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Lin O, Alperstein S, Barkan GA, Cuda JM, Kezlarian B, Jhala D, Jin X, Mehrotra S, Monaco SE, Rao J, Saieg M, Thrall M, Pantanowitz L. American Society of Cytopathology Telecytology validation recommendations for rapid on-site evaluation (ROSE). J Am Soc Cytopathol 2024; 13:111-121. [PMID: 38310002 DOI: 10.1016/j.jasc.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 02/05/2024]
Abstract
Telecytology has multiple applications, including rapid onsite evaluation (ROSE) of fine-needle aspiration (FNA) specimens. It can enhance cytopathology practice by increasing productivity, reducing costs, and providing subspecialty expertise in areas with limited access to a cytopathologist. However, there are currently no specific validation guidelines to ensure safe practice and compliance with regulations. This initiative, promoted by the American Society of Cytopathology (ASC), intends to propose recommendations for telecytology implementation. These recommendations propose that the validation process should include testing of all hardware and software, both separately and as a whole; training of all individuals who will participate in telecytology with regular competency evaluations; a structured approach using retrospective slides with defined diagnoses for validation and prospective cases for verification and quality assurance. Telecytology processes must be integrated into the laboratory's quality management system and benchmarks for discrepancy rates between preliminary and final diagnoses should be established and monitored. Special attention should be paid to minimize discrepancies that downgrade malignant cases to benign (false positive on telecytology). Currently, billing and reimbursement codes for telecytology are not yet available. Once, they are, recommendation of the appropriate usage of these codes would be a part of the recommendations. These proposed guidelines are intended to be a resource for laboratories that are considering implementing telecytology. These recommendations can help to ensure the safe and effective use of telecytology and maximize its benefits for patients.
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Affiliation(s)
- Oscar Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Susan Alperstein
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, New York, New York
| | - Güliz A Barkan
- Department of Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, Illinois
| | - Jacqueline M Cuda
- Department of Pathology and Laboratory Services, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Brie Kezlarian
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Darshana Jhala
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Pittsburgh, Pennsylvania
| | - Xiaobing Jin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Swati Mehrotra
- Department of Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, Illinois
| | - Sara E Monaco
- Department of Pathology, Geisinger Medical Center, Danville, Pennsylvania
| | - Jianyu Rao
- Department of Pathology and Laboratory, UCLA Health, Los Angeles, California
| | - Mauro Saieg
- Department of Pathology, Santa Casa Medical School, Sao Paulo, Brazil
| | - Michael Thrall
- Department of Pathology, Houston Methodist Hospital, Houston, Texas
| | - Liron Pantanowitz
- Department of Pathology and Laboratory Services, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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Murray NP. Biomarkers of minimal residual disease and treatment. Adv Clin Chem 2024; 119:33-70. [PMID: 38514211 DOI: 10.1016/bs.acc.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Minimal residual disease (MRD) has been defined as a very small numbers of cancer cells that remain in the body after curative treatment. Its presence or absence will ultimately determine prognosis. With the introduction of new technologies the presence of MRD in patients with solid tumours can be detected and characterized. As MRD predicts future relapse, be it early or late treatment failure, in an otherwise asymptomatic patient its treatment and when to start treatment remains to be determined. Thus the concepts of personalized medicine using different biomarkers to classify the biological properties of MRD maybe come possible. Based on this determinations it may be possible to use targeted therapies rather than all patients with the same type of cancer receiving a standard treatment. However, it is important to understand the limitations of the different technologies, what these techniques are detecting and how they may help in the treatment of patients with cancer. The majority of published studies are in patients with metastatic cancer and there are few reports in patients with MRD. In this chapter the concept of MRD, the methods used to detect it and what treatments may be effective based on the biological characteristics of the tumour cells as determined by different biomarkers is reviewed. MRD depends on the phenotypic properties of the tumour cells to survive in their new environment and the anti-tumour immune response. This is a dynamic process and changes with time in the wake of immunosuppression caused by the tumour cells and/or the effects of treatment to select resistant tumour cells. With the use of biomarkers to typify the characteristics of MRD and the development of new drugs a personalized treatment can be designed rather than all patients given the same treatment. Patients who are initially negative for MRD may not require further treatment with liquid biopsies used to monitor the patients during follow-up in order to detect those patients who may become MRD positive. The liquid biopsy used during the follow up of MRD positive patients can be used to detect changes in the biological properties of the tumour cells and thus may need treatment changes to overcome tumour cell resistance.
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Affiliation(s)
- Nigel P Murray
- Minimal Residual Disease Laboratory, Faculty of Medicine, University Finis Terrae, Santiago, Chile.
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Lin DI, Huang RSP, Ladas I, Keller RB, Patel NR, Lakis S, Decker B, Janovitz T, Mata DA, Ross JS, Vergilio JA, Elvin JA, Herbst RS, Mack PC, Killian JK. Precision needle-punch tumor enrichment from paraffin blocks improves the detection of clinically actionable genomic alterations and biomarkers. Front Oncol 2024; 14:1328512. [PMID: 38444675 PMCID: PMC10912171 DOI: 10.3389/fonc.2024.1328512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 03/07/2024] Open
Abstract
Background While many molecular assays can detect mutations at low tumor purity and variant allele frequencies, complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) require higher tumor purity for accurate measurement. Scalable, quality-controlled, tissue-conserving methods to increase tumor nuclei percentage (TN%) from tumor specimens are needed for complex biomarkers and hence necessary to maximize patient matching to approved therapies or clinical trial enrollment. We evaluated the clinical utility and performance of precision needle-punch enrichment (NPE) compared with traditional razor blade macroenrichment of tumor specimens on molecular testing success. Methods Pathologist-directed NPE was performed manually on formalin-fixed, paraffin embedded (FFPE) blocks. Quality control of target capture region and quantity of residual tumor in each tissue block was determined via a post-enrichment histologic slide recut. Resultant tumor purity and biomarker status were determined by the computational analysis pipeline component of the FDA-approved next-generation sequencing (NGS) assay, FoundationOne®CDx. Following NPE implementation for real-world clinical samples, assay performance and biomarker (MSI, TMB, gLOH) detection were analyzed. Results In real-world clinical samples, enrichment rate via NPE was increased to ~50% over a 2.5-year period, exceeding the prior use of razor blade macro-enrichment (<30% of cases) prior to NPE implementation due to proven efficacy in generating high quality molecular results from marginal samples and the ease of use for both pathologist and histotechnologists. NPE was associated with lower test failures, higher computational tumor purity, and higher rates of successful TMB, MSI and gLOH determination when stratified by pre-enriched (incipient) tumor nuclei percentage. In addition, challenging cases in which tumor content was initially insufficient for testing were salvaged for analysis of biomarker status, gene amplification/deletion, and confident mutant or wild-type gene status determination. Conclusions Pathologist-directed precision enrichment from tissue blocks (aka NPE) increases tumor purity, and consequently, yields a greater number of successful tests and complex biomarker determinations. Moreover, this process is rapid, safe, inexpensive, scalable, and conserves patient surgical pathology material. NPE may constitute best practice with respect to enriching tumor cells from low-purity specimens for biomarker detection in molecular laboratories.
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Affiliation(s)
- Douglas I Lin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Richard S P Huang
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Ioannis Ladas
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Rachel B Keller
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Nimesh R Patel
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Sotirios Lakis
- Foundation Medicine GmbH, Pathology Department, Penzberg, Germany
| | - Brennan Decker
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Tyler Janovitz
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Douglas A Mata
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jeffrey S Ross
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jo-Anne Vergilio
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Julia A Elvin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Roy S Herbst
- Department of Medical Oncology, Yale School of Medicine, Yale Cancer Center, New Haven, CT, United States
| | - Philip C Mack
- Division of Hematology and Oncology, Department of Medicine, Tisch Cancer Institute at Mount Sinai, New York, NY, United States
| | - Jonathan K Killian
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
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Brown JE, Noormohammadi AH, Courtman NF. Immunoreactivity of canine, feline, and equine D-dimer with antibodies to human D-dimer. J Vet Intern Med 2024; 38:187-196. [PMID: 37950415 PMCID: PMC10800179 DOI: 10.1111/jvim.16888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/15/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Commercially available D-dimer assays use antibodies against human D-dimer, with limited sensitivity and specificity data in companion animals. OBJECTIVES To evaluate the immunoreactivity of D-dimer in plasma of dogs, horses, and cats with commercially available antibodies to human D-dimer. ANIMALS Plasma samples were collected from healthy dogs and horses, and from surplus feline plasma submitted for diagnostic purposes. METHODS Descriptive research study. A cross-linked fibrin lysate was prepared from plasma samples, and SDS-PAGE and immunoblotting were performed with a variety of commercially available antibodies to human D-dimer. RESULTS The selected antibodies demonstrated variable reactivity with D-dimer of each species. The monoclonal antibody DD44 bound canine D-dimer with good specificity and sensitivity, but this antibody did not react with feline or equine D-dimer. The polyclonal antibody D2D bound putative D-dimer in dogs, cats, and horses with good specificity, and higher sensitivity compared to human D-dimer. CONCLUSIONS AND CLINICAL IMPORTANCE The variable performance of commercially available human D-dimer assays between species is, in part, because of inter-species variation in D-dimer immunoreactivity. The use of these assays should follow validation studies. Monoclonal antibody DD44 could be a focus for the development of a canine-specific assay.
