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1.
Arch Pathol Lab Med ; 2024 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-38740387

RESUMEN

CONTEXT.­: Title 45, section 164.524 of the Code of Federal Regulations states that health care systems must provide patient health records upon that patient's request. For complex testing, such as next-generation sequencing (NGS), this raises questions related to what data should be released and the laboratory considerations regarding the release of this data. OBJECTIVE.­: To describe the laboratory implications of releasing different NGS data files and the limitations for the clinical use of different NGS data files. DESIGN.­: The College of American Pathologists workgroup, composed of laboratorians with expertise regarding NGS testing, reviewed pertinent literature, including title 45, section 164.524, and the Health and Human Services "Guidance on Individuals' Right to Access Health Information." RESULT.­: From an accreditation standpoint, validation of NGS includes both the wet bench and data processing (bioinformatics) portions, and appropriately validated laboratory testing is required to ensure quality patient results. NGS testing generates intermediate data files that have not completed the fully validated process but are often kept by the laboratory. These files may be requested by patients, but most patients will not be aware of the test validation process and the limitations of data that have not gone through a fully validated process. CONCLUSIONS.­: Laboratories should encourage patients to receive their health data and to help individuals understand the content, uses, and limitations of laboratory data they have requested or received. NGS data used in a nonvalidated manner should not be used for clinical purposes without confirmation by a clinically validated method.

2.
Pathology ; 56(3): 404-412, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38341302

RESUMEN

TP53 mutational status in myeloid neoplasms is prognostic and in acute myeloid leukaemia (AML) may lead to alternative induction therapy; therefore, rapid assessment is necessary for precision treatment. Assessment of multiple prognostic genes by next generation sequencing in AML is standard of care, but the turn-around time often cannot support rapid clinical decision making. Studies in haematological neoplasms suggest p53 immunohistochemistry (IHC) correlates with TP53 mutational status, but they have used variable criteria to define TP53 overexpression. p53 IHC was performed and interpreted on AZF-fixed, acid decalcified bone marrow biopsies on 47 cases of clonal myeloid neoplasms with TP53 mutations between 2016 and 2019 and 16 control samples. Results were scored by manual and digital analysis. Most TP53-mutated cases (81%) overexpressed p53 by digital analysis and manual analysis gave similar results. Among the nine TP53-mutated IHC-negative cases, seven (78%) were truncating mutations and two (22%) were single-hit missense mutations. Using a digital cut-off of at least 3% ≥1+ positive nuclei, the sensitivity and specificity are 81% and 100%; cases with loss-of-function mutations were more likely to be negative. In this cohort, p53 immunopositivity correlated with TP53 mutational status, especially missense mutations, with excellent specificity. Truncating TP53 mutations explain most IHC-negative cases, impacting the sensitivity. We demonstrate that p53 IHC can screen for TP53 mutations allowing quicker treatment decisions for most patients. However, not all patients will be identified, so molecular studies are required. Furthermore, cut-offs for positivity vary in the literature, consequently laboratories should independently validate their processes before adopting p53 IHC for clinical use. p53 IHC performs well to screen for TP53 mutations in AZF-fixed bone marrow. Performance in our setting differs from the literature, which shows variability of pre-analytic factors and cut-offs used to screen for TP53 mutations. Each laboratory should validate p53 IHC to screen for TP53 mutations in their unique setting.


Asunto(s)
Leucemia Mieloide Aguda , Trastornos Mieloproliferativos , Humanos , Proteína p53 Supresora de Tumor/genética , Médula Ósea/patología , Inmunohistoquímica , Mutación , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Biopsia
3.
Prev Med Rep ; 38: 102599, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38292027

RESUMEN

Human papillomavirus (HPV) self-collect shows promise to increase cervical cancer screening rates in underscreened populations, such as Somali patients, but little is known about how to integrate such an approach in primary care. In this study, primary care providers and staff who provide primary care services to Somali women were asked for their views on integrating HPV self-collect into routine care to address cervical cancer screening disparities. Thirty primary care providers and staff participated in semi-structured interviews exploring their views on HPV self-collect and their anticipated needs or barriers to implementing this approach into the clinic generally and with specific patient populations, such as Somali women. A thematic analysis using the constructivist version of grounded theory was undertaken. Providers and staff anticipate positive patient reaction to the option of HPV self-collect, and were interested in using this approach both for Somali patients and for all patients in general. HPV self-collect was viewed as straightforward to integrate into existing clinic workflows. Providers largely lacked awareness of the evidence supporting primary HPV testing and HPV self-collect specifically, sharing concerns about effectiveness of self-collect and the lack of a physical exam. Providers felt clinic-wide staff education and patient education, along with strategies to address disparities, such as cultural and linguistic tailoring would be needed for successful implementation. Integrating HPV self-collect as an option in the cervical cancer screening process in a primary care clinical encounter offers considerable opportunity to address health disparities and may benefit all patients.

