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Hirschhorn JW, Sasaki MM, Kegl A, Akter T, Dickerson T, Narlieva M, Nhan N, Liu T, Jim P, Young S, Orner E, Thwe P, Lucic D, Goldstein DY. Performance evaluation of the high-throughput quantitative Alinity m BK virus assay. J Clin Microbiol 2024; 62:e0135423. [PMID: 38526061 PMCID: PMC11005350 DOI: 10.1128/jcm.01354-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
BK virus (BKV) infection or reactivation in immunocompromised individuals can lead to adverse health consequences including BKV-associated nephropathy (BKVAN) in kidney transplant patients and BKV-associated hemorrhagic cystitis (BKV-HC) in allogeneic hematopoietic stem cell transplant recipients. Monitoring BKV viral load plays an important role in post-transplant patient care. This study evaluates the performance of the Alinity m BKV Investigational Use Only (IUO) assay. The linearity of the Alinity m BKV IUO assay had a correlation coefficient of 1.000 and precision of SD ≤ 0.25 Log IU/mL for all panel members tested (2.0-7.3 Log IU/