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Affiliation(s)
- Juliet E. Brown
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVictoriaAustralia
| | - Amir H. Noormohammadi
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVictoriaAustralia
| | - Natalie F. Courtman
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVictoriaAustralia
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Kanji CR, Mbavha BT, Masimirembwa C, Thelingwani RS. Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry. PLoS One 2023; 18:e0292131. [PMID: 37788265 PMCID: PMC10547200 DOI: 10.1371/journal.pone.0292131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated the analytical performance of the GenoPharm® custom open array platform which evaluates 120 SNPs across 46 pharmacogenes. Using commercially available reference samples (Coriell Biorepository) and in-house extracted DNA, we assessed accuracy, precision, and linearity of GenoPharm®. We then used GenoPharm® on 218 samples from two Southern African black populations and determined allele and genotype frequencies for selected actionable variants. Across all assays, the GenoPharm® panel demonstrated 99.5% concordance with the Coriell reference samples, with 98.9% reproducibility. We observed high frequencies of key genetic variants in people of African ancestry: CYP2B6*6 (0.35), CYP2C9*8, *11 (0.13, 0.03), CYP2D6*17 (0.21) and *29 (0.11). GenoPharm® open array is therefore an accurate, reproducible and sensitive test that can be used for clinical pharmacogenetic testing and is inclusive of variants specific to the people of African ancestry.
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Affiliation(s)
- Comfort Ropafadzo Kanji
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
- Department of Clinical Pharmacology, University of Zimbabwe (UZ), Harare, Zimbabwe
| | - Bianza Tinotenda Mbavha
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
| | - Collen Masimirembwa
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
| | - Roslyn Stella Thelingwani
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
- CradleOmics, Harare, Zimbabwe
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Lange PF, Schilling O, Huesgen PF. Positional proteomics: is the technology ready to study clinical cohorts? Expert Rev Proteomics 2023; 20:309-318. [PMID: 37869791 DOI: 10.1080/14789450.2023.2272046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 10/24/2023]
Abstract
INTRODUCTION Positional proteomics provides proteome-wide information on protein termini and their modifications, uniquely enabling unambiguous identification of site-specific, limited proteolysis. Such proteolytic cleavage irreversibly modifies protein sequences resulting in new proteoforms with distinct protease-generated neo-N and C-termini and altered localization and activity. Misregulated proteolysis is implicated in a wide variety of human diseases. Protein termini, therefore, constitute a huge, largely unexplored source of specific analytes that provides a deep view into the functional proteome and a treasure trove for biomarkers. AREAS COVERED We briefly review principal approaches to define protein termini and discuss recent advances in method development. We further highlight the potential of positional proteomics to identify and trace specific proteoforms, with a focus on proteolytic processes altered in disease. Lastly, we discuss current challenges and potential for applying positional proteomics in biomarker and pre-clinical research. EXPERT OPINION Recent developments in positional proteomics have provided significant advances in sensitivity and throughput. In-depth analysis of proteolytic processes in clinical cohorts thus appears feasible in the near future. We argue that this will provide insights into the functional state of the proteome and offer new opportunities to utilize proteolytic processes altered or targeted in disease as specific diagnostic, prognostic and companion biomarkers.
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Affiliation(s)
- Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, Department for Chemistry, University of Cologne, Cologne, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
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Lin G, Li J. Circulating HPV DNA in HPV-associated cancers. Clin Chim Acta 2023; 542:117269. [PMID: 36841427 DOI: 10.1016/j.cca.2023.117269] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023]
Abstract
Human papillomavirus (HPV) infections are the primary cause of almost all cervical cancers, anal cancers, and a variable proportion of other anogenital tumors, as well as head and neck cancers. Circulating HPV DNA (cHPV-DNA) is emerging as a biomarker with extensive potential in the management of HPV-driven malignancies. There has been a rapid advancement in the development of techniques for analyzing cHPV-DNA for the detection, characterization, and monitoring of HPV-associated cancers. As clinical evidence accumulates, it is becoming evident that cHPV-DNA can be used as a diagnostic tool. By conducting clinical trials assessing the clinical utility of cHPV-DNA, the full potential of cHPV-DNA for the screening, diagnosis, and treatment of HPV-related malignancies can be corroborated. In this review, we examine the current landscape of applications for cHPV-DNA liquid biopsies throughout the cancer care continuum, highlighting future opportunities for research and integration into clinical practice.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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8
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Recent Advances in Optimizing Radiation Therapy Decisions in Early Invasive Breast Cancer. Cancers (Basel) 2023; 15:cancers15041260. [PMID: 36831598 PMCID: PMC9954587 DOI: 10.3390/cancers15041260] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Adjuvant whole breast irradiation after breast-conserving surgery is a well-established treatment standard for early invasive breast cancer. Screening, early diagnosis, refinement in surgical techniques, the knowledge of new and specific molecular prognostic factors, and now the standard use of more effective neo/adjuvant systemic therapies have proven instrumental in reducing the rates of locoregional relapses. This underscores the need for reliably identifying women with such low-risk disease burdens in whom elimination of radiation from the treatment plan would not compromise oncological safety. This review summarizes the current evidence for radiation de-intensification strategies and details ongoing prospective clinical trials investigating the omission of adjuvant whole breast irradiation in molecularly defined low-risk breast cancers and related evidence supporting the potential for radiation de-escalation in HER2+ and triple-negative clinical subtypes. Furthermore, we discuss the current evidence for the de-escalation of regional nodal irradiation after neoadjuvant chemotherapy. Finally, we also detail the current knowledge of the clinical value of stromal tumor-infiltrating lymphocytes and liquid-based biomarkers as prognostic factors for locoregional relapse.
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9
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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10
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Robak T, Robak P. Measurable residual disease in hairy cell leukemia: Technical considerations and clinical significance. Front Oncol 2022; 12:976374. [DOI: 10.3389/fonc.2022.976374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Hairy cell leukemia (HCL) is a rare type of chronic lymphoid leukemia originating from a mature B lymphocyte. A diagnosis of HCL is based on cytology, confirmed by multiparametric flow cytometry (MFC) studies using anti-B-cell monoclonal antibodies, together with a panel of antibodies more specific to HCL, such as CD11c, CD25, CD103 and CD123. Recently, the BRAF V600E mutation has been described as a disease-defining genetic event. Measurable residual disease (MRD) is defined as the lowest level of HCL cells that can be detected accurately and reproducibly using validated methods; as MRD negativity is associated with high rates of durable complete response, by clearing MRD, the long-term outcome may be improved in patients with advanced HCL. MRD is typically detected using bone marrow, and in some cases, peripheral blood; however, in HCL, discrepancies frequently exist between MRD results obtained from blood, bone marrow aspirate and core biopsy. Among the methods used for MRD detection, MFC appears to be a more sensitive technique than immunohistochemistry. Molecular tests are also used, such as real-time quantitative PCR for unique immunoglobulin heavy chain (IgH) gene rearrangements and PCR techniques with clone specificity for BRAF V600E. Clone-specific PCR (spPCR) is able to detect one HCL cell in 106 normal cells, and is particularly suitable for patients found to be negative for MRD by MFC. Recently, the Hairy Cell Leukemia Consortium created a platform to work on a definition for MRD, and establish the optimal time point, tissue type and method for measuring MRD. This
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Pascual J, Attard G, Bidard FC, Curigliano G, De Mattos-Arruda L, Diehn M, Italiano A, Lindberg J, Merker JD, Montagut C, Normanno N, Pantel K, Pentheroudakis G, Popat S, Reis-Filho JS, Tie J, Seoane J, Tarazona N, Yoshino T, Turner NC. ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2022; 33:750-768. [PMID: 35809752 DOI: 10.1016/j.annonc.2022.05.520] [Citation(s) in RCA: 202] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/16/2022] Open
Abstract
Circulating tumour DNA (ctDNA) assays conducted on plasma are rapidly developing a strong evidence base for use in patients with cancer. The European Society for Medical Oncology convened an expert working group to review the analytical and clinical validity and utility of ctDNA assays. For patients with advanced cancer, validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, and may be used in routine clinical practice, provided the limitations of the assays are taken into account. Tissue based testing remains the preferred test for many cancer patients, due to limitations of ctDNA assays detecting fusion events and copy number changes, although ctDNA assays may be routinely used when faster results will be clinically important, or when tissue biopsies are not possible or inappropriate. Reflex tumour testing should be considered following a non-informative ctDNA result, due to false negative results with ctDNA testing. In patients treated for early-stage cancers, detection of molecular residual disease (MRD) or molecular relapse (MR), has high evidence of clinical validity in anticipating future relapse in many cancers. MRD/MR detection cannot be recommended in routine clinical practice, as currently there is no evidence for clinical utility in directing treatment. Additional potential applications of ctDNA assays, under research development and not recommended for routine practice, include identifying patients not responding to therapy with early dynamic changes in ctDNA levels, monitoring therapy for the development of resistance mutations prior to clinical progression, and in screening asymptomatic people for cancer. Recommendation for reporting of results, future development of ctDNA assays, and future clinical research are made.
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Affiliation(s)
- Javier Pascual
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Gerhardt Attard
- Urological Cancer Research, University College London, London, UK
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris, France; University of Versailles Saint-Quentin-en-Yvelines (UVSQ)/Paris-Saclay University, Saint Cloud, France
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy; Division of Early Drug Development, European Institute of Oncology, IRCCS, Milano, Italy
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, US
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonie, Bordeaux, France; DITEP, Gustave Roussy, Villejuif, France; Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Jason D Merker
- Departments of Pathology and Laboratory Medicine & Genetics, UNC School of Medicine, Chapel Hill, NC, US
| | - Clara Montagut
- Medical Oncology Department, Hospital del Mar-IMIM, CIBERONC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, 'Fondazione G. Pascale' - IRCCS, Naples, Italy
| | - Klaus Pantel
- Institute for Tumour Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - George Pentheroudakis
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - Sanjay Popat
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joan Seoane
- Preclinical and Translational Research Programme, Vall d'Hebron Institute of Oncology (VHIO), ICREA, CIBERONC, Barcelona, Spain,; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Nicholas C Turner
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
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Scionti F, Di Martino MT, Caracciolo D, Pensabene L, Tagliaferri P, Arbitrio M. Tools in Pharmacogenomics Biomarker Identification for Cancer Patients. Methods Mol Biol 2022; 2401:1-12. [PMID: 34902118 DOI: 10.1007/978-1-0716-1839-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The understanding of the biological differences which underlie the inter-individual variability in drug response improved the efficacy of cancer therapy in the era of precision medicine. In fact molecularly targeted drugs and immunotherapy represent a revolution in cancer treatment. The identification of genetic predictive and/or prognostic biomarkers linked to drug pharmacokinetics (PK) and pharmacodynamics (PD) is allowed by the development of high-throughput omics tools for detecting and understanding biological differences among individuals, in order to improve drug efficacy and minimize risk of toxicity. Personalized medicine in cancer treatment reduces costs of the healthcare system. Unfortunately, pharmacogenomics biomarkers discovery is influenced by complexity, need of high-quality evidence, and a validation process for regulatory purposes. This chapter is focused on the critic analysis of presently available pharmacogenomics tools for discovering or testing genetic polymorphic variants in drug metabolizing enzyme to be introduced in clinical practice for the prospective stratification of cancer patients.