4.
Am J Clin Pathol ; 161(4): 380-387, 2024 Apr 03.
Artículo en Inglés | MEDLINE | ID: mdl-38044670

RESUMEN

OBJECTIVES: Novel histopathologic prognostic factors are needed to identify patients with follicular lymphoma (FL) at risk of inferior outcomes. Our primary objective was to evaluate the Ki-67 proliferative index in follicular and interfollicular areas in tissue biopsy specimens from patients with newly diagnosed FL and correlate with clinical outcomes. Our secondary objective was to correlate PD-L1 and LAG-3 with clinical outcomes. METHODS: Seventy cases of low-grade FL from the University of Minnesota were evaluated with Ki-67 immunohistochemical stain. Ki-67 expression as a continuous variable was interpreted digitally and manually in follicular and interfollicular areas. Progression-free survival (PFS) and overall survival (OS) were analyzed by Cox regression, and hazard ratios (HRs) per 10-point increase in Ki-67 were calculated. RESULTS: Progression-free survival at 4 years was 28% (95% CI, 19%-41%). Interfollicular, but not follicular, Ki-67 was associated with PFS by manual (HR, 1.33; P = .01) and digital (HR, 1.38; P = .02) analysis. Digital and manual Ki-67 were only moderately correlated but demonstrated similar effects on PFS. At 4 years, OS was 90% with no association with follicular or interfollicular Ki-67 proliferation. CONCLUSIONS: Higher interfollicular Ki-67 by either digital or manual analysis is associated with a poorer PFS in patients with low-grade FL. These results suggest further validation of this marker is warranted to improve pathologic risk stratification at FL diagnosis. PD-L1 and LAG-3 were not associated with PFS or OS.


Asunto(s)
Linfoma Folicular , Humanos , Linfoma Folicular/diagnóstico , Linfoma Folicular/patología , Supervivencia sin Progresión , Antígeno Ki-67/análisis , Antígeno B7-H1 , Pronóstico , Supervivencia sin Enfermedad
5.
Arch Pathol Lab Med ; 2023 Aug 23.
Artículo en Inglés | MEDLINE | ID: mdl-37610100

RESUMEN

CONTEXT.­: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry settings that developed technologies rooted in principles and products of nature. However, with such technologic developments come many important considerations, including adverse risks, high cost, and ethical questions. OBJECTIVE.­: To educate pathologists about gene editing technologies, inform them of potential indications and risks, outline regulatory and practical issues that could affect hospital-based practice and laboratory testing, and advocate that pathologists need to be present at discussions among industry and regulators pertaining to gene editing-based therapies. DESIGN.­: A Gene Editing Workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop an educational paper to serve as a stimulus to increase pathologist involvement and inquiry in gene editing therapeutic and diagnostic implementation. RESULTS.­: Through multiple discussions and literature review, the workgroup identified potential gaps in pathologists' knowledge of gene editing. Additional topics that could impact pathology and laboratory medicine were also identified and summarized in order to facilitate pathologists as stakeholders in gene editing therapy administration and monitoring and potential use in diagnostics. CONCLUSIONS.­: Gene editing therapy is a complex but potentially transformative area of medicine. This article serves as an introduction to pathologists to assist them in future discussions with colleagues and potentially identify and alter pathology practices that relate to gene editing.

