ratio (OR)=7.2], cytological (OR=1.8) or bone samples (OR=8.5) and a percentage of tumour cells ≤20% (OR=41.4) were significantly associated with non-contributive results. By combining these parameters in a scoring system, we were able to predict the contributive or non-contributive result of a molecular analysis with sensitivity and specificity higher than 80% in a validation set of samples. Predicting the contributive or non-contributive result of a molecular analysis is feasible in samples on the basis of simple features. A combination of these features could be used to better choose samples to analyse in order to reduce the rate of non-contributive molecular results and related treatment delays and costs in patients with advanced cancers.
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116
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Omilian AR, Zirpoli GR, Cheng TYD, Yao S, Stein L, Davis W, Head KL, Nair P, Khoury T, Ambrosone CB, Bshara W. Storage Conditions and Immunoreactivity of Breast Cancer Subtyping Markers in Tissue Microarray Sections. Appl Immunohistochem Mol Morphol 2019; 28:267-273. [PMID: 31205070 DOI: 10.1097/pai.0000000000000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Loss of immunoreactivity in tissue sections has been shown to occur when slide sections are stored at room temperature for prolonged periods of time. We conducted a systematic investigation to determine the extent of staining loss in various storage conditions to determine an optimal storage method. We investigated 6 antibodies that are commonly used for breast cancer subtyping in research studies with immunohistochemistry (ER, PR, HER2, CK5/6, EGFR, and Ki67) in formalin-fixed paraffin-embedded breast tissue microarrays consisting of 148 patients. Tissue microarrays were sectioned at various time points: fresh, 1 week, 1 month, 6 months, and 12 months before staining. Slides sectioned at each time point were stored in 5 storage conditions: desiccator, paraffin dipped, 4°C, -20°C, and -80°C. Immunohistochemistry scores were assessed over time with McNemar Test and Bowker Test of Symmetry. Desiccator storage was the only storage condition that did not show any loss in immunoreactivity for any antibody or time point in our study. Paraffin coated slides were the most difficult storage method operationally and also showed the most loss in immunoreactivity. Storing sections in a desiccator was the most effective method for minimizing immunoreactivity loss. Cold storage at 4°C is an intermediate option that is not as protective as a desiccator, but offers the advantage of being accessible to virtually all research labs.
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Affiliation(s)
- Angela R Omilian
- Departments of Cancer Prevention and Control.,Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University Medical Campus, Boston, MA
| | - Ting-Yuan David Cheng
- Departments of Cancer Prevention and Control.,Department of Epidemiology, University of Florida, Gainesville, FL
| | - Song Yao
- Departments of Cancer Prevention and Control
| | - Leighton Stein
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Karen L Head
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Priya Nair
- Departments of Cancer Prevention and Control
| | - Thaer Khoury
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Wiam Bshara
- Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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117
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Lerch ML, Bauer DR, Theiss A, Chafin D, Otter M, Baird GS. Monitoring Dehydration and Clearing in Tissue Processing for High-Quality Clinical Pathology. Biopreserv Biobank 2019; 17:303-311. [PMID: 31107113 PMCID: PMC6703239 DOI: 10.1089/bio.2018.0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The development of precision testing for disease diagnosis has advanced medicine by specifically matching patients with drugs to treat specific diseases. High-quality diagnostics start with high-quality tissue specimens. The development and optimization of tissue handling and processing have lagged behind bioassay development. Ultrasound time-of-flight (TOF) technology has been successfully used to monitor the critical processing step of tissue fixation with formalin. In this study, we expand the use of this technology to monitor tissue dehydration and clearing by analyzing TOF signals from 270 different specimens, representing 13 different tissue types obtained through surgical resections. We determined the time constant τ90 for each tissue type for the following tissue processing solvents: 70% ethanol, 90% ethanol, 100% ethanol, and xylene. The TOF signals were correlated with tissue morphology to ensure that high-quality tissue was produced. Tissues can be grouped into those exhibiting fast and slow reagent diffusion. We monitored incomplete dehydration of tissue by skipping a key processing step, dehydration in absolute ethanol, and then correlated the τ90 with poor histomorphology, demonstrating that the technique can detect significant processing errors. Ultrasound TOF technology can therefore be used to monitor all phases of tissue processing cycle and yields an important preanalytical quality metric.
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Affiliation(s)
- Melissa L Lerch
- 1Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington
| | | | | | | | | | - Geoffrey S Baird
- 1Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington
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118
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Giusti L, Angeloni C, Lucacchini A. Update on proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2019; 16:513-520. [DOI: 10.1080/14789450.2019.1615452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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119
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Hsiao SJ, Zehir A, Sireci AN, Aisner DL. Detection of Tumor NTRK Gene Fusions to Identify Patients Who May Benefit from Tyrosine Kinase (TRK) Inhibitor Therapy. J Mol Diagn 2019; 21:553-571. [PMID: 31075511 PMCID: PMC7456740 DOI: 10.1016/j.jmoldx.2019.03.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/17/2019] [Accepted: 03/01/2019] [Indexed: 01/04/2023] Open
Abstract
Chromosomal rearrangements involving the NTRK1, NTRK2, and NTRK3 genes (NTRK genes), which encode the high-affinity nerve growth factor receptor (TRKA), brain-derived neurotrophic factor/neurotrophin-3 (BDNF/NT-3) growth factor receptor (TRKB), and neurotrophin-3 (NT-3) growth factor receptor (TRKC) tyrosine kinases (TRK proteins), act as oncogenic drivers in a broad range of pediatric and adult tumor types. NTRK gene fusions have been shown to be actionable genomic events that are predictive of response to TRK kinase inhibitors, making their routine detection an evolving clinical priority. In certain exceedingly rare tumor types, NTRK gene fusions may be seen in the overwhelming majority of cases, whereas in a range of common cancers, reported incidences are in the range of 0.1% to 2%. Herein, we review the structure of the three NTRK genes and the nature and incidence of NTRK gene fusions in different solid tumor types, and we summarize the clinical data showing the importance of identifying tumors harboring such genomic events. We also outline the laboratory techniques that can be used to diagnose NTRK gene fusions in clinical samples. Finally, we propose a diagnostic algorithm for solid tumors to facilitate the identification of patients with TRK fusion cancer. This algorithm accounts for the widely varying frequencies by tumor histology and the underlying prevalence of TRK expression in the absence of NTRK gene fusions and is based on a combination of fluorescence in situ hybridization, next-generation sequencing, and immunohistochemistry assays.