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Affiliation(s)
- Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Messina, Italy
| | | | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Licia Pensabene
- Department of Medical and Surgical Sciences, Pediatric Unit, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | | | - Mariamena Arbitrio
- Institute of Research and Biomedical Innovation (IRIB), National Research Council (CNR), Catanzaro, Italy.
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13
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Wang NC, Kaplan J, Lee J, Hodgin J, Udager A, Rao A. Stress Testing Pathology Models with Generated Artifacts. J Pathol Inform 2021; 12:54. [PMID: 35070483 PMCID: PMC8721870 DOI: 10.4103/jpi.jpi_6_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Machine learning models provide significant opportunities for improvement in health care, but their "black-box" nature poses many risks. METHODS We built a custom Python module as part of a framework for generating artifacts that are meant to be tunable and describable to allow for future testing needs. We conducted an analysis of a previously published digital pathology classification model and an internally developed kidney tissue segmentation model, utilizing a variety of generated artifacts including testing their effects. The artifacts simulated were bubbles, tissue folds, uneven illumination, marker lines, uneven sectioning, altered staining, and tissue tears. RESULTS We found that there is some performance degradation on the tiles with artifacts, particularly with altered stains but also with marker lines, tissue folds, and uneven sectioning. We also found that the response of deep learning models to artifacts could be nonlinear. CONCLUSIONS Generated artifacts can provide a useful tool for testing and building trust in machine learning models by understanding where these models might fail.
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Affiliation(s)
- Nicholas Chandler Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jeremy Kaplan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Joonsang Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey Hodgin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aaron Udager
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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14
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A Cost-Effective and Non-Invasive pfeRNA-Based Test Differentiates Benign and Suspicious Pulmonary Nodules from Malignant Ones. Noncoding RNA 2021; 7:ncrna7040080. [PMID: 34940762 PMCID: PMC8709422 DOI: 10.3390/ncrna7040080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022] Open
Abstract
The ability to differentiate between benign, suspicious, and malignant pulmonary nodules is imperative for definitive intervention in patients with early stage lung cancers. Here, we report that plasma protein functional effector sncRNAs (pfeRNAs) serve as non-invasive biomarkers for determining both the existence and the nature of pulmonary nodules in a three-stage study that included the healthy group, patients with benign pulmonary nodules, patients with suspicious nodules, and patients with malignant nodules. Following the standards required for a clinical laboratory improvement amendments (CLIA)-compliant laboratory-developed test (LDT), we identified a pfeRNA classifier containing 8 pfeRNAs in 108 biospecimens from 60 patients by sncRNA deep sequencing, deduced prediction rules using a separate training cohort of 198 plasma specimens, and then applied the prediction rules to another 230 plasma specimens in an independent validation cohort. The pfeRNA classifier could (1) differentiate patients with or without pulmonary nodules with an average sensitivity and specificity of 96.2% and 97.35% and (2) differentiate malignant versus benign pulmonary nodules with an average sensitivity and specificity of 77.1% and 74.25%. Our biomarkers are cost-effective, non-invasive, sensitive, and specific, and the qPCR-based method provides the possibility for automatic testing of robotic applications.
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15
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Perazzio SF, Palmeira P, Moraes-Vasconcelos D, Rangel-Santos A, de Oliveira JB, Andrade LEC, Carneiro-Sampaio M. A Critical Review on the Standardization and Quality Assessment of Nonfunctional Laboratory Tests Frequently Used to Identify Inborn Errors of Immunity. Front Immunol 2021; 12:721289. [PMID: 34858394 PMCID: PMC8630704 DOI: 10.3389/fimmu.2021.721289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
Inborn errors of immunity (IEI), which were previously termed primary immunodeficiency diseases, represent a large and growing heterogeneous group of diseases that are mostly monogenic. In addition to increased susceptibility to infections, other clinical phenotypes have recently been associated with IEI, such as autoimmune disorders, severe allergies, autoinflammatory disorders, benign lymphoproliferative diseases, and malignant manifestations. The IUIS 2019 classification comprises 430 distinct defects that, although rare individually, represent a group affecting a significant number of patients, with an overall prevalence of 1:1,200-2,000 in the general population. Early IEI diagnosis is critical for appropriate therapy and genetic counseling, however, this process is deeply dependent on accurate laboratory tests. Despite the striking importance of laboratory data for clinical immunologists, several IEI-relevant immunoassays still lack standardization, including standardized protocols, reference materials, and external quality assessment programs. Moreover, well-established reference values mostly remain to be determined, especially for early ages, when the most severe conditions manifest and diagnosis is critical for patient survival. In this article, we intend to approach the issue of standardization and quality control of the nonfunctional diagnostic tests used for IEI, focusing on those frequently utilized in clinical practice. Herein, we will focus on discussing the issues of nonfunctional immunoassays (flow cytometry, enzyme-linked immunosorbent assays, and turbidimetry/nephelometry, among others), as defined by the pure quantification of proteins or cell subsets without cell activation or cell culture-based methods.
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Affiliation(s)
- Sandro Félix Perazzio
- Division of Rheumatology, Universidade Federal de São Paulo, Sao Paulo, Brazil.,Immunology Division, Fleury Medicine and Health Laboratory, Sao Paulo, Brazil
| | - Patricia Palmeira
- Laboratório de Investigação Médica (LIM-36), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
| | - Dewton Moraes-Vasconcelos
- Laboratório de Investigação Médica (LIM-56), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
| | - Andréia Rangel-Santos
- Laboratório de Investigação Médica (LIM-36), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
| | | | - Luis Eduardo Coelho Andrade
- Division of Rheumatology, Universidade Federal de São Paulo, Sao Paulo, Brazil.,Immunology Division, Fleury Medicine and Health Laboratory, Sao Paulo, Brazil
| | - Magda Carneiro-Sampaio
- Laboratório de Investigação Médica (LIM-36), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil.,Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), Sao Paulo, Brazil
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16
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Scherz V, Greub G, Bertelli C. Building up a clinical microbiota profiling: a quality framework proposal. Crit Rev Microbiol 2021; 48:356-375. [PMID: 34752719 DOI: 10.1080/1040841x.2021.1975642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Extensive characterization of the human microbiota has revealed promising relationships between microbial composition and health or disease, generating interest in biomarkers derived from microbiota profiling. However, microbiota complexity and technical challenges strongly influencing the results limit the generalization of microbiota profiling and question its clinical utility. In addition, no quality management scheme has been adapted to the specificities of microbiota profiling, notably due to the heterogeneity in methods and results. In this review, we discuss possible adaptation of classical quality management tools routinely used in diagnostic laboratories to microbiota profiling and propose a specific framework. Multiple quality controls are needed to cover all steps, from sampling to data processing. Standard operating procedures, primarily developed for wet lab analyses, must be adapted to the use of bioinformatic tools. Finally, requirements for test validation and proficiency testing must take into account expected discrepancies in results due to the heterogeneity of the processes. The proposed quality management framework should support the implementation of routine microbiota profiling by clinical laboratories to support patient care. Furthermore, its use in research laboratories would improve publication reproducibility as well as transferability of methods and results to routine practice.
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Affiliation(s)
- Valentin Scherz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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17
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Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains. J Clin Microbiol 2021; 59:e0260220. [PMID: 34432486 DOI: 10.1128/jcm.02602-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 109 copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like intergenogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost. It will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.
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18
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Rosas-Alonso R, Queiruga J, Arias P, Del Monte Á, Yuste F, Rodríguez-Antolín C, Losantos-Garcia I, Borobia AM, Rodríguez-Nóvoa S. Analytical validation of a laboratory-development multigene pharmacogenetic assay. Pharmacogenet Genomics 2021; 31:177-184. [PMID: 34116532 DOI: 10.1097/fpc.0000000000000438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The implementation of pharmacogenetics (PGx) in clinical practice is an essential tool for personalized medicine. However, clinical laboratories must validate their procedures before being used to perform PGx studies in patients, in order to confirm that they are adequate for the intended purposes. METHODS We designed a validation process for our in-house pharmacogenetic PCR-based method assay. RESULTS The concordance to reference, repeatability and reproducibility was 100%. Sensitivity and specificity were 100% for the detection of variant diplotypes in CYP2C9, CYP3A5, TPMT, DPYD and UGT1A1 genes. The sensitivity was lower in the detection of CYP2C19 variants due to a limitation in the design that prevents the detection of CYP2C19 *2/*10 diplotype. CONCLUSIONS The success of implementing clinical pharmacogenetic testing into routine clinical practice is dependent on the precision of genotyping. Limitations must be bearing in mind to guarantee the quality of PGx assays in clinical laboratory practice. We provided objective evidence that the necessary requirements in our laboratory-development assay were fulfilled.