6.
Arch Pathol Lab Med ; 2023 Aug 22.
Artículo en Inglés | MEDLINE | ID: mdl-37603682

RESUMEN

CONTEXT­: Gene editing-based therapies are currently in development in the areas of oncology, inherited disease, and infectious disease. These potentially life-altering therapies are derived from decades of research in both academic and industry settings that developed technologies rooted in principles and products of nature. However, with such technologic developments come many important considerations, including adverse risks, high cost, and ethical questions. OBJECTIVE­: To educate pathologists about gene editing technologies, inform them of potential indications and risks, outline regulatory and practical issues that could affect hospital-based practice and laboratory testing, and advocate that pathologists need to be present at discussions among industry and regulators pertaining to gene editing-based therapies. DESIGN­: A Gene Editing Workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop an educational paper to serve as a stimulus to increase pathologist involvement and inquiry in gene editing therapeutic and diagnostic implementation. RESULTS­: Through multiple discussions and literature review, the workgroup identified potential gaps in pathologists' knowledge of gene editing. Additional topics that could impact pathology and laboratory medicine were also identified and summarized in order to facilitate pathologists as stakeholders in gene editing therapy administration and monitoring and potential use in diagnostics. CONCLUSIONS­: Gene editing therapy is a complex but potentially transformative area of medicine. This article serves as an introduction to pathologists to assist them in future discussions with colleagues and potentially identify and alter pathology practices that relate to gene editing.

7.
Blood Adv ; 7(16): 4599-4607, 2023 08 22.
Artículo en Inglés | MEDLINE | ID: mdl-37236162

RESUMEN

While molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans. Differences in NGS panel size, use, and gene content were reported. Gene content for myeloid processes was reported to be generally excellent, while genes for lymphoid processes were less well covered. The turnaround time (TAT) for acute cases, including acute myeloid leukemia, was reported to range from 2 to 7 calendar days to 15 to 21 calendar days, with different approaches to achieving rapid TAT described. To help guide NGS panel design and standardize gene content, consensus gene lists based on current and future NGS panels in development were generated. Most survey respondents expected molecular testing at academic laboratories to continue to be viable in the future, with rapid TAT for acute cases likely to remain an important factor. Molecular testing reimbursement was reported to be a major concern. The results of this survey and subsequent discussions improve the shared understanding of differences in testing practices for hematologic malignancies between institutions and will help provide a more consistent level of patient care.


Asunto(s)
Objetivos , Neoplasias Hematológicas , Humanos , Neoplasias Hematológicas/diagnóstico , Neoplasias Hematológicas/genética , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos
8.
Arch Pathol Lab Med ; 147(1): 62-70, 2023 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-35472701

RESUMEN

CONTEXT.­: Programmed death ligand-1 (PD-L1) immunohistochemistry companion diagnostic assays play a crucial role as predictive markers in patients being considered for immune checkpoint inhibitor therapy. However, because of a convergence of several factors, including recognition of increased types of cancers susceptible to immunotherapy, increasing numbers of immune checkpoint inhibitors, and release of multiple PD-L1 immunohistochemistry antibodies with differing reporting systems, this complex testing environment has led to significant levels of confusion for pathologists and medical oncologists. OBJECTIVE.­: To identify which processes and procedures have contributed to the current challenges surrounding programmed death receptor-1 (PD-1)/PD-L1 companion diagnostics and to propose potential remedies to this issue. This is based upon input from key industrial stakeholders in conjunction with the College of American Pathologists Personalized Health Care Committee. DESIGN.­: A meeting of representatives of pharmaceutical and in vitro diagnostic companies along with the Personalized Health Care Committee reviewed the process of release of the PD-L1 companion diagnostic assays using a modified root cause analysis format. The modified root cause analysis envisioned an ideal circumstance of development and implementation of a companion diagnostic to identify shortcomings in the rollout of the PD-L1 assay and to suggest actions to improve future companion diagnostic assay releases. RESULTS.­: The group recommended improvements to key principles in companion diagnostics implementation related to multi-stakeholder communication, increased regulatory flexibility to incorporate postapproval medical knowledge, improved cross-disciplinary information exchange between medical oncology and pathology societies, and enhanced postmarket training programs. CONCLUSIONS.­: The rapidly changing nature of and increasing complexity associated with companion diagnostics require a fundamental review of processes related to their design, implementation, and oversight.