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Affiliation(s)
- Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony N Sireci
- Department of Medical Affairs, Loxo Oncology, Inc., Stamford, Connecticut
| | - Dara L Aisner
- Department of Pathology, University of Colorado, Aurora, Colorado.
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120
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Jones W, Greytak S, Odeh H, Guan P, Powers J, Bavarva J, Moore HM. Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles. Sci Rep 2019; 9:6980. [PMID: 31061401 PMCID: PMC6502812 DOI: 10.1038/s41598-019-43282-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/08/2019] [Indexed: 11/09/2022] Open
Abstract
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
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Affiliation(s)
| | | | - Hana Odeh
- National Cancer Institute, Bethesda, MD, USA
| | - Ping Guan
- National Cancer Institute, Bethesda, MD, USA
| | - Jason Powers
- Q2 Solutions - EA Genomics, Morrisville, NC, USA
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121
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Mueller C, Gambarotti M, Benini S, Picci P, Righi A, Stevanin M, Hombach-Klonisch S, Henderson D, Liotta L, Espina V. Unlocking bone for proteomic analysis and FISH. J Transl Med 2019; 99:708-721. [PMID: 30659273 PMCID: PMC10752433 DOI: 10.1038/s41374-018-0168-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/04/2018] [Accepted: 09/14/2018] [Indexed: 11/08/2022] Open
Abstract
Bone tissue is critically lagging behind soft tissues and biofluids in our effort to advance precision medicine. The main challenges have been accessibility and the requirement for deleterious decalcification processes that impact the fidelity of diagnostic histomorphology and hinder downstream analyses such as fluorescence in-situ hybridization (FISH). We have developed an alternative fixation chemistry that simultaneously fixes and decalcifies bone tissue. We compared tissue morphology, immunohistochemistry (IHC), cell signal phosphoprotein analysis, and FISH in 50 patient matched primary bone cancer cases that were either formalin fixed and decalcified, or theralin fixed with and without decalcification. Use of theralin improved tissue histomorphology, whereas overall IHC was comparable to formalin fixed, decalcified samples. Theralin-fixed samples showed a significant increase in protein and DNA extractability, supporting technologies such as laser-capture microdissection and reverse phase protein microarrays. Formalin-fixed bone samples suffered from a fixation artifact where protein quantification of β-actin directly correlated with fixation time. Theralin-fixed samples were not affected by this artifact. Moreover, theralin fixation enabled standard FISH staining in bone cancer samples, whereas no FISH staining was observed in formalin-fixed samples. We conclude that the use of theralin fixation unlocks the molecular archive within bone tissue allowing bone to enter the standard tissue analysis pipeline. This will have significant implications for bone cancer patients, in whom personalized medicine has yet to be implemented.
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Affiliation(s)
- Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Marco Gambarotti
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefania Benini
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Piero Picci
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Righi
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Monica Stevanin
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Dana Henderson
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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122
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Three-dimensional imaging and quantitative analysis in CLARITY processed breast cancer tissues. Sci Rep 2019; 9:5624. [PMID: 30948791 PMCID: PMC6449377 DOI: 10.1038/s41598-019-41957-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
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123
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DNA extraction from FFPE tissue samples - a comparison of three procedures. Contemp Oncol (Pozn) 2019; 23:52-58. [PMID: 31061638 PMCID: PMC6500389 DOI: 10.5114/wo.2019.83875] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/26/2019] [Indexed: 12/29/2022] Open
Abstract
Aim of the study One of the critical steps in molecular oncology diagnostics is obtaining high quality genomic DNA. Therefore, it is important to evaluate and compare the techniques used to extract DNA from tissue samples. Since formalin-fixed, paraffin-embedded (FFPE) tissues are routinely used for both retrospective and prospective studies, we compared three commercially available methods of nucleic acid extraction in terms of quantity and quality of isolated DNA. Material and methods Slides prepared from 42 FFPE blocks were macro-dissected. Resulting material was divided and processed simultaneously using three extraction kits: QIAamp DNA FFPE Tissue Kit (QIAGEN), Cobas DNA Sample Preparation Kit (Roche Molecular Systems) and Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega). Subsequently, quantity and quality of obtained DNA samples were analysed spectrophotometrically (NanoDrop 2000, Thermo Scientific). Results of quantitative analysis were confirmed by a fluorometric procedure (Qubit 3.0 Fluorometer, Life Technologies). Results The results demonstrated that the yields of total DNA extracted using either Maxwell or Cobas methods were significantly higher compared to the QIAamp method (p < 0.001). The Maxwell Extraction Kit delivered DNA samples of the highest quality (p < 0.01). However, the highest total yield of extracted DNA was achieved with the Cobas technique, which may be due to a higher volume of eluate compared to the Maxwell method. Conclusions To our knowledge, this is the first paper which directly compares three extraction methods: Cobas, Maxwell and QIAamp. The data herein provide information required for the selection of a protocol that best suits the needs of the overall study design in terms of the quantity and quality of the extracted DNA.
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124
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Wehmas LC, Wood CE, Gagne R, Williams A, Yauk C, Gosink MM, Dalmas D, Hao R, O'Lone R, Hester S. Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples. Toxicol Sci 2019; 162:535-547. [PMID: 29228314 DOI: 10.1093/toxsci/kfx278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 h followed by ethanol (18F); or 10% buffered formalin (3F). Samples from OH, 18F, and 3F groups were processed to FFPE blocks and sectioned for RNA isolation. Additional sections from 3F received the following demodification protocols to mitigate RNA damage: short heated incubation with Tris-Acetate-EDTA buffer; overnight heated incubation with an organocatalyst using 2 different isolation kits; or overnight heated incubation without organocatalyst. Ribo-depleted, stranded, total RNA libraries were built and sequenced using the Illumina HiSeq 2500 platform. Overnight incubation (± organocatalyst) increased RNA yield >3-fold and RNA integrity numbers and fragment analysis values by > 1.5- and >3.0-fold, respectively, versus 3F. Postsequencing metrics also showed reduced bias in gene coverage and deletion rates for overnight incubation groups. All demodification groups had increased overlap for differentially expressed genes (77%-84%) and enriched pathways (91%-97%) with FR, with the highest overlap in the organocatalyst groups. These results demonstrate simple changes in RNA isolation methods that can enhance genomic analyses of FFPE samples.