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Affiliation(s)
- Rocío Rosas-Alonso
- Pharmacogenetic Laboratory, Genetics Department, Hospital Universitario La Paz
- Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ
| | - Javier Queiruga
- Clinical Pharmacology Department, School of Medicine, Hospital Universitario La Paz. IdiPAZ. Universidad Autónoma de Madrid
| | - Pedro Arias
- Pharmacogenetic Laboratory, Genetics Department, Hospital Universitario La Paz
| | - Álvaro Del Monte
- Pharmacogenetic Laboratory, Genetics Department, Hospital Universitario La Paz
| | - Fernando Yuste
- Pharmacogenetic Laboratory, Genetics Department, Hospital Universitario La Paz
| | - Carlos Rodríguez-Antolín
- Clinical Pharmacology Department, School of Medicine, Hospital Universitario La Paz. IdiPAZ. Universidad Autónoma de Madrid
| | | | - Alberto M Borobia
- Clinical Pharmacology Department, School of Medicine, Hospital Universitario La Paz. IdiPAZ. Universidad Autónoma de Madrid
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19
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Hallermayr A, Benet-Pagès A, Steinke-Lange V, Mansmann U, Rentsch M, Holinski-Feder E, Pickl JMA. Liquid Biopsy Hotspot Variant Assays: Analytical Validation for Application in Residual Disease Detection and Treatment Monitoring. Clin Chem 2021; 67:1483-1491. [PMID: 34392332 DOI: 10.1093/clinchem/hvab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Analysis of circulating tumor DNA (ctDNA) in plasma is a powerful approach to guide decisions in personalized cancer treatment. Given the low concentration of ctDNA in plasma, highly sensitive methods are required to reliably identify clinically relevant variants. METHODS We evaluated the suitability of 5 droplet digital PCR (ddPCR) assays targeting KRAS, BRAF, and EGFR variants for ctDNA analysis in clinical use. RESULTS We investigated assay performance characteristics for very low amounts of variants, showing that the assays had very low limits of blank (0% to 0.11% variant allele frequency, VAF) and limits of quantification (0.41% to 0.7% VAF). Nevertheless, striking differences in detection and quantification of low mutant VAFs between the 5 tested assays were observed, highlighting the need for assay-specific analytical validation. Besides in-depth evaluation, a guide for clinical interpretation of obtained VAFs in plasma was developed, depending on the limits of blank and limits of quantification values. CONCLUSION It is possible to provide comprehensive clinical reports on actionable variants, allowing minimal residual disease detection and treatment monitoring in liquid biopsy.
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Affiliation(s)
- Ariane Hallermayr
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Pettenkofer School of Public Health, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Anna Benet-Pagès
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Markus Rentsch
- Department of General, Visceral and Thorax Surgery, Klinikum Ingolstadt, Germany.,Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University of Munich, Campus Großhadern, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Julia M A Pickl
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
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20
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Zhao Z, Sacks DB. Call for Action: Journals Need to Insist on Full Reporting of the Analytical Characteristics of Biomarkers. Lab Med 2021; 52:7-9. [PMID: 33258475 DOI: 10.1093/labmed/lmaa097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhen Zhao
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - David B Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland
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21
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Zhou F, Shum E, Moreira AL. Molecular cytology of the respiratory tract and pleura. Cytopathology 2021; 33:14-22. [PMID: 34333812 DOI: 10.1111/cyt.13045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/06/2021] [Accepted: 07/24/2021] [Indexed: 01/01/2023]
Abstract
There is growing evidence that molecular testing is feasible on all types of cytological preparation, which is fortunate as more diagnostic markers and biomarkers for targeted therapies are discovered for use in pulmonary and pleural malignancies. In this article we will discuss the pre-analytic, analytic, and post-analytic (interpretive) considerations for successful implementation of molecular tests for diagnostic and predictive markers in respiratory and pleural cytology. The vast majority of laboratories are familiar with, and have validated their molecular protocols for, formalin-fixed paraffin-embedded surgical specimens, which are not directly applicable to cytology specimens. Thus, rigorous validation must be performed for each type of fixative and cytology preparation before it is implemented in the clinical setting.
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Affiliation(s)
- Fang Zhou
- Department of Pathology, New York University Langone Health, New York, NY, USA
| | - Elaine Shum
- Division of Hematology and Medical Oncology, Department of Medicine, New York University Langone Health, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, New York University Langone Health, New York, NY, USA
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22
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Rosenbaum JN, Berry AB, Church AJ, Crooks K, Gagan JR, López-Terrada D, Pfeifer JD, Rennert H, Schrijver I, Snow AN, Wu D, Ewalt MD. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2021; 23:1218-1240. [PMID: 34245921 DOI: 10.1016/j.jmoldx.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.
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Affiliation(s)
- Jason N Rosenbaum
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna B Berry
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Swedish Cancer Institute and Institute of Systems Biology, Seattle, Washington
| | - Alanna J Church
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristy Crooks
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey R Gagan
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dolores López-Terrada
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - John D Pfeifer
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Hanna Rennert
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Iris Schrijver
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anthony N Snow
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - David Wu
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mark D Ewalt
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
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Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
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24
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Guo M, Shlyakhova N, Khanna A, Tinnirello AA, Schmeler KM, Hwang J, Sturgis EM, Stewart J. Validation of cobas 4800 HPV assay in SurePath Papanicolaou specimens for cervical cancer screening. J Am Soc Cytopathol 2021; 10:399-405. [PMID: 33967024 DOI: 10.1016/j.jasc.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/05/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION The cobas (Roche Diagnostics, Indianapolis, IN) HPV assay was approved by the US Food and Drug Administration for human papillomavirus (HPV) testing in SurePath (Becton Dickinson, Franklin Lakes, NJ) Papanicolaou specimens for cervical cancer prevention. To validate the cobas HPV assay in SurePath specimens in our institution, we compared its accuracy and clinical efficacy to that of the Cervista (Hologic, Marlborough, MA) HPV HR assay. METHODS This study used 138 Papanicolaou (Pap) cytology specimens collected in SurePath preservative fluid at our institution in 2018. After Pap cytology testing, the residual specimens were split for testing with the cobas and Cervista assays. Polymerase chain reaction (PCR)-based HPV testing (GP5+/GP6+) was performed on specimens with discrepant results. Clinical follow-up data were reviewed. RESULTS The cobas HPV and Cervista HPV HR assays showed good concordance (89.1%), with a kappa value of 0.78 (95% CI: 0.675-0.885). Fifteen specimens showed discrepant results between the 2 assays. Of 7 cases with cobas+/Cervista- results, 5 (71%) were confirmed positive by PCR. Of 8 cases with cobas-/Cervista+ results, 4 (50%) were confirmed positive by PCR. cobas HPV and Cervista HPV HR showed the same HPV-positive rate in cases of pathologically diagnosed ASC-H, LSIL, or HSIL. The sensitivities and specificities for detecting high-risk HPV of cobas HPV (93.7%, 97.3%) and Cervista HPV HR (92.1%, 94.7%) were comparable. The cobas HPV assay had false-negative results in 4 cases (5.2%) including 1 false-negative case that failed to predict CIN3. CONCLUSIONS The cobas HPV assay is valid in SurePath Pap cytology specimens for cervical cancer screening but has limitations of false-negative results with clinical implications.
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Affiliation(s)
- Ming Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Natalya Shlyakhova
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abha Khanna
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Agata A Tinnirello
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica Hwang
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erich M Sturgis
- Department of Head and Neck Surgery The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas
| | - John Stewart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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25
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Krishnan V, Utiramerur S, Ng Z, Datta S, Snyder MP, Ashley EA. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 2021; 22:85. [PMID: 33627090 PMCID: PMC7903625 DOI: 10.1186/s12859-020-03934-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/15/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortium have enabled the evaluation of analytical methods. The performance of such methods is not uniform across the different genomic regions of interest and variant types. Several benchmarking methods such as hap.py, vcfeval, and vcflib are available to assess the analytical performance characteristics of variant calling algorithms. However, assessing the performance characteristics of an overall LDT assay still requires stringing together several such methods and experienced bioinformaticians to interpret the results. In addition, these methods are dependent on the hardware, operating system and other software libraries, making it impossible to reliably repeat the analytical assessment, when any of the underlying dependencies change in the assay. Here we present a scalable and reproducible, cloud-based benchmarking workflow that is independent of the laboratory and the technician executing the workflow, or the underlying compute hardware used to rapidly and continually assess the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples. RESULTS The benchmarking workflow was used to evaluate the performance characteristics for secondary analysis pipelines commonly used by Clinical Genomics laboratories in their LDT assays such as the GATK HaplotypeCaller v3.7 and the SpeedSeq workflow based on FreeBayes v0.9.10. Five reference sample truth sets generated by Genome in a Bottle (GIAB) consortium, six samples from the Personal Genome Project (PGP) and several samples with validated clinically relevant variants from the Centers for Disease Control were used in this work. The performance characteristics were evaluated and compared for multiple reportable ranges, such as whole exome and the clinical exome. CONCLUSIONS We have implemented a benchmarking workflow for clinical diagnostic laboratories that generates metrics such as specificity, precision and sensitivity for germline SNPs and InDels within a reportable range using whole exome or genome sequencing data. Combining these benchmarking results with validation using known variants of clinical significance in publicly available cell lines, we were able to establish the performance of variant calling pipelines in a clinical setting.