Asunto(s)
Antígeno B7-H1 , Neoplasias , Humanos , Neoplasias/diagnóstico , Inmunohistoquímica , Inmunoterapia/métodos
9.
Arch Pathol Lab Med ; 147(8): 872-884, 2023 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-36508682

RESUMEN

CONTEXT.­: Neurotrophic receptor tyrosine kinase (NTRK) fusion testing has both diagnostic and therapeutic implications for patient care. With 2 tumor-agnostic US Food and Drug Administration-approved tropomyosin receptor kinase (TRK) inhibitors, testing is increasingly used for therapeutic decision making. However, the testing landscape for NTRK fusions is complex, and optimal testing depends on the clinicopathologic scenario. OBJECTIVE.­: To compare different NTRK testing methods to help pathologists understand test features and performance characteristics and make appropriate selections for NTRK fusion detection for their laboratory and individual patient specimens. DATA SOURCES.­: A literature search for NTRK gene fusions and TRK protein was performed, including papers that discussed treatment, testing methodology, and detection or prevalence of fusion-positive cases. CONCLUSIONS.­: As standard of care in some tumor types, next-generation sequencing (NGS) panel testing is a cost effective and reliable way to detect a broad range of NTRK fusions. The design of the panel and use of DNA or RNA will affect performance characteristics. Pan-TRK immunohistochemistry may be used as a rapid, less expensive screen in cases that will not undergo routine NGS testing, or on specimens unsuitable for NGS testing. Fluorescence in situ hybridization may be appropriate for low-tumor-content specimens that are unsuitable for NGS testing. Quantitative reverse transcription polymerase chain reaction is best suited for monitoring low-level disease of a specific, previously identified target. This information should help laboratories develop a laboratory-specific NTRK testing algorithm that best suits their practice setting and patients' needs.


Asunto(s)
Neoplasias , Receptor trkA , Humanos , Receptor trkA/genética , Receptor trkC/genética , Hibridación Fluorescente in Situ , Laboratorios , Neoplasias/diagnóstico , Neoplasias/genética , Neoplasias/tratamiento farmacológico , Proteínas de Fusión Oncogénica/genética
10.
JCO Precis Oncol ; 6: e2200454, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36446042

RESUMEN

PURPOSE: Immune checkpoint inhibition (ICI) therapy represents one of the great advances in the field of oncology, highlighted by the Nobel Prize in 2018. Multiple predictive biomarkers for ICI benefit have been proposed. These include assessment of programmed death ligand-1 expression by immunohistochemistry, and determination of mutational genotype (microsatellite instability or mismatch repair deficiency or tumor mutational burden) as a reflection of neoantigen expression. However, deployment of these assays has been challenging for oncologists and pathologists alike. METHODS: To address these issues, ASCO and the College of American Pathologists convened a virtual Predictive Factor Summit from September 14 to 15, 2021. Representatives from the academic community, US Food and Drug Administration, Centers for Medicare and Medicaid Services, National Institutes of Health, health insurance organizations, pharmaceutical companies, in vitro diagnostics manufacturers, and patient advocate organizations presented state-of-the-art predictive factors for ICI, associated problems, and possible solutions. RESULTS: The Summit provided an overview of the challenges and opportunities for improvement in assay execution, interpretation, and clinical applications of programmed death ligand-1, microsatellite instability-high or mismatch repair deficient, and tumor mutational burden-high for ICI therapies, as well as issues related to regulation, reimbursement, and next-generation ICI biomarker development. CONCLUSION: The Summit concluded with a plan to generate a joint ASCO/College of American Pathologists strategy for consideration of future research in each of these areas to improve tumor biomarker tests for ICI therapy.


Asunto(s)
Inhibidores de Puntos de Control Inmunológico , Neoplasias , Anciano , Estados Unidos , Humanos , Inhibidores de Puntos de Control Inmunológico/farmacología , Inestabilidad de Microsatélites , Patólogos , Medicare , Biomarcadores de Tumor/genética , Neoplasias/diagnóstico
11.
Blood Cells Mol Dis ; 93: 102636, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-34864445

RESUMEN

Vacuoles, E1, X-linked, autoimmunity, somatic (VEXAS) syndrome is characterized by a pathogenic mutation in UBA1, which leads to protean complications including autoimmunity and myelodysplasia. A 56-year-old man with steroid-dependent, later steroid-refractory cutaneous polyarteritis nodosa and Sweet syndrome developed recurrent daily fever, macrocytic anemia, thrombocytopenia, acute hypoxic respiratory failure, and anasarca. He was eventually diagnosed with Epstein-Barr virus (EBV) viremia and hemophagocytic lymphohistiocytosis (HLH). He improved clinically with rituximab, ruxolitinib, and increased glucocorticoids before expiring from Pseudomonas sepsis. UBA1 exon 3 mutational analysis in myeloid enriched peripheral blood revealed a c.122T>C (p.Met41Thr) pathogenic variant, consistent with VEXAS syndrome. We describe the first case of EBV-associated HLH in a patient diagnosed with VEXAS syndrome. Early identification of this syndrome will be important in order to offer potential therapies before life-threatening complications arise.