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Affiliation(s)
- Leah C Wehmas
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Charles E Wood
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Remi Gagne
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada K1A 0K9
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada K1A 0K9
| | - Carole Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada K1A 0K9
| | | | - Deidre Dalmas
- GlaxoSmithKline, King of Prussia, Pennsylvania 19406
| | | | - Raegan O'Lone
- ILSI Health and Environmental Sciences Institute, Washington, District of Columbia 20005
| | - Susan Hester
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709
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125
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Carithers LJ, Agarwal R, Guan P, Odeh H, Sachs MC, Engel KB, Greytak SR, Barcus M, Soria C, Lih CJJ, Williams PM, Branton PA, Sobin L, Fombonne B, Bocklage T, Andry C, Duffy ER, Sica G, Dhir R, Jewell S, Roche N, Moore HM. The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality. Arch Pathol Lab Med 2019; 143:1106-1118. [PMID: 30785788 DOI: 10.5858/arpa.2018-0172-oa] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown. OBJECTIVE.— To elucidate molecular effects associated with clinically relevant preanalytical variability, the National Cancer Institute initiated the Biospecimen Preanalytical Variables (BPV) program. DESIGN.— The BPV program, a well-controlled series of systematic, blind and randomized studies, investigated whether a delay to fixation (DTF) or time in fixative (TIF) affects the quantity and quality of DNA and RNA isolated from FFPE colon, kidney, and ovarian tumors in comparison to case-matched snap-frozen controls. RESULTS.— DNA and RNA yields were comparable among FFPE biospecimens subjected to different DTF and TIF time points. DNA and RNA quality metrics revealed assay- and time point-specific effects of DTF and TIF. A quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was superior when assessing RNA quality, consistently detecting differences between FFPE and snap-frozen biospecimens and among DTF and TIF time points. RNA Integrity Number and DV200 (representing the percentage of RNA fragments longer than 200 nucleotides) displayed more limited sensitivity. Differences in DNA quality (Q-ratio) between FFPE and snap-frozen biospecimens and among DTF and TIF time points were detected with a qPCR-based assay. CONCLUSIONS.— DNA and RNA quality may be adversely affected in some tumor types by a 12-hour DTF or a TIF of 72 hours. Results presented here as well as those of additional BPV molecular analyses underway will aid in the identification of acceptable delays and optimal fixation times, and quality assays that are suitable predictors of an FFPE biospecimen's fit-for-purpose.
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Affiliation(s)
- Latarsha J Carithers
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Rachana Agarwal
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Ping Guan
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Hana Odeh
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Michael C Sachs
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Kelly B Engel
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Sarah R Greytak
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Mary Barcus
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Conrado Soria
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Chih-Jian Jason Lih
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - P Mickey Williams
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Philip A Branton
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Leslie Sobin
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Benjamin Fombonne
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Therese Bocklage
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Chris Andry
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Elizabeth R Duffy
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Gabriel Sica
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Rajiv Dhir
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Scott Jewell
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Nancy Roche
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
| | - Helen M Moore
- From Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland (Drs Carithers, Guan, Odeh, Sachs, Branton, and Moore); Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland (Drs Agarwal, Barcus, Lih, Williams, Sobin, Roche, and Mr Soria); Preferred Solutions Group, Preferred Scientific Group, Washington, District of Columbia (Dr Engel); Kelly Government Solutions, Kelly Services, Rockville, Maryland (Dr Greytak and Mr Fombonne); the Department of Pathology, University of New Mexico, Albuquerque (Dr Bocklage); the Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (Dr Andry and Ms Duffy); the Department of Pathology and Laboratory Medicine, Emory University, Winship Cancer Institute, Atlanta, Georgia (Dr Sica); the Department of Pathology, University of Pittsburg, Pittsburgh, Pennsylvania (Dr Dhir); and Van Andel Research Institute, Pathology and Biorepository Core, VARI Core Technologies and Services, Grand Rapids, Michigan (Dr Jewell)
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Decalf J, Albert ML, Ziai J. New tools for pathology: a user's review of a highly multiplexed method for in situ analysis of protein and RNA expression in tissue. J Pathol 2019; 247:650-661. [PMID: 30570141 DOI: 10.1002/path.5223] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/18/2022]
Abstract
Tumor cell heterogeneity and tumor cell-stromal interactions are being explored as determinants of disease progression and treatment resistance in solid tumor and hematological malignancies. As such, tools simultaneously capable of highly multiplexed profiling of tissues' protein and RNA content, as well as interrogation of rare or single cells, are required to precisely characterize constituent tumor cell populations, infiltrating lymphocytes and stromal elements. Access to spatial relationships will enable more precise characterization of tumors, support patient stratification and may help to identify novel drug targets. Multiple platforms are being developed to address these critical unmet needs. The NanoString digital spatial profiling (DSP) platform enables highly multiplexed, spatial assessment of protein and/or RNA targets in tissues by detecting oligonucleotide barcodes conjugated via a photocleavable linker to primary antibodies or nucleic acid probes. Although this platform enables high-dimensional spatial interrogation of tissue protein and RNA expression, a detailed understanding of its composition, function and chemistry is advisable to guide experimental design and data interpretation. The purpose of this review is to provide an independent, comprehensive description of the DSP technology, including an overview of NanoString's capture and antibody barcode conjugation chemistries, experimental workflow, data output and analysis methods. The DSP technology will be discussed in the context of other highly multiplexed immunohistochemistry methods, including imaging mass cytometry and multiplexed ion beam imaging, to inform potential users of the advantages and limitations of each. Additional issues such as preanalytical variability, sampling and specimen adequacy will be considered with respect to the platforms to inform potential experimental design. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jérémie Decalf
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Matthew L Albert
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - James Ziai
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
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127
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Devouassoux-Shisheboran M, Le Frère-Belda MA, Leary A. [Biopathology of ovarian carcinomas early and advanced-stages: Article drafted from the French guidelines in oncology entitled "Initial management of patients with epithelial ovarian cancer" developed by FRANCOGYN, CNGOF, SFOG, GINECO-ARCAGY under the aegis of CNGOF and endorsed by INCa]. ACTA ACUST UNITED AC 2019; 47:155-167. [PMID: 30686728 DOI: 10.1016/j.gofs.2018.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Ovarian carcinomas represent a heterogeneous group of lesions with specific therapeutic management for each histological subtype. Thus, the correct histological diagnosis is mandatory. MATERIAL AND METHODS References were searched by PubMed from January 2000 to January 2018 and original articles in French and English literature were selected. RESULTS AND CONCLUSIONS In case of ovarian mass suspicious for cancer, a frozen section analysis may be proposed, if it could impact the surgical management. A positive histological diagnosis of ovarian carcinoma (type and grade) has to be rendered on histological (and not cytological) material before any chemotherapy with multiples and large sized biopsies. In case of needle biopsy, at least three fragments with needles>16G are needed. Histological biopsies need to be formalin-fixed (4% formaldehyde) less than 1h after resection and at least 6hours fixation is mandatory for small size biopsies. Tissue transfer to pathological labs up to 48hours under vacuum and at +4°C (in case of large surgical specimens) may be an alternative. Gross examination should include the description of all specimens and their integrity, the site of the tumor and the dimension of all specimens and nodules. Multiples sampling is needed, including the capsule, the solid areas, at least 1 to 2 blocks per cm of tumor for mucinous lesions, the Fallopian tube in toto, at least 3 blocks on grossly normal omentum and one block on the largest omental nodule. WHO classification should be used to classify the carcinoma (type and grade), with the use of a panel of immunohistochemical markers. High-grade ovarian carcinomas (serous and endometrioid) should be tested for BRCA mutation and in case of a detectable tumor mutation, the patient should be referred to an oncogenetic consultation.