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Affiliation(s)
- Vandhana Krishnan
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA
| | - Sowmithri Utiramerur
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA. .,Clinical Genomics Program, Stanford Health Care, Stanford, CA, USA. .,Roche Diagnostics Solutions, Research and Early Development, Pleasanton, CA, USA.
| | - Zena Ng
- Clinical Genomics Program, Stanford Health Care, Stanford, CA, USA
| | - Somalee Datta
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA.,School of Medicine, Research IT - Technology and Digital Solutions, Stanford University, Redwood City, CA, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.,Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA
| | - Euan A Ashley
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA. .,Department of Cardiovascular Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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26
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Provenzano M, Rotundo S, Chiodini P, Gagliardi I, Michael A, Angotti E, Borrelli S, Serra R, Foti D, De Sarro G, Andreucci M. Contribution of Predictive and Prognostic Biomarkers to Clinical Research on Chronic Kidney Disease. Int J Mol Sci 2020; 21:ijms21165846. [PMID: 32823966 PMCID: PMC7461617 DOI: 10.3390/ijms21165846] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic kidney disease (CKD), defined as the presence of albuminuria and/or reduction in estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73 m2, is considered a growing public health problem, with its prevalence and incidence having almost doubled in the past three decades. The implementation of novel biomarkers in clinical practice is crucial, since it could allow earlier diagnosis and lead to an improvement in CKD outcomes. Nevertheless, a clear guidance on how to develop biomarkers in the setting of CKD is not yet available. The aim of this review is to report the framework for implementing biomarkers in observational and intervention studies. Biomarkers are classified as either prognostic or predictive; the first type is used to identify the likelihood of a patient to develop an endpoint regardless of treatment, whereas the second type is used to determine whether the patient is likely to benefit from a specific treatment. Many single assays and complex biomarkers were shown to improve the prediction of cardiovascular and kidney outcomes in CKD patients on top of the traditional risk factors. Biomarkers were also shown to improve clinical trial designs. Understanding the correct ways to validate and implement novel biomarkers in CKD will help to mitigate the global burden of CKD and to improve the individual prognosis of these high-risk patients.
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Affiliation(s)
- Michele Provenzano
- Renal Unit, Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (I.G.); (A.M.)
- Correspondence: (M.P.); (M.A.); Tel.: +39-3407544146 (M.P.); +39-3396814750 (M.A.)
| | - Salvatore Rotundo
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (S.R.); (D.F.)
| | - Paolo Chiodini
- Medical Statistics Unit, University of Campania Luigi Vanvitelli, I-80138 Naples, Italy;
| | - Ida Gagliardi
- Renal Unit, Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (I.G.); (A.M.)
| | - Ashour Michael
- Renal Unit, Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (I.G.); (A.M.)
| | - Elvira Angotti
- Clinical Biochemistry Unit, Azienda Ospedaliera Universitaria Mater Domini Hospital, I-88100 Catanzaro, Italy;
| | - Silvio Borrelli
- Renal Unit, University of Campania “Luigi Vanvitelli”, I-80138 Naples, Italy;
| | - Raffaele Serra
- Interuniversity Center of Phlebolymphology (CIFL), “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy;
| | - Daniela Foti
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (S.R.); (D.F.)
| | - Giovambattista De Sarro
- Pharmacology Unit, Department of Health Sciences, School of Medicine, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy;
| | - Michele Andreucci
- Renal Unit, Department of Health Sciences, “Magna Graecia” University of Catanzaro, I-88100 Catanzaro, Italy; (I.G.); (A.M.)
- Correspondence: (M.P.); (M.A.); Tel.: +39-3407544146 (M.P.); +39-3396814750 (M.A.)
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27
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Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L. Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection. Clin Transl Sci 2020; 14:204-213. [PMID: 32931151 PMCID: PMC7877843 DOI: 10.1111/cts.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5, *13, *36, *68; CYP2B6*29; and CYP2C19*36). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.
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Affiliation(s)
- Stuart A Scott
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Aniwaa Owusu Obeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Neal Cody
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Paola Nicoletti
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lisong Shi
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth Kornreich
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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28
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Nikiforova MN, Lepe M, Tolino LA, Miller ME, Ohori NP, Wald AI, Landau MS, Kaya C, Malapelle U, Bellevicine C, Troncone G, Nikiforov YE, Baloch Z. Thyroid cytology smear slides: An untapped resource for ThyroSeq testing. Cancer Cytopathol 2020; 129:33-42. [PMID: 32697051 DOI: 10.1002/cncy.22331] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Molecular testing of thyroid nodules with indeterminate fine-needle aspiration (FNA) cytology is commonly used to guide patient management and is typically performed on freshly collected FNA samples. In this study, the authors evaluated the performance of the ThyroSeq test in cytology smear slides. METHODS Air-dried Diff-Quik (DQ)-stained and alcohol-fixed Papanicolaou (Pap)-stained smears were used to determine required cellularity and sensitivity of mutation detection and to compare ThyroSeq v3 Genomic Classifier (GC) results obtained in cytology smears and fresh FNA samples from the same nodules. RESULTS ThyroSeq testing of 31 cytology smears revealed that 25 smears (81%) were adequate for ThyroSeq analysis, including 14 Pap-stained smears (100%) and 11 DQ-stained smears (65%), whereas 6 DQ-stained smears (35%) failed RNA sequencing. The overall accuracy for detecting molecular alterations was 98%, with 100% concordance for mutations and gene expression alterations, 96% concordance for fusions, and 94% concordance for copy number alterations. Cytology smears were adequate for ThyroSeq analysis when at least 200 to 300 cells were present in 1 to 3 slides. ThyroSeq detected all studied mutations down to 5% allele frequency and BRAF mutations down to 1% allele frequency. Testing of smears yielded a positive ThyroSeq GC result in all nodules originally classified as positive. CONCLUSIONS Thyroid FNA cytology smear slides with adequate cellularity can be successfully used for ThyroSeq GC testing in approximately 80% of cases, with an even higher success rate in Pap-stained smears. Compared with FNA samples collected into preservative solution, 94% to 100% of different genetic alterations could be accurately detected in smears, validating cytology smears as an alternative for ThyroSeq testing in patients with indeterminate thyroid cytology.
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Affiliation(s)
- Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Marcos Lepe
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lindsey A Tolino
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Megan E Miller
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - N Paul Ohori
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Abigail I Wald
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael S Landau
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Cihan Kaya
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Umberto Malapelle
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Perelman School of Medicine, Philadelphia, Pennsylvania
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29
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Montoya-Fuentes H, Rodriguez-Martin A, Pena-Iniguez DI, Gonzalez-Bonilla CR, Rosales-Gomez RC, Gallegos-Arreola MP, Santoscoy-Ascencio G, Gutierrez-Rubio SA. Molecular Detection and Typing of Human Papillomavirus in Men from Northwestern Mexico. Arch Med Res 2020; 51:675-682. [PMID: 32682576 DOI: 10.1016/j.arcmed.2020.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/20/2020] [Accepted: 06/30/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND A few studies of Human Papillomavirus (HPV) distribution and frequency have shown a real context of infection in men. The study aimed to know the HPV types distribution in men from Northwestern Mexico, in general, per age and year. METHODS A total of 1,769 males were recruited from 5 years (2011-2015), from an HPV PCR testing laboratory service. Penile scraps from urethral meatus and coronal sulcus were taken for DNA isolation. There were detected 32 high and low-risk HPV types by HPV Type 3.5 LCD-Array system. RESULTS A high frequency of HPV-6 and HPV-66 and a reduced frequency of HPV-18 and HPV-11 was detected. Young men had a high risk of HPV infection regarding men aged 40 years and older. The theoretical coverage for the HPV vaccine in men was calculated, where the bivalent vaccine showed coverage of 21.66% in high-risk HPV positive cases. CONCLUSION The men from Northwestern Mexico have a different distribution of high and low-risk HPV types and high risk of HPV infection in younger men, with a theoretical coverage for HPV bivalent vaccine of 1 of 10 positive men for any HPV type.
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Affiliation(s)
- Hector Montoya-Fuentes
- Laboratorio de Microbiología Molecular, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - Araceli Rodriguez-Martin
- Departamento de Biología Molecular, Unidad de Patología Clínica, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - Daniel Ivan Pena-Iniguez
- Laboratorio de Microbiología Molecular, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | | | - Roberto Carlos Rosales-Gomez
- Laboratorio de Microbiología Molecular, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México; Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonala, Jalisco, México
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - Guillermo Santoscoy-Ascencio
- Departamento de Biología Molecular, Unidad de Patología Clínica, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - Susan Andrea Gutierrez-Rubio
- Instituto de Terapéutica Experimental y Clínica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México.
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30
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Kim J, Yeo I, Kim H, Sohn A, Kim Y, Kim Y. Web portal for analytical validation of MRM-MS assay abided with integrative multinational guidelines. Sci Rep 2020; 10:10848. [PMID: 32616742 PMCID: PMC7331696 DOI: 10.1038/s41598-020-67731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Multiple reaction monitoring-mass spectrometry became a mainstream method for quantitative proteomics, which made the validation of a method and the analyzed data important. In this portal for validation of the MRM-MS assay, we developed a website that automatically evaluates uploaded MRM-MS data, based on biomarker assay guidelines from the European Medicines Agency, the US Food & Drug Administration, and the Korea Food & Drug Administration. The portal reads a Skyline output file and produces the following results—calibration curve, specificity, sensitivity, carryover, precision, recovery, matrix effect, recovery, dilution integrity, stability, and QC—according to the standards of each independent agency. The final tables and figures that pertain to the 11 evaluation categories are displayed in an individual page. Spring boot was used as a framework for development of the webpage, which follows MVC Pattern. JSP, HTML, XML, and Java Script were used to develop the webpage. A server was composed of Apache Tomcat, MySQL. Input files were skyline-derived output files (csv file), and each files were organized by specific columns in order. SQL, JAVA were interworked to evaluate all the categories and show the results. Method Validation Portal can be accessed via any kind of explorer from https://pnbvalid.snu.ac.kr.
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Affiliation(s)
- Jaenyeon Kim
- Interdisciplinary Program of Bioengineering, Seoul National University College of Engineering, Seoul, South Korea
| | - Injoon Yeo
- Interdisciplinary Program of Bioengineering, Seoul National University College of Engineering, Seoul, South Korea
| | - Hyunsoo Kim
- Institute of Medical and Biological Engineering, MRC, Seoul National University, Seoul, South Korea
| | - Areum Sohn
- Institute of Medical and Biological Engineering, MRC, Seoul National University, Seoul, South Korea
| | - Yoseop Kim
- Interdisciplinary Program of Bioengineering, Seoul National University College of Engineering, Seoul, South Korea
| | - Youngsoo Kim
- Interdisciplinary Program of Bioengineering, Seoul National University College of Engineering, Seoul, South Korea. .,Institute of Medical and Biological Engineering, MRC, Seoul National University, Seoul, South Korea. .,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea. .,Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.