Asunto(s)
Infecciones por Virus de Epstein-Barr , Linfohistiocitosis Hemofagocítica , Síndromes Mielodisplásicos , Infecciones por Virus de Epstein-Barr/complicaciones , Infecciones por Virus de Epstein-Barr/tratamiento farmacológico , Herpesvirus Humano 4 , Humanos , Linfohistiocitosis Hemofagocítica/complicaciones , Linfohistiocitosis Hemofagocítica/diagnóstico , Linfohistiocitosis Hemofagocítica/tratamiento farmacológico , Masculino , Persona de Mediana Edad , Rituximab
12.
Arch Pathol Lab Med ; 146(1): 70-77, 2022 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-33769456

RESUMEN

CONTEXT.­: Next-generation sequencing is a powerful clinical tool for cancer management but can produce incidental/secondary findings that require special consideration. OBJECTIVE.­: To discuss clinical and laboratory issues related to incidental or secondary germline findings in the clinical setting of tumor testing and inform future guidelines in this area. DESIGN.­: A College of American Pathologists workgroup including representation from the American Society of Clinical Oncology, the Association for Molecular Pathology, and the American College of Medical Genetics and Genomics created a review of items that should be considered when developing guidelines for incidental or secondary findings when performing clinical tumor testing. RESULTS.­: Testing recommendations should be cognizant of the differences among anticipated incidental, unanticipated incidental, and secondary findings, and whether normal tissue is also tested. In addition to defining which variants will be reported, robust recommendations must also take into account test design and validation, reimbursement, cost, infrastructure, impact on reflex testing, and maintenance of proficiency. Care providers need to consider the potential of a test to uncover incidental or secondary findings, the recommendation of upfront counseling, the need for consent, the timing of testing and counseling, and that the exact significance of a finding may not be clear. CONCLUSIONS.­: As clinical oncology testing panels have become a mainstay of clinical cancer care, guidelines addressing the unique aspects of incidental and secondary findings in oncology testing are needed. This paper highlights clinical and laboratory considerations with regard to incidental/secondary findings and is a clarion call to create recommendations.


Asunto(s)
Laboratorios , Neoplasias , Pruebas Genéticas , Células Germinativas , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Hallazgos Incidentales , Oncología Médica , Neoplasias/diagnóstico , Neoplasias/genética
14.
Front Genet ; 12: 712602, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34745204

RESUMEN

Pharmacogenomics (PGx) studies how a person's genes affect the response to medications and is quickly becoming a significant part of precision medicine. The clinical application of PGx principles has consistently been cited as a major opportunity for improving therapeutic outcomes. Several recent studies have demonstrated that most individuals (> 90%) harbor PGx variants that would be clinically actionable if prescribed a medication relevant to that gene. In multiple well-conducted studies, the results of PGx testing have been shown to guide therapy choice and dosing modifications which improve treatment efficacy and reduce the incidence of adverse drug reactions (ADRs). Although the value of PGx testing is evident, its successful implementation in a clinical setting presents a number of challenges to molecular diagnostic laboratories, healthcare systems, providers and patients. Different molecular methods can be applied to identify PGx variants and the design of the assay is therefore extremely important. Once the genotyping results are available the biggest technical challenge lies in turning this complex genetic information into phenotypes and actionable recommendations that a busy clinician can effectively utilize to provide better medical care, in a cost-effective, efficient and reliable manner. In this paper we describe a successful and highly collaborative implementation of the PGx testing program at the University of Minnesota and MHealth Fairview Molecular Diagnostic Laboratory and selected Pharmacies and Clinics. We offer detailed descriptions of the necessary components of the pharmacogenomic testing implementation, the development and technical validation of the in-house SNP based multiplex PCR based assay targeting 20 genes and 48 SNPs as well as a separate CYP2D6 copy number assay along with the process of PGx report design, results of the provider and pharmacists usability studies, and the development of the software tool for genotype-phenotype translation and gene-phenotype-drug CPIC-based recommendations. Finally, we outline the process of developing the clinical workflow that connects the providers with the PGx experts within the Molecular Diagnostic Laboratory and the Pharmacy.