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Affiliation(s)
- M Devouassoux-Shisheboran
- Institut multisite de biopathologie des hôpitaux de Lyon : site Sud, centre de biologie et pathologie Sud, centre hospitalier Lyon Sud, 165, chemin du Grand-Revoyet, 69495 Pierre-Bénite cedex, France.
| | - M-A Le Frère-Belda
- Service de pathologie, hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
| | - A Leary
- Inserm U981, service d'oncologie médicale, Gustave-Roussy Cancer Campus, 114, rue Édouard-Vaillant, 94800 Villejuif, France
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Abstract
Paraffin embedding is a standard technique used in clinical and research laboratories to create a formalin-fixed, paraffin-embedded (FFPE) block of tissue. Formalin-fixed tissue undergoes tissue processing and then is embedded in paraffin (wax) to create a FFPE block or paraffin block. The paraffin block can be cut using a microtome to generate thin sections of tissue contained in paraffin to be stained or paraffin tissue ribbons suitable for nucleic acid extraction. In addition, the FFPE blocks can be stored at room temperature for years. Herein, we provide a basic knowledge, and introduce common methods of the paraffin embedding process.
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Affiliation(s)
- Alireza Sadeghipour
- Department of Pathology, Iran University of Medical Sciences, Tehran, Tehran Province, Iran.
| | - Pegah Babaheidarian
- Department of Pathology, Iran University of Medical Sciences, Tehran, Tehran Province, Iran
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Lantuejoul S, Damotte D, Hofman V, Adam J. Programmed death ligand 1 immunohistochemistry in non-small cell lung carcinoma. J Thorac Dis 2019; 11:S89-S101. [PMID: 30775032 PMCID: PMC6353738 DOI: 10.21037/jtd.2018.12.103] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide with low response rates to conventional chemotherapy. New promising therapies have emerged based on programmed cell death protein 1 (PD-1) immunity checkpoint inhibitors (ICI), including anti-PD-1, such as nivolumab and pembrolizumab, or programmed death ligand 1 (PD-L1) inhibitors, such as atezolizumab, durvalumab, and avelumab. The prescription of pembrolizumab has been approved by FDA and EMA for advanced stages non-small cell lung carcinoma (NSCLC), restricted for first-line setting to patients whose tumor presents ≥50% of PD-L1 positive tumor cells (TC), and ≥1% for second-line and beyond, leading to consider PD-L1 assay as a companion diagnostic tool for pembrolizumab. Very recently, the EMA has approved durvalumab for the treatment of patients with unresectable stage III NSCLC not progressing after chemoradiotherapy and whose tumors express PD-L1 on ≥1% of TC. Four standardized PD-L1 immunohistochemistry assays have been used in clinical trials; 22C3 and 28-8 PharmDx assays on Dako/Agilent platforms, and SP142 and SP263 assays on Ventana platforms, each test having been developed initially for a specific ICI. They differ in terms of primary monoclonal antibody, platform, detection system and scoring methods with different thresholds of positivity validated in clinical trials. Several studies have shown a close analytical performance of the 22C3, 28-8 and SP263 assays regarding TC staining in NSCLC, with poor concordance with SP142 assay and for immune cells. However, as dedicated platforms are not available in all pathology laboratories and because of the high cost of these assays, laboratory developed tests are widely used in many countries. Their validation must guarantee the same sensitivities and specificities as compared to standardized assays. Overall, PD-L1 test is of great help to select patients who could benefit for ICI and most pathologists have included this test in their daily practice for advanced stages NSCLC, besides ALK and ROS1 IHC.
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Affiliation(s)
- Sylvie Lantuejoul
- Département de Biopathologie, Centre Léon Bérard UNICANCER, Lyon, France
- Département de Recherche Translationnelle et d’Innovations, Centre Léon Bérard UNICANCER, Lyon, France
- Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
- PATTERN: Group of French Thoracic Pathologists for Innovation and Translational Research, Synergie Lyon Cancer Foundation, Lyrican, France
| | - Diane Damotte
- PATTERN: Group of French Thoracic Pathologists for Innovation and Translational Research, Synergie Lyon Cancer Foundation, Lyrican, France
- Département de Pathologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Recherche des Cordeliers, Université Paris Descartes, Paris, France
| | - Véronique Hofman
- PATTERN: Group of French Thoracic Pathologists for Innovation and Translational Research, Synergie Lyon Cancer Foundation, Lyrican, France
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Hospital, University Côte d’Azur, Nice, France
- Biobank BB-0033-0025, FHU OncoAge, Nice Hospital, University Côte d’Azur, Nice, France
| | - Julien Adam
- PATTERN: Group of French Thoracic Pathologists for Innovation and Translational Research, Synergie Lyon Cancer Foundation, Lyrican, France
- Département de Biologie et Pathologie Médicales, Gustave-Roussy, Villejuif, France
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Abstract
The personnel who operate a biomedical biobank should function as a unit to efficiently manage the numerous types of biospecimens that are to be utilized for both clinical and research purposes. Therefore, new staff must be appropriately trained before becoming fully integrated into the work environment. This chapter focuses on several key aspects to this training that should be completed by all personnel. This first step is an orientation where the new trainee is provided with the priorities and expectations of the biobank. The next and perhaps most important step is training on the various safety precautions. The trainee should learn how to protect patient privacy if human biospecimens are involved. They should gain a basic understanding of different types of biospecimens and their vulnerabilities to suboptimal storage conditions. The trainee must learn the various aspects of the day to day work which encompasses the methods and equipment needed for procuring, labeling, handling, tracking, storing, disbursing, and shipping biospecimens. They should become familiar with aspects of quality assurance.