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31
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Becker MG, Liang D, Cooper B, Le Y, Taylor T, Lee ER, Wu S, Sandstrom P, Ji H. Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays. Viruses 2020; 12:E627. [PMID: 32532083 PMCID: PMC7354553 DOI: 10.3390/v12060627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/07/2020] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays outperform conventional Sanger sequencing in scalability, sensitivity, and quantitative detection of minority resistance variants. Thus far, HIVDR assays have been applied primarily in research but rarely in clinical settings. One main obstacle is the lack of standardized validation and performance evaluation systems that allow regulatory agencies to benchmark and accredit new assays for clinical use. By revisiting the existing principles for molecular assay validation, here we propose a new validation and performance evaluation system that helps to both qualitatively and quantitatively assess the performance of an NGS-based HIVDR assay. To accomplish this, we constructed a 70-specimen proficiency test panel that includes plasmid mixtures at known ratios, viral RNA from infectious clones, and anonymized clinical specimens. We developed assessment criteria and benchmarks for NGS-based HIVDR assays and used these to assess data from five separate MiSeq runs performed in two experienced HIVDR laboratories. This proposed platform may help to pave the way for the standardization of NGS HIVDR assay validation and performance evaluation strategies for accreditation and quality assurance purposes in both research and clinical settings.
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Affiliation(s)
- Michael G. Becker
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Dun Liang
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Breanna Cooper
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Yan Le
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Tracy Taylor
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Sutan Wu
- SutanStats, St. Louis, MO 63017, USA;
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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32
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Taube JM, Akturk G, Angelo M, Engle EL, Gnjatic S, Greenbaum S, Greenwald NF, Hedvat CV, Hollmann TJ, Juco J, Parra ER, Rebelatto MC, Rimm DL, Rodriguez-Canales J, Schalper KA, Stack EC, Ferreira CS, Korski K, Lako A, Rodig SJ, Schenck E, Steele KE, Surace MJ, Tetzlaff MT, von Loga K, Wistuba II, Bifulco CB. The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J Immunother Cancer 2020; 8:e000155. [PMID: 32414858 PMCID: PMC7239569 DOI: 10.1136/jitc-2019-000155] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES The interaction between the immune system and tumor cells is an important feature for the prognosis and treatment of cancer. Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their spatial arrangement within the tumor microenvironment. METHODS The Society for Immunotherapy of Cancer (SITC) convened a task force of pathologists and laboratory leaders from academic centers as well as experts from pharmaceutical and diagnostic companies to develop best practice guidelines for the optimization and validation of mIHC/mIF assays across platforms. RESULTS Representative outputs and the advantages and disadvantages of mIHC/mIF approaches, such as multiplexed chromogenic IHC, multiplexed immunohistochemical consecutive staining on single slide, mIF (including multispectral approaches), tissue-based mass spectrometry, and digital spatial profiling are discussed. CONCLUSIONS mIHC/mIF technologies are becoming standard tools for biomarker studies and are likely to enter routine clinical practice in the near future. Careful assay optimization and validation will help ensure outputs are robust and comparable across laboratories as well as potentially across mIHC/mIF platforms. Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force.
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Affiliation(s)
- Janis M Taube
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Guray Akturk
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Elizabeth L Engle
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Shirley Greenbaum
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Palo Alto, California, USA
| | | | - Travis J Hollmann
- Dermatopathology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | | | - Edwin R Parra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Kurt A Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Cláudia S Ferreira
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Konstanty Korski
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Ana Lako
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Scott J Rodig
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Michael T Tetzlaff
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Katharina von Loga
- Biomedical Research Centre, Royal Marsden NHS Foundation Trust, London, UK
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Design and Reporting Considerations for Genetic Screening Tests. J Mol Diagn 2020; 22:599-609. [DOI: 10.1016/j.jmoldx.2020.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/20/2022] Open
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Fortschegger M, Preuner S, Printz D, Poetsch AR, Geyeregger R, Pichler H, Lawitschka A, Lion T. Detection and Monitoring of Lineage-Specific Chimerism by Digital Droplet PCR-Based Testing of Deletion/Insertion Polymorphisms. Biol Blood Marrow Transplant 2020; 26:1218-1224. [PMID: 32092354 DOI: 10.1016/j.bbmt.2020.02.016] [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: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/13/2020] [Indexed: 12/31/2022]
Abstract
Analysis of specific leukocyte subsets for post-transplantation monitoring of chimerism provides greater sensitivity and clinical informativeness on dynamic changes in donor- and recipient-derived cells. Limitations of the most commonly used approach to chimerism testing relying on PCR-based analysis of microsatellite markers prompted us to assess the applicability of digital droplet (dd) PCR amplification of deletion/insertion polymorphisms (DIPs) for lineage-specific chimerism testing in the related stem cell transplantation setting, where the identification of informative markers facilitating the discrimination between donor-derived and recipient-derived cells can be challenging. We analyzed 100 genetically related patient-donor pairs by ddPCR analysis using commercially available DIP kits including large sets of polymorphic markers. At least 1 informative marker was identified in all related pairs analyzed, and 2 or more discriminating markers were detected in the majority (82%) of instances. The achievable detection limit is dependent on the number of cells available for analysis and was as low as 0.1% in the presence of ≥20,000 leukocytes available for DNA extraction. Moreover, the reproducibility and accuracy of quantitative chimerism analysis compared favorably to highly optimized microsatellite assays. Thus, the use of ddPCR-based analysis of DIP markers is an attractive approach to lineage-specific monitoring of chimerism in any allogeneic transplantation setting.
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Affiliation(s)
| | - Sandra Preuner
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Dieter Printz
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Anna R Poetsch
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - René Geyeregger
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | | | | | - Thomas Lion
- St Anna Children's Cancer Research Institute, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
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35
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Zneimer SM. Validation of Fluorescence In Situ Hybridization (FISH) for Chromosome 5 Monosomy and Deletion. ACTA ACUST UNITED AC 2020; 105:e96. [PMID: 31922364 DOI: 10.1002/cphg.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In order to comply with regulations set by established local, state, and federal agencies and other regulatory organizations, such as the College of American Pathologists and the International Organization for Standardization, a clinical laboratory needs to develop procedures for the processes of validating laboratory-developed tests (LDTs) and establishing performance specifications for these assays prior to use in clinical testing. This is applicable to all fluorescence in situ hybridization (FISH) assays. Even Food and Drug Administration-approved FISH assays must undergo some form of verification before implementation in the clinical laboratory. The process of validating an assay as an LDT must include a plan, a procedure, and a report. The validation studies described here include metaphase and interphase FISH methodology for identification of the LSI EGR1/D5S23, D5S721 dual-color probe, which labels distinct biomarkers consistent with myeloid hematologic disorders, including myelodysplasias and acute myeloid leukemia. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Validation plan for fluorescence in situ hybridization (FISH) probes for chromosome 5 monosomy and deletion Support Protocol: Normal cut-off calculation Basic Protocol 2: Validation procedure for FISH probes for chromosome 5 monosomy and deletion Basic Protocol 3: Validation report for FISH probes for chromosome 5 monosomy and deletion.
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Affiliation(s)
- Susan M Zneimer
- Medical Operation Systems Consulting (MOSYS), Camas, Washington.,Symbiotica, Inc., Vacaville, California
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36
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Abstract
The apolipoproteins are well known for their roles in both health and disease, as components of plasma lipoprotein particles, such as high-density lipoprotein (HDL), low-density lipoprotein (LDL), very-low-density lipoprotein (VLDL), chylomicrons, and metabolic, vascular- and inflammation-related disorders, such as cardiovascular disease, atherosclerosis, metabolic syndrome, and diabetes. Increasingly, their roles in neurovascular and neurodegenerative disorders are also being elucidated. They play major roles in lipid and cholesterol transport between blood and organs and are, therefore, critical to maintenance and homeostasis of the lipidome, with apolipoprotein-lipid interactions, including cholesterol, fatty acids, triglycerides, phospholipids, and isoprostanes. Further, they have important pleiotropic roles related to aging and longevity, which are largely managed through their many structural variants, including multiple isoforms, and a diversity of post-translational modifications. Consequently, tools for the characterization and accurate quantification of apolipoproteins, including their diverse array of variant forms, are required to understand their salutary and disease related roles. In this chapter we outline three distinct quantitative approaches suitable for targeting apolipoproteins: (1) multiplex immunoassays, (2) mass spectrometric immunoassay, and (3) multiple reaction monitoring, mass spectrometric quantification. We also discuss management of pre-analytical and experimental design variables.
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Lim YK, Kweon OJ, Lee MK, Kim HR. Assessing the measurement uncertainty of qualitative analysis in the clinical laboratory. J LAB MED 2019. [DOI: 10.1515/labmed-2019-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Measurement uncertainty is a parameter that is associated with the dispersion of measurements. Assessment of the measurement uncertainty is recommended in qualitative analyses in clinical laboratories; however, the measurement uncertainty of qualitative tests has been neglected despite the introduction of many adequate methods. We herein provide an overview of three reasonable statistical methods for quantifying the measurement uncertainties of qualitative assays, namely Bayes’ theorem, the normal distribution method, and the information theoretic approach. Unlike in quantitative analysis, the measurement uncertainty of qualitative analysis is expressed using a conditional probability, likelihood ratio, and entropy. With the necessary theoretical background, the practical applications for clinical laboratories are also provided using statistical calculations. Using statistical approaches, we hope that our review will contribute to the use of measurement uncertainty in qualitative analyses in the clinical laboratory environment.