15.
Microbiol Spectr ; 9(1): e0008621, 2021 09 03.
Artículo en Inglés | MEDLINE | ID: mdl-34259552

RESUMEN

Although nasopharyngeal samples have been considered the gold standard for COVID-19 testing, variability in viral load across different anatomical sites could cause nasopharyngeal samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples have logistical advantages over nasopharyngeal samples, making them amenable to population-scale screening. To evaluate sampling alternatives for population screening, we collected nasopharyngeal, saliva, and nasal samples from two cohorts with varied levels and types of symptoms. In a mixed cohort of 60 symptomatic and asymptomatic participants, we found that saliva had 88% concordance with nasopharyngeal samples when tested in the same testing lab (n = 41) and 68% concordance when tested in different testing labs (n = 19). In a second cohort of 20 participants hospitalized for COVID-19, saliva had 74% concordance with nasopharyngeal samples tested in the same testing lab but detected virus in two participants that tested negative with nasopharyngeal samples on the same day. Medical record review showed that the saliva-based testing sensitivity was related to the timing of symptom onset and disease stage. We find that no sample site will be perfectly sensitive for COVID-19 testing in all situations, and the significance of negative results will always need to be determined in the context of clinical signs and symptoms. Saliva retained high clinical sensitivity for early-stage and presymptomatic COVID-19 while allowing easier collection, minimizing the exposure of health care workers, and need for personal protective equipment and making it a viable option for population-scale testing. IMPORTANCE Methods for COVID-19 detection are necessary for public health efforts to monitor the spread of disease. Nasopharyngeal samples have been considered the best approach for COVID-19 testing. However, alternative samples like self-collected saliva offer advantages for population-scale screening. Meta-analyses of recent studies suggest that saliva is useful for detecting SARS-CoV-2; however, differences in disease prevalence, sample collection, and analysis methods still confound strong conclusions on the utility of saliva compared to nasopharyngeal samples. Here, we find that the sensitivity of saliva testing is related to both the timing of the sample collection relative to symptom onset and the disease stage. Importantly, several clinical vignettes in our cohorts highlight the challenges of medical decision making with limited knowledge of the associations between laboratory test data and the natural biology of infection.


Asunto(s)
Prueba de COVID-19/métodos , COVID-19/diagnóstico , SARS-CoV-2/aislamiento & purificación , Saliva/virología , Adulto , Anciano , Anciano de 80 o más Años , Enfermedades Asintomáticas , COVID-19/virología , Estudios de Cohortes , Pruebas Diagnósticas de Rutina/instrumentación , Pruebas Diagnósticas de Rutina/métodos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Nasofaringe/virología , SARS-CoV-2/genética , Adulto Joven
16.
J Mol Diagn ; 23(9): 1085-1096, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34116245

RESUMEN

Widespread high-throughput testing for identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by RT-PCR has been a foundation in the response to the coronavirus disease 2019 (COVID-19) pandemic. Quality assurance metrics for these RT-PCR tests are still evolving as testing is widely implemented. As testing increases, it is important to understand performance characteristics and the errors associated with these tests. Herein, we investigate a high-throughput, laboratory-developed SARS-CoV-2 RT-PCR assay to determine whether modeling can generate quality control metrics that identify false-positive (FP) results due to contamination. This study reviewed repeated clinical samples focusing on positive samples that test negative on re-extraction and PCR, likely representing false positives. To identify and predict false-positive samples, we constructed machine learning-derived models based on the extraction method used. These models identified variables associated with false-positive results across all methods, with sensitivities for predicting FP results ranging between 67% and 100%. Application of the models to all results predicted a total FP rate of 0.08% across all samples, or 2.3% of positive results, similar to reports for other RT-PCR tests for RNA viruses. These models can predict quality control parameters, enabling laboratories to generate decision trees that reduce interpretation errors, allow for automated reflex testing of samples with a high FP probability, improve workflow efficiency, and increase diagnostic accuracy for patient care.