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Affiliation(s)
- Ryan R Williams
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Diviya Gupta
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William H Yong
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Brain Tumor Translational Resource, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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Parker LA, Chilet-Rosell E, Hernández-Aguado I, Pastor-Valero M, Gea S, Lumbreras B. Diagnostic Biomarkers: Are We Moving from Discovery to Clinical Application? Clin Chem 2018; 64:1657-1667. [DOI: 10.1373/clinchem.2018.292854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022]
Abstract
Abstract
BACKGROUND
Despite considerable research investment, moving from biomarker discovery to clinical application has presented unique challenges. We aimed to evaluate progress toward clinical application of a sample of molecular- and “omics”-based diagnostic tests over a 10-year period.
METHODS
We used Scopus to locate studies, published before the December 31, 2016, citing 107 original-research articles published in 2006 that assessed the diagnostic value of a molecular- or “omics”-based test. We identified diagnostic studies of the same test and disease and determined whether the article represented progress in the validation of the molecular test. We classified the types of progress: (a) clinical validation (measuring diagnostic accuracy in a series of patients similar to the population in which the test will be used in practice), (b) technical improvement, (c) extended diagnostic application (modification of the diagnostic question attended initially by the test), (d) economic evaluation, or (e) clinical use or implementation.
RESULTS
In the 10-year period analyzed, 4257 articles cited the 107 diagnostic studies; 118 (2.8%) were diagnostic studies of the same test, and of these papers, 25 (21.2%) did not constitute progress toward validation of the test for use in clinical practice (potential research waste). Of the 107 molecular- or “omics”-based tests described in 2006, only 28 (26.2%) appeared to have made progress toward clinical application. Only 4 (9.1%) of 44 proteomics-based tests had made progress toward clinical application.
CONCLUSIONS
Articles evaluating molecular- or “omics”-based diagnostic tests are numerous in biomedical journals. Few tests have made progress toward clinical application in the 10 years following their discovery.
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Affiliation(s)
- Lucy A Parker
- Department of Public Health, University Miguel Hernández, Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Elisa Chilet-Rosell
- Department of Public Health, University Miguel Hernández, Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ildefonso Hernández-Aguado
- Department of Public Health, University Miguel Hernández, Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - María Pastor-Valero
- Department of Public Health, University Miguel Hernández, Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Sonia Gea
- Department of Public Health, University Miguel Hernández, Alicante, Spain
| | - Blanca Lumbreras
- Department of Public Health, University Miguel Hernández, Alicante, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
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132
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Nohle DG, Mandt RL, Couce ME, Parwani AV, Ayers LW. Acceptable Weight Ranges for Research Tissue Procurement and Biorepositories, 2015-2017. Biopreserv Biobank 2018; 16:463-466. [PMID: 30379574 PMCID: PMC6308276 DOI: 10.1089/bio.2018.0068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: The Cooperative Human Tissue Network, Midwestern Division, is a National Cancer Institute-funded program that provides quality research biospecimens to qualified investigators. Consented human tissues are procured according to researcher specifications for weight (size) and preservation type; weights of samples in significant demand and limited supply are negotiated. Weights of procured tissues are entered into a dedicated biospecimen database. This study seeks to provide guidance for acceptable tissue weights for researchers. Methods: Tissue weights by year and anatomic site were retrieved from the database for primary malignant tissues. The total number of tissues included was 5141. Statistical evaluation of data included the number of tissues for each year, anatomic site as well as minimum, maximum, average weights, standard deviation, and standard error. Anatomic sites with few tissues were excluded. Results: “Stock price” type graphs were constructed to show an average as “volume” with both full weight ranges and range that accommodated 80% of tissues. Average weight and number of sample trends varied by anatomic site. Tissues fell into four weight groups; 10 and 90 percentile boundaries were calculated for each. Smallest average research tissue weights for middle 80% were recorded for prostate and oropharynx (140 mg). Second weight group included tonsil, thyroid, breast, oral cavity, larynx, pancreas, salivary gland, skin, tongue, lung, and parotid (265 mg). The third group included stomach, cervix, colon, esophagus, endometrium, bone, brain, bladder, small bowel, uterus, liver, kidney lymph node, adrenal, and ovary (513 mg). The fourth and heaviest weight group included soft tissue tumors and spleen (1201 mg). Conclusions: Since tissue weights are not usually included in recommendations for research tissue procurement or for frozen tissues stored in biorepositories, we offer this data as a practical guide to researcher acceptable tissue weights for selected sites based on a 3-year researcher request and acceptance history.
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Affiliation(s)
- David G Nohle
- Ohio Consortium, Cooperative Human Tissue Network (CHTN) Midwestern Division, Columbus, Ohio.,Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Randal L Mandt
- Ohio Consortium, Cooperative Human Tissue Network (CHTN) Midwestern Division, Columbus, Ohio.,Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Marta E Couce
- Ohio Consortium, Cooperative Human Tissue Network (CHTN) Midwestern Division, Columbus, Ohio.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Anil V Parwani
- Ohio Consortium, Cooperative Human Tissue Network (CHTN) Midwestern Division, Columbus, Ohio.,Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Leona W Ayers
- Ohio Consortium, Cooperative Human Tissue Network (CHTN) Midwestern Division, Columbus, Ohio.,Department of Pathology, The Ohio State University, Columbus, Ohio
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133
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Liu P, Tseng G, Wang Z, Huang Y, Randhawa P. Diagnosis of T-cell-mediated kidney rejection in formalin-fixed, paraffin-embedded tissues using RNA-Seq-based machine learning algorithms. Hum Pathol 2018; 84:283-290. [PMID: 30296518 DOI: 10.1016/j.humpath.2018.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/21/2018] [Accepted: 09/29/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnosis is being increasingly used in transplant pathology to render more objective and quantitative determinations that also provide mechanistic and prognostic insights. This study performed RNA-Seq on biopsies from kidneys with stable function (STA) and biopsies with classical findings of T-cell-mediated rejection (TCMR). Machine learning tools were used to develop prediction models for distinguishing TCMR and STA samples using the top genes identified by DSeq2. The prediction models were tested on 703 biopsies with Affymetrix chip gene expression profiles available in the public domain. Linear discriminant analysis predicted TCMR in 55 of 67 biopsies labeled TCMR, and 65 of 105 biopsies designated as antibody-mediated rejection. The random forest and support vector machine models showed comparable performance. These data illustrate the feasibility of using RNA-Seq for molecular diagnosis of TCMR in formalin-fixed tissue. Application of the derived diagnostic algorithms to publicly available data sets demonstrates frequent coexistence of TCMR in biopsies designated as antibody-mediated rejection. This underrecognition of TCMR in renal allograft biopsies has significant implications with respect to patient care.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - George Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Zijie Wang
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Yuchen Huang
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
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134
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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135
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Neumeister VM, Juhl H. Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis. CURRENT PATHOBIOLOGY REPORTS 2018; 6:265-274. [PMID: 30595971 PMCID: PMC6290693 DOI: 10.1007/s40139-018-0179-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purpose of Review Precision medicine promises patient tailored, individualized diagnosis and treatment of diseases and relies on clinical specimen integrity and accuracy of companion diagnostic testing. Therefore, pre-analytics, which are defined as the collection, processing, and storage of clinical specimens, are critically important to enable optimal diagnostics, molecular profiling, and clinical decision-making around harvested specimens. This review article discusses the impact of tumor pre-analytics on molecular pathology focusing on biospecimen protein expression and analysis. Recent Findings Due to busy clinical schedules and workflows that have been established for many years and to lack of standardization and limited assessment tools to quantify variability in pre-analytical processing, the effects of pre-analytics on biospecimen integrity are often overlooked. Several studies have recently emphasized an emerging crisis in science and reproducibility of results. Summary Biomarker instability due to pre-analytical variables affects comprehensive analysis and molecular phenotyping of patients’ tissue. This problematic emphasizes the critical need for standardized protocols and technologies to be applied in the clinical and research setting.