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Affiliation(s)
- Yong Kwan Lim
- Department of Laboratory Medicine , Armed Forces Capital Hospital , Gyeonggi-do , Republic of Korea
- Department of Laboratory Medicine , Chung-Ang University College of Medicine , Seoul , Republic of Korea
| | - Oh Joo Kweon
- Department of Laboratory Medicine , Chung-Ang University College of Medicine , Seoul , Republic of Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine , Chung-Ang University College of Medicine , Seoul , Republic of Korea
| | - Hye Ryoun Kim
- Department of Laboratory Medicine , Chung-Ang University College of Medicine , Seoul , Republic of Korea
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Sesler CL, Grigorenko EV. Analytical Validation of qPCR-Based Multivariate Index Assays in a Clinical Laboratory: Practical Challenges and Limitations. J Appl Lab Med 2019; 3:267-281. [PMID: 33636934 DOI: 10.1373/jalm.2017.025924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/02/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Multivariate index assays (MIAs) to evaluate disease status and/or therapeutic efficacy are increasingly being used in clinical laboratories as laboratory-developed tests (LDTs). Before clinical use, diagnostic and analytical performance specifications of LDTs must be established. Several regulatory guidelines have been published that address specific components of validation procedures, but the interpretation for the analytical validation of MIAs is ambiguous and creates confusion when implementing a novel MIA in the clinical laboratory. CONTENT CLSI guidelines and published methods were evaluated to develop a validation strategy to establish analytical sensitivity, precision, specificity, and stability for qPCR-based MIAs. Limitations and challenges identified while evaluating guidelines and literature and implementing this strategy are discussed in this review, including sample sourcing and integrity, laboratory contamination, and sample throughput. Due to the diversity of qPCR-based MIAs, we discuss additional considerations for researchers intending to transfer MIAs to a clinical laboratory. SUMMARY A practical strategy to assess the analytical performance characteristics for validation of qPCR-based MIAs was developed and tested before diagnostic clinical use. Several important limitations, challenges, and considerations were identified during development of the analytical validation procedures that are not addressed in regulatory guidelines or published literature. The described strategy can provide insight for future developers of MIAs and clinical laboratories implementing MIAs as LDTs.
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Ascierto PA, Bifulco C, Palmieri G, Peters S, Sidiropoulos N. Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis. J Mol Diagn 2019; 21:756-767. [PMID: 31251989 DOI: 10.1016/j.jmoldx.2019.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. Many preanalytic variables can influence the accuracy and reliability of NGS results. Standardization of preanalytic variables is, however, complicated by the plethora of specimen acquisition and processing methods. Variables across the tissue journey, including specimen acquisition, specimen fixation, and sectioning, as well as postfixation processing, such as nucleic acid extraction, library preparation, and choice of sequencing methods, are critical for the reliability of NGS analysis; thus, standardization would be beneficial. In this article, each step in the tissue journey is outlined, with specific focus on preanalytic variables that can influence NGS results. Practical considerations for standardization of these variables are provided to facilitate accurate, reliable, and reproducible NGS-based molecular characterization of tumors, ultimately informing diagnosis and guiding treatment.
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Affiliation(s)
- Paolo A Ascierto
- Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - Carlo Bifulco
- Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, Oregon
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry - National Research Council, Sassari, Italy
| | - Solange Peters
- Department of Oncology, Lausanne University, Lausanne, Switzerland
| | - Nikoletta Sidiropoulos
- University of Vermont Health Network, Larner College of Medicine at the University of Vermont, Burlington, Vermont
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40
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Moncur JT, Bartley AN, Bridge JA, Kamel-Reid S, Lazar AJ, Lindeman NI, Long TA, Merker JD, Rai AJ, Rimm DL, Rothberg PG, Vasalos P, Kim AS. Performance Comparison of Different Analytic Methods in Proficiency Testing for Mutations in the BRAF, EGFR, and KRAS Genes: A Study of the College of American Pathologists Molecular Oncology Committee. Arch Pathol Lab Med 2019; 143:1203-1211. [PMID: 30969158 DOI: 10.5858/arpa.2018-0396-cp] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The performance of laboratory testing has recently come under increased scrutiny as part of important and ongoing debates on regulation and reimbursement. To address this critical issue, this study compares the performance of assay methods, using either commercial kits or assays designed and implemented by single laboratories ("home brews"), including next-generation sequencing methods, on proficiency testing provided by the College of American Pathologists Molecular Oncology Committee. OBJECTIVE.— To compare the performance of different assay methods on College of American Pathologists proficiency testing for variant analysis of 3 common oncology analytes: BRAF, EGFR, and KRAS. DESIGN.— There were 6897 total responses across 35 different proficiency testing samples interrogating 13 different variants as well as wild-type sequences for BRAF, EGFR, and KRAS. Performance was analyzed by test method, kit manufacturer, variants tested, and preanalytic and postanalytic practices. RESULTS.— Of 26 reported commercial kits, 23 achieved greater than 95% accuracy. Laboratory-developed tests with no kit specified demonstrated 96.8% or greater accuracy across all 3 analytes (1123 [96.8%] acceptable of 1160 total responses for BRAF; 848 [97.5%] acceptable of 870 total responses for EGFR; 942 [97.0%] acceptable of 971 total responses for KRAS). Next-generation sequencing platforms (summed across all analytes and 2 platforms) demonstrated 99.4% accuracy for these analytes (165 [99.4%] acceptable of 166 total next-generation sequencing responses). Slight differences in performance were noted among select commercial assays, dependent upon the particular design and specificity of the assay. Wide differences were noted in the lower limits of neoplastic cellularity laboratories accepted for testing. CONCLUSIONS.— These data demonstrate the high degree of accuracy and comparable performance across all laboratories, regardless of methodology. However, care must be taken in understanding the diagnostic specificity and reported analytic sensitivity of individual methods.
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Affiliation(s)
- Joel T Moncur
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Angela N Bartley
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Julia A Bridge
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Suzanne Kamel-Reid
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alexander J Lazar
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Neal I Lindeman
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Thomas A Long
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Jason D Merker
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alex J Rai
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - David L Rimm
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Paul G Rothberg
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Patricia Vasalos
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Annette S Kim
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
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Barbieri RR, Manta FSN, Moreira SJM, Sales AM, Nery JAC, Nascimento LPR, Hacker MA, Pacheco AG, Machado AM, Sarno EM, Moraes MO. Quantitative polymerase chain reaction in paucibacillary leprosy diagnosis: A follow-up study. PLoS Negl Trop Dis 2019; 13:e0007147. [PMID: 30835722 PMCID: PMC6428338 DOI: 10.1371/journal.pntd.0007147] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/21/2019] [Accepted: 01/09/2019] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE The diagnosis of paucibacillary (PB) leprosy cases remains a challenge because of the absence of a confirmatory laboratory method. While quantitative polymerase chain reaction (qPCR) has been shown to provide reliable sensitivity and specificity in PB diagnoses, a thorough investigation of its efficacy in clinical practice has not yet been published. The present study evaluated patients with suspected leprosy skin lesions by using qPCR to identify PB individuals in the Leprosy Outpatient clinic at the Oswaldo Cruz Foundation in Rio de Janeiro, Brazil. METHODS One hundred seventy-two suspected PB cases were included in the study. The patients were evaluated by a dermatologist at three different times. The clinical dermato-neurological examination and collected samples were performed on the first visit. On the second visit, the results of the histopathological analysis and PCR assay (DNA-based Mycobacterium leprae qPCR-targeting 16S gene) results were analyzed, and a decision regarding multi-drug therapy was made. A year later, the patients were re-examined, and the consensus diagnosis was established. RESULTS In 58% (100/172) of cases, a conclusive diagnosis via histopathological analysis was not possible; however, 30% (30/100) of these cases had a positive PCR. One hundred ten patients (110/172) attended the third visit. The analysis showed that while the sensitivity of the histopathological test was very low (35%), a qPCR alone was more effective for identifying leprosy, with 57% sensitivity. CONCLUSION The use of qPCR in suspected PB cases with an inconclusive histology improved the sensitivity of leprosy diagnoses.
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Affiliation(s)
- Raquel R. Barbieri
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda S. N. Manta
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suelen J. M. Moreira
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anna M. Sales
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José A. C. Nery
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Mariana A. Hacker
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Antônio G. Pacheco
- PROCC—Programa de Computação Científica—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alice M. Machado
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Euzenir M. Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Milton O. Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute—Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
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Park W, Lopes G. Perspectives: Neutrophil-to-lymphocyte Ratio as a Potential Biomarker in Immune Checkpoint Inhibitor for Non-Small-Cell Lung Cancer. Clin Lung Cancer 2018; 20:143-147. [PMID: 30683629 DOI: 10.1016/j.cllc.2018.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/25/2018] [Accepted: 12/08/2018] [Indexed: 12/18/2022]
Abstract
There is a rising need for optimal biomarkers to better tailor treatments for patients with cancer in the era of immunotherapy. In addition to programmed death-ligand 1 (PD-L1) and tumor mutation burden (TMB), neutrophil-to-lymphocyte (NLR) is regaining interest as a biomarker in immunotherapy for its availability, accessibility, and reproducibility. High NLR, according to different thresholds, is consistently reported to correlate with poor prognosis in different treatments in several cancers. Yet, most data come from retrospective analysis, and proof of mechanism and principle evaluations are limited. Prospective studies or adequately sized retrospective analyses of prospectively collected data are required to best assess its role in clinical practice. Moreover, effective myeloid or neutrophil modulators in tumor microenvironment can potentially contribute as a new therapeutic strategy. This perspective will summarize our current knowledge and will discuss where we stand now and propose future directions.