Asunto(s)
Prueba de Ácido Nucleico para COVID-19/métodos , ARN Viral/aislamiento & purificación , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Automatización de Laboratorios , Portador Sano/virología , Sistemas de Apoyo a Decisiones Clínicas , Reacciones Falso Positivas , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Aprendizaje Automático , SARS-CoV-2/genética , Carga Viral , Flujo de Trabajo
18.
Artículo en Inglés | MEDLINE | ID: mdl-33832922

RESUMEN

Somatic mutations in hotspot regions of the cytosolic or mitochondrial isoforms of the isocitrate dehydrogenase gene (IDH1 and IDH2, respectively) contribute to the pathogenesis of acute myeloid leukemia (AML) by producing the oncometabolite 2-hydroxyglutarate (2-HG). The allosteric IDH1 inhibitor, ivosidenib, suppresses 2-HG production and induces clinical responses in relapsed/refractory IDH1-mutant AML. Herein, we describe a clinical case of AML in which we detected the neomorphic IDH1 p.R132C mutation in consecutive patient samples with a mutational hotspot targeted next-generation sequencing (NGS) assay. The patient had a clinical response to ivosidenib, followed by relapse and disease progression. Subsequent sequencing of the relapsed sample using a newly developed all-exon, hybrid-capture-based NGS panel identified an additional IDH1 p.S280F mutation known to cause renewed 2-HG production and drug resistance. Structural modeling confirmed that serine-to-phenylalanine substitution at this codon sterically hinders ivosidenib from binding to the mutant IDH1 dimer interface and predicted a similar effect on the pan-IDH inhibitor AG-881. Joint full-exon NGS and structural modeling enables monitoring IDH1 inhibitor-treated AML patients for acquired drug resistance and choosing follow-up therapy.


Asunto(s)
Resistencia a Antineoplásicos/genética , Inhibidores Enzimáticos/farmacología , Exones , Isocitrato Deshidrogenasa/efectos de los fármacos , Isocitrato Deshidrogenasa/genética , Leucemia Mieloide Aguda/genética , Anciano , Sitios de Unión , Inhibidores Enzimáticos/química , Femenino , Predisposición Genética a la Enfermedad/genética , Glicina/análogos & derivados , Glicina/uso terapéutico , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Isocitrato Deshidrogenasa/química , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/patología , Mutación , Piridinas , Recurrencia
20.
Arch Pathol Lab Med ; 145(6): 704-716, 2021 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-33237994

RESUMEN

CONTEXT.­: Chimeric antigen receptor T-cell (CAR-T) technology has shown great promise in both clinical and preclinical models in mediating potent and specific antitumor activity. With the advent of US Food and Drug Administration-approved CAR-T therapies for B-cell lymphoblastic leukemia and B-cell non-Hodgkin lymphomas, CAR-T therapy is poised to become part of mainstream clinical practice. OBJECTIVE.­: To educate pathologists on CAR-T and chimeric antigen receptor-derived cellular therapy, provide a better understanding of their role in this process, explain important regulatory aspects of CAR-T therapy, and advocate for pathologist involvement in the delivery and monitoring of chimeric antigen receptor-based treatments. Much of the focus of this article addresses US Food and Drug Administration-approved therapies; however, more general issues and future perspectives are considered for therapies in development. DESIGN.­: A CAR-T workgroup, facilitated by the College of American Pathologists Personalized Health Care Committee and consisting of pathologists of various backgrounds, was convened to develop a summary guidance paper for the College of American Pathologists Council on Scientific Affairs. RESULTS.­: The workgroup identified gaps in pathologists' knowledge of CAR-T therapy, including uncertainty in the role of the clinical laboratory in supporting CAR-T therapy. The workgroup considered these issues and summarized the findings to assist pathologists to become stakeholders in CAR-T therapy administration. CONCLUSIONS.­: This manuscript serves to both educate pathologists on CAR-T therapy and serve as a point of initial discussions in areas of CAR-T science, clinical therapy, and regulatory issues as CAR-T therapies continue to be introduced into clinical practice.


Asunto(s)
Inmunoterapia Adoptiva/métodos , Linfoma de Células B/terapia , Leucemia-Linfoma Linfoblástico de Células Precursoras/terapia , Receptores de Antígenos de Linfocitos T/inmunología , Receptores Quiméricos de Antígenos/inmunología , Linfocitos T/inmunología , Educación Médica Continua/métodos , Humanos , Linfoma de Células B/inmunología , Patólogos/educación , Leucemia-Linfoma Linfoblástico de Células Precursoras/inmunología , Linfocitos T/metabolismo , Estados Unidos , United States Food and Drug Administration
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