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Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
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136
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Zhou J, Sun HC, Wang Z, Cong WM, Wang JH, Zeng MS, Yang JM, Bie P, Liu LX, Wen TF, Han GH, Wang MQ, Liu RB, Lu LG, Ren ZG, Chen MS, Zeng ZC, Liang P, Liang CH, Chen M, Yan FH, Wang WP, Ji Y, Cheng WW, Dai CL, Jia WD, Li YM, Li YX, Liang J, Liu TS, Lv GY, Mao YL, Ren WX, Shi HC, Wang WT, Wang XY, Xing BC, Xu JM, Yang JY, Yang YF, Ye SL, Yin ZY, Zhang BH, Zhang SJ, Zhou WP, Zhu JY, Liu R, Shi YH, Xiao YS, Dai Z, Teng GJ, Cai JQ, Wang WL, Dong JH, Li Q, Shen F, Qin SK, Fan J. Guidelines for Diagnosis and Treatment of Primary Liver Cancer in China (2017 Edition). Liver Cancer 2018; 7:235-260. [PMID: 30319983 PMCID: PMC6167671 DOI: 10.1159/000488035] [Citation(s) in RCA: 400] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/24/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) (about 85-90% of primary liver cancer) is particularly prevalent in China because of the high prevalence of chronic hepatitis B infection. HCC is the fourth most common malignancy and the third leading cause of tumor-related deaths in China. It poses a significant threat to the life and health of Chinese people. SUMMARY This guideline presents official recommendations of the National Health and Family Planning Commission of the People's Republic of China on the surveillance, diagnosis, staging, and treatment of HCC occurring in China. The guideline was written by more than 50 experts in the field of HCC in China (including liver surgeons, medical oncologists, hepatologists, interventional radiologists, and diagnostic radiologists) on the basis of recent evidence and expert opinions, balance of benefits and harms, cost-benefit strategies, and other clinical considerations. KEY MESSAGES The guideline presents the Chinese staging system, and recommendations regarding patients with HCC in China to ensure optimum patient outcomes.
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Affiliation(s)
- Jian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Hui-Chuan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Zheng Wang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Wen-Ming Cong
- Department of Pathology, the Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jian-Hua Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Meng-Su Zeng
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Mei Yang
- Department of Hepatic Surgery, the Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Ping Bie
- Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Lian-Xin Liu
- Department of General Surgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tian-Fu Wen
- Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Guo-Hong Han
- Department of Liver Diseases and Digestive Interventional Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Mao-Qiang Wang
- Department of Interventional Radiology, Chinese PLA General Hospital, Beijing, China
| | - Rui-Bao Liu
- Department of Interventional Radiology, the Tumor Hospital of Harbin Medical University, Harbin, China
| | - Li-Gong Lu
- Department of Interventional Oncology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zheng-Gang Ren
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Min-Shan Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhao-Chong Zeng
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ping Liang
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Beijing, China
| | - Chang-Hong Liang
- Department of Radiology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Min Chen
- Editorial Department of Chinese Journal of Digestive Surgery, Chongqing, China
| | - Fu-Hua Yan
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wen-Ping Wang
- Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen-Wu Cheng
- Department of integrated treatment, Tumor Hospital of Fudan University, Shanghai, China
| | - Chao-Liu Dai
- Department of Hepatobiliary and Spleenary Surgery, the Affiliated Shengjing Hospital, China Medical University, Shenyang, China
| | - Wei-Dong Jia
- Department of Hepatic Surgery, Affiliated Provincial Hospital, Anhui Medical University, Hefei, China
| | - Ya-Ming Li
- Department of Nuclear Medicine, the First Hospital of China Medical University, Shenyang, China
| | - Ye-Xiong Li
- Department of Radiation Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Liang
- Department of Oncology, Peking University International Hospital, Beijing, China
| | - Tian-Shu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guo-Yue Lv
- Department of General Surgery, the First Hospital of Jilin University, Jilin, China
| | - Yi-Lei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, China
| | - Wei-Xin Ren
- Department of Interventional Radiology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hong-Cheng Shi
- Department of Nuclear Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen-Tao Wang
- Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Xiao-Ying Wang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Bao-Cai Xing
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jian-Ming Xu
- Department of Gastrointestinal Oncology, Affiliated Hospital Cancer Center, Academy of Military Medical Sciences, Beijing, China
| | - Jian-Yong Yang
- Department of Interventional Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye-Fa Yang
- Department of Hepatic Surgery and Interventional Radiology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Sheng-Long Ye
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Zheng-Yu Yin
- Department of Hepatobiliary Surgery, Zhongshan Hospital of Xiamen University, Xiamen, China
| | - Bo-Heng Zhang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Shui-Jun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei-Ping Zhou
- Department of Hepatic Surgery, the Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Ji-Ye Zhu
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
| | - Rong Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying-Hong Shi
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Yong-Sheng Xiao
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Zhi Dai
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China
| | - Gao-Jun Teng
- Department of Radiology, Zhongda Hospital, Medical School, Southeast University, Nanjing, China
| | - Jian-Qiang Cai
- Department of Abdominal Surgical Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei-Lin Wang
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jia-Hong Dong
- Department of Hepatobiliary and Pancreas Surgery, Beijing Tsinghua Changgung Hospital (BTCH), School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Qiang Li
- Department of Hepatobiliary Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Feng Shen
- Department of Hepatic Surgery, the Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shu-Kui Qin
- Department of Medical Oncology, PLA Cancer Center, Nanjing Bayi Hospital, Nanjing, China,**Dr. Shu-Kui Qin, Department of Medical Oncology, PLA Cancer Center, Nanjing Bayi Hospital, Nanjing 210002 (China), E-Mail
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, China,*Dr. Jia Fan, Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032 (China), E-Mail
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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD. Residual tissue repositories as a resource for population-based cancer proteomic studies. Clin Proteomics 2018; 15:26. [PMID: 30087585 PMCID: PMC6074037 DOI: 10.1186/s12014-018-9202-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/27/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected fresh frozen or optimal cutting temperature (OCT) embedded specimens. However, such specimens are often difficult to obtain, in limited in supply, and clinical information and outcomes on patients are inherently delayed as compared to banked samples. Annotated formalin fixed, paraffin embedded (FFPE) tumor tissue specimens are available for research use from a variety of tissue banks, such as from the surveillance, epidemiology and end results (SEER) registries' residual tissue repositories. Given the wealth of outcomes information associated with such samples, the reuse of archived FFPE blocks for deep proteomic characterization with mass spectrometry technologies would provide a valuable resource for population-based cancer studies. Further, due to the widespread availability of FFPE specimens, validation of specimen integrity opens the possibility for thousands of studies that can be conducted worldwide. METHODS To examine the suitability of the SEER repository tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with expression proteomics and 18 with phosphoproteomics, using isobaric labeling. Linear modeling and gene set enrichment analysis was used to evaluate the impacts of collection site and storage time. RESULTS All samples, regardless of age, yielded suitable protein mass after extraction for expression analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although peptide, protein, and phosphopeptide identifications were reduced by 50, 20 and 76% respectively, from comparable OCT specimens, we found no statistically significant differences in protein quantitation correlating with collection site or specimen age. GSEA analysis of GO-term level measurements of protein abundance differences between FFPE and OCT embedded specimens suggest that the formalin fixation process may alter representation of protein categories in the resulting dataset. CONCLUSIONS These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for proteomic investigations if paired with rigorously verified mass spectrometry workflows.
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Affiliation(s)
- Paul D. Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Ryan L. Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Thomas L. Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Hala Makhlouf
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20850 USA
| | - Rodrigo F. Chuaqui
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20850 USA
| | - Emily S. Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Jerry S. H. Lee
- Center for Strategic Scientific Initiatives, National Cancer Institute, Bethesda, MD 20892 USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Danielle M. Carrick
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, MD 20850 USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
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139
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Andreasen S, Tan Q, Agander TK, Hansen TVO, Steiner P, Bjørndal K, Høgdall E, Larsen SR, Erentaite D, Olsen CH, Ulhøi BP, Heegaard S, Wessel I, Homøe P. MicroRNA dysregulation in adenoid cystic carcinoma of the salivary gland in relation to prognosis and gene fusion status: a cohort study. Virchows Arch 2018; 473:329-340. [DOI: 10.1007/s00428-018-2423-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/20/2018] [Accepted: 07/22/2018] [Indexed: 01/14/2023]
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140
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Greytak SR, Engel KB, Moore HM. Maximizing the Utility of Archival Formalin-Fixed Paraffin-Embedded Blocks for Nucleic Acid Analysis. Biopreserv Biobank 2018; 16:245-246. [PMID: 30004789 DOI: 10.1089/bio.2018.29042.sjg] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Helen M Moore
- 3 Biorepositories and Biospecimen Research Branch, National Cancer Institute , Bethesda, Maryland
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141
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Andreasen S. Molecular features of adenoid cystic carcinoma with an emphasis on microRNA expression. APMIS 2018; 126 Suppl 140:7-57. [DOI: 10.1111/apm.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery; Zealand University Hospital; Køge Denmark
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142
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Greytak SR, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall AJ, Wheeler DA, Doddapaneni HV, Moore HM. National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue. Biopreserv Biobank 2018; 16:247-250. [PMID: 29920119 DOI: 10.1089/bio.2018.0046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
| | | | - Erik Zmuda
- 3 Cytogenetics/Molecular Genetics Laboratory at Nationwide Children's Hospital , Columbus, Ohio
| | - Esmeralda Casas-Silva
- 4 Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute , Bethesda, Maryland
| | - Ping Guan
- 4 Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute , Bethesda, Maryland
| | - Katherine A Hoadley
- 5 Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Andrew J Mungall
- 6 Canada's Michael Smith Genome Sciences Center , BC Cancer Agency, Vancouver, Canada
| | - David A Wheeler
- 7 Human Genome Sequencing Center , Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha V Doddapaneni
- 7 Human Genome Sequencing Center , Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Helen M Moore
- 4 Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute , Bethesda, Maryland
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143
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Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA. Cancers (Basel) 2018; 10:cancers10060195. [PMID: 29891792 PMCID: PMC6025404 DOI: 10.3390/cancers10060195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 02/06/2023] Open
Abstract
Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability. The conservation of samples at room temperature (RT) by duplication can facilitate their protection. We describe a security system for the collection of non-small cell lung cancers (NSCLC) stored in the biobank of the Nice Hospital Center, France, by duplication and conservation of lyophilized (dried), encapsulated DNA kept at RT. Therefore, three frozen tissue collections from non-smoking, early stage and sarcomatoid carcinoma NSCLC patients were selected for this study. DNA was extracted, lyophilized and encapsulated at RT under anoxic conditions using the DNAshell technology. In total, 1974 samples from 987 patients were encapsulated. Six and two capsules from each sample were stored in the biobanks of the Nice and Grenoble (France) Hospitals, respectively. In conclusion, DNA maintained at RT allows for the conservation, duplication and durability of collections of interest stored in biobanks. This is a low-cost and safe technology that requires a limited amount of space and has a low environmental impact.
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144
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Molecular Pathology and Pre-Analytic Variables: Impact on Clinical Practice From a Breast Pathology Perspective. CURRENT PATHOBIOLOGY REPORTS 2018. [DOI: 10.1007/s40139-018-0169-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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145
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Cheah PL, Koh CC, Khang TF, Goh KL, Lau PC, Chin KF, Teoh KH, Toh YF, Looi LM. Esophageal squamous cell carcinomas in a Malaysian cohort show a lack of association with human papillomavirus. J Dig Dis 2018; 19:272-278. [PMID: 29722130 DOI: 10.1111/1751-2980.12605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/23/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE With an age-standardized incidence rate of 2 per 100 000, esophageal cancer is not common among Malaysians, but they are nevertheless important due to its poor prognosis. The study is to clarify whether the human papillomavirus (HPV) is associated with esophageal cancer in Malaysians as there has been no report to date on this in Malaysians and other South East Asians. METHODS Altogether 67 esophageal squamous cell carcinomas histologically diagnosed between 1 January 2004 and 31 December 2014 at the Department of Pathology, University of Malaya Medical Center, Malaysia were considered for HPV analysis using two commercially available methods, polymerase chain reaction with flow-through hybridization (21 HPV GenoArray Diagnostic Kit) and multiplex real-time polymerase chain reaction (Anyplex II HPV28 Detection). The DNA amplifiability of the formalin-fixed, paraffin-embedded tumor was checked by amplification of a 268 bp segment of the human β-globin gene (GH20/PC04) prior to HPV detection. RESULTS HPV detection was finally carried out in 51 patients. HPV16 was detected in the moderately differentiated, stage IV lower esophageal tumor of a 32-year-old Malaysian-born Chinese woman by both methods. Except for a predilection for Indians, the clinical characteristics of esophageal squamous cell carcinomas in this Malaysian cohort were generally similar to those of other populations. CONCLUSION It appears that HPV is rare and an unlikely oncovirus in esophageal squamous cell carcinomas of Malaysians.
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Affiliation(s)
- Phaik-Leng Cheah
- Division of Anatomical Pathology, Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Cing-Chai Koh
- Division of Anatomical Pathology, Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Khean-Lee Goh
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Peng-Choong Lau
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kin-Fah Chin
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kean-Hooi Teoh
- Division of Anatomical Pathology, Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yen-Fa Toh
- Division of Anatomical Pathology, Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Division of Anatomical Pathology, Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Lantuejoul S, Adam J, Girard N, Duruisseaux M, Mansuet-Lupo A, Cazes A, Rouquette I, Gibault L, Garcia S, Antoine M, Vignaud JM, Galateau-Sallé F, Sagan C, Badoual C, Penault-Llorca F, Damotte D. Tests immunohistochimiques PD-L1 dans les cancers du poumon non à petites cellules : recommandations par le groupe PATTERN de pathologistes thoraciques. Ann Pathol 2018; 38:110-125. [DOI: 10.1016/j.annpat.2018.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 01/09/2023]
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147
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Abstract
Immunohistochemistry is a widely available technique that is less challenging and can provide clinically meaningful results quickly and cost-efficiently in comparison with other techniques. In addition, immunohistochemistry allows for the evaluation of cellular localization of proteins in the context of tumor structure. In an era of precision medicine, pathologists are required to classify lung cancer into specific subtypes and assess biomarkers relevant to molecular-targeted therapies. This review summarizes the hot topics of immunohistochemistry in lung cancer, including (i) adenocarcinoma vs squamous cell carcinoma; (ii) neuroendocrine markers; (iii) ALK, ROS1, and EGFR; (iv) PD-L1 (CD274); (v) lung carcinoma vs malignant mesothelioma; and (vi) NUT carcinoma. Major pitfalls in evaluating immunohistochemical results are also described.
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Affiliation(s)
- Kentaro Inamura
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
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148
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Targeted Transcriptional Profiling of Kidney Transplant Biopsies. Kidney Int Rep 2018; 3:722-731. [PMID: 29854981 PMCID: PMC5976814 DOI: 10.1016/j.ekir.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction Studies are needed to assess the quality of transcriptome analysis in paired human tissue samples preserved by different methods and different gene amplification platforms to enable data comparisons across experimenters. Methods RNA was extracted from kidney biopsies, either submerged in RNA-stabilizing solution (RSS) or stored in formalin-fixed, paraffin-embedded (FFPE) blocks. RNA quality and integrity were compared. Gene expression of the common rejection module and other immune cell genes were quantified for both tissue preservation methods in the same sample using conventional quantitative polymerase chain reaction (QPCR) by 2 different commercial platforms, (fluidigm [FD]) or barcoded-oligos (nanostring [NS]). Results RNA quality was inferior in FFPE tissues. Despite this, gene expression for 19 measured genes on the same sample, stored in FFPE or RSS, were strongly correlated on the FD (r = 0.81) or NS platforms (r = 0.82). For the same samples, interplatform gene expression correlations were excellent (r = 0.80) for RSS and moderate (r = 0.66) for FFPE. Significant differences in gene expression were confirmed on both platforms (FD: P = 1.1E-03; NS: P = 2.5E-04) for biopsy-confirmed acute rejection. Conclusion Our study provided supportive evidence that despite a low RNA quality of archival FFPE kidney transplantation tissue, small quantities of this tissue can be obtained from existing paraffin blocks to provide a viable and rich biospecimen source for focused gene expression assays. In addition, reliable and reproducible gene expression evaluation can be performed on these FFPE tissues using either a QPCR-based or a barcoded-oligo approach, which provides opportunities for collaborative analytics.
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149
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Abstract
Among various methods now available to isolate distinct cell populations or even single cells for DNA/RNA and proteomic analysis, laser capture microdissection (LCM) offers a unique opportunity to study cells in their topological contexts. This chapter focuses on the preparation of LCM membrane slides, tissue staining and laser microdissection of cells of interest from frozen or formalin-fixed, paraffin-embedded glioblastoma tissue.
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150
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Bishop DP, Cole N, Zhang T, Doble PA, Hare DJ. A guide to integrating immunohistochemistry and chemical imaging. Chem Soc Rev 2018. [DOI: 10.1039/c7cs00610a] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A ‘how-to’ guide for designing chemical imaging experiments using antibodies and immunohistochemistry.
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Affiliation(s)
- David P. Bishop
- Elemental Bio-imaging Facility
- University of Technology Sydney
- Broadway
- Australia
- Atomic Pathology Laboratory
| | - Nerida Cole
- Elemental Bio-imaging Facility
- University of Technology Sydney
- Broadway
- Australia
- Atomic Pathology Laboratory
| | - Tracy Zhang
- Atomic Pathology Laboratory
- The Florey Institute of Neuroscience and Mental Health
- The University of Melbourne
- Parkville
- Australia
| | - Philip A. Doble
- Atomic Pathology Laboratory
- The Florey Institute of Neuroscience and Mental Health
- The University of Melbourne
- Parkville
- Australia
| | - Dominic J. Hare
- Elemental Bio-imaging Facility
- University of Technology Sydney
- Broadway
- Australia
- Atomic Pathology Laboratory
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