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Affiliation(s)
- Wungki Park
- Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY; Divisions of Hematology and Medical Oncology, Departments of Medicine, Miller School of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL.
| | - Gilberto Lopes
- Divisions of Hematology and Medical Oncology, Departments of Medicine, Miller School of Medicine, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL
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Arbitrio M, Di Martino MT, Scionti F, Barbieri V, Pensabene L, Tagliaferri P. Pharmacogenomic Profiling of ADME Gene Variants: Current Challenges and Validation Perspectives. High Throughput 2018; 7:E40. [PMID: 30567415 PMCID: PMC6306724 DOI: 10.3390/ht7040040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 01/04/2023] Open
Abstract
In the past decades, many efforts have been made to individualize medical treatments, taking into account molecular profiles and the individual genetic background. The development of molecularly targeted drugs and immunotherapy have revolutionized medical treatments but the inter-patient variability in the anti-tumor drug pharmacokinetics (PK) and pharmacodynamics can be explained, at least in part, by genetic variations in genes encoding drug metabolizing enzymes and transporters (ADME) or in genes encoding drug receptors. Here, we focus on high-throughput technologies applied for PK screening for the identification of predictive biomarkers of efficacy or toxicity in cancer treatment, whose application in clinical practice could promote personalized treatments tailored on individual's genetic make-up. Pharmacogenomic tools have been implemented and the clinical utility of pharmacogenetic screening could increase safety in patients for the identification of drug metabolism-related biomarkers for a personalized medicine. Although pharmacogenomic studies were performed in adult cohorts, pharmacogenetic pediatric research has yielded promising results. Additionally, we discuss the current challenges and theoretical bases for the implementation of pharmacogenetic tests for translation in the clinical practice taking into account that pharmacogenomics platforms are discovery oriented and must open the way for the setting of robust tests suitable for daily practice.
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Affiliation(s)
- Mariamena Arbitrio
- Institute of Neurological Sciences, UOS of Pharmacology, 88100 Catanzaro, Italy.
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Vito Barbieri
- Medical Oncology Unit, Mater Domini Hospital, Salvatore Venuta University Campus, 8810 Catanzaro, Italy.
| | - Licia Pensabene
- Department of Medical and Surgical Sciences Pediatric Unit, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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Chauvin A, Boisvert FM. Clinical Proteomics in Colorectal Cancer, a Promising Tool for Improving Personalised Medicine. Proteomes 2018; 6:proteomes6040049. [PMID: 30513835 PMCID: PMC6313903 DOI: 10.3390/proteomes6040049] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures currently used for detecting this cancer, as well as for predicting the response to treatment and the outcome of a patient's resistance in guiding clinical practice, are key elements driving the search for biomarkers. In the present overview, the different biomarkers (diagnostic, prognostic, treatment resistance) discovered through proteomics studies in various colorectal cancer study models (blood, stool, biopsies), including the different proteomic techniques used for the discovery of these biomarkers, are reviewed, as well as the various tests used in clinical practice and those currently in clinical phase. These studies define the limits and perspectives related to proteomic biomarker research for personalised medicine in colorectal cancer.
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Affiliation(s)
- Anaïs Chauvin
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
| | - François-Michel Boisvert
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
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The cornerstone of integrating circulating tumor DNA into cancer management. Biochim Biophys Acta Rev Cancer 2018; 1871:1-11. [PMID: 30419316 DOI: 10.1016/j.bbcan.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022]
Abstract
Recent circulating tumor DNA (ctDNA) research has demonstrated its potential as a non-invasive biomarker for cancer. However, the deployment of ctDNA assays in routine clinical practice remains challenging owing to variability in analytical approaches and the assessment of clinical significance. A well-developed, analytically valid ctDNA assay is a prerequisite for integrating ctDNA into cancer management, and an appropriate analytical technology is crucial for the development of a ctDNA assay. Other determinants including pre-analytical procedures, test validation, internal quality control (IQC), and continual proficiency testing (PT) are also important for the accuracy of ctDNA assays. In the present review, we will focus on the most widely used ctDNA detection technologies and the key quality management measures used to assure the accuracy of ctDNA assays. The aim of this review is to provide useful information for technology selection during ctDNA assay development and assure a reliable test result in clinical practice.
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47
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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Caudle KE, Keeling NJ, Klein TE, Whirl-Carrillo M, Pratt VM, Hoffman JM. Standardization can accelerate the adoption of pharmacogenomics: current status and the path forward. Pharmacogenomics 2018; 19:847-860. [PMID: 29914287 DOI: 10.2217/pgs-2018-0028] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Successfully implementing pharmacogenomics into routine clinical practice requires an efficient process to order genetic tests and report the results to clinicians and patients. Lack of standardized approaches and terminology in clinical laboratory processes, ordering of the test and reporting of test results all impede this workflow. Expert groups such as the Association for Molecular Pathology and the Clinical Pharmacogenetics Implementation Consortium have published recommendations for standardizing laboratory genetic testing, reporting and terminology. Other resources such as PharmGKB, ClinVar, ClinGen and PharmVar have established databases of nomenclature for pharmacogenetic alleles and variants. Opportunities remain to develop new standards and further disseminate existing standards which will accelerate the implementation of pharmacogenomics.
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Affiliation(s)
- Kelly E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nicholas J Keeling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Pharmacy Administration, University of Mississippi School of Pharmacy, Oxford, MS 38655, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Victoria M Pratt
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - James M Hoffman
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Office of Quality & Patient Care, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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Chou R, Easterbrook P, Hellard M. Methodological challenges in appraising evidence on diagnostic testing for WHO guidelines on hepatitis B and hepatitis C virus infection. BMC Infect Dis 2017; 17:694. [PMID: 29143626 PMCID: PMC5688453 DOI: 10.1186/s12879-017-2766-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Linking persons with hepatitis B (HBV) and hepatitis C (HCV) infection with appropriate prevention and treatment requires that they first be diagnosed. The World Health Organization (WHO) has developed its first guidelines on testing for chronic HBV and HCV infection, using a framework based on methods from the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) Working Group for the formulation of recommendations, including determining the strength of recommendations and quality of evidence. Recommendations were formulated based on the overall quality of the evidence, in addition to other considerations, including the balance between benefits and harms, values and preferences, feasibility and resource implications. This article summarizes methodological challenges and additional considerations encountered in applying these procedures to diagnostic testing for viral hepatitis, and strategies to address these. Direct evidence on the effects of tests and test strategies on clinical outcomes was not available. Given the availability of effective treatments for HBV and HCV that are generally acceptable to patients, the Guidelines Development Group (GDG) considered diagnostic accuracy a reasonable surrogate for clinical outcomes. In order to increase the number of patients identified with chronic HBV and HCV infection who could benefit from treatments, the GDG determined that tests and testing strategies associated with slightly lower diagnostic accuracy could be recommended when associated with lower costs; increased testing access, uptake, and linkage to care; greater feasibility; or if preferred by patients.
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Affiliation(s)
- Roger Chou
- Department of Medical Informatics and Clinical Epidemiology, Pacific Northwest Evidence-based Practice Center, Oregon Health & Science University, Portland, Oregon, USA.
| | - Philippa Easterbrook
- Global Hepatitis Programme, HIV Department, World Health Organization, Geneva, Switzerland
| | - Margaret Hellard
- Centre for Population Health, Burnet Institute, Melbourne, Australia
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50
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Singhi AD, Arnold CA, Lam-Himlin DM, Nikiforova MN, Voltaggio L, Canto MI, McGrath KM, Montgomery EA. Targeted next-generation sequencing supports epidermoid metaplasia of the esophagus as a precursor to esophageal squamous neoplasia. Mod Pathol 2017; 30:1613-1621. [PMID: 28731047 DOI: 10.1038/modpathol.2017.73] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/15/2017] [Accepted: 05/20/2017] [Indexed: 12/17/2022]
Abstract
Esophageal epidermoid metaplasia is a rare condition that involves the proximal-to-middle third of the esophagus. It is sharply demarcated and defined histologically by epithelial hyperplasia, a prominent granular cell layer, and superficial hyperorthokeratosis. In addition, preliminary studies have suggested an association between esophageal epidermoid metaplasia and esophageal squamous neoplasia (squamous dysplasia and esophageal squamous cell carcinoma). To further characterize esophageal epidermoid metaplasia and better define its relationship to squamous neoplasia of the esophagus, we performed targeted next-generation sequencing on uninvolved esophageal squamous mucosa and matching esophageal epidermoid metaplasia specimens from 18 patients. Further, we evaluated both synchronous and metachronous high-grade squamous dysplasia/esophageal squamous cell carcinoma by next-generation sequencing from 5 of the 18 (28%) patients, and compared these findings to corresponding esophageal epidermoid metaplasia specimens. Targeted next-generation sequencing revealed 12 of 18 (67%) esophageal epidermoid metaplasia specimens' harbored alterations in genes often associated with esophageal squamous cell carcinoma. The most frequently mutated genes consisted of TP53 (n=10), PIK3CA (n=2), EGFR (n=2), MYCN (n=1), HRAS (n=1), and the TERT promoter (n=1). Sequencing of synchronous and metachronous high-grade squamous dysplasia/esophageal squamous cell carcinoma identified shared genetic alterations with corresponding esophageal epidermoid metaplasia specimens that suggests a clonal relationship between these entities. In addition, the presence of a TP53 mutation in esophageal epidermoid metaplasia specimens correlated with concurrent or progression to high-grade squamous dysplasia/esophageal squamous cell carcinoma. No genetic alterations were detected in uninvolved esophageal squamous mucosa. On the basis of these findings, we conclude esophageal epidermoid metaplasia is a precursor to in situ and invasive esophageal squamous neoplasia. Further, the detection of TP53 mutations in esophageal epidermoid metaplasia specimens may serve as an early detection biomarker for high-grade squamous dysplasia/esophageal squamous cell carcinoma.
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Affiliation(s)
- Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
| | | | | | - Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
| | | | - Marcia I Canto
- Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Kevin M McGrath
- Department of Pathology, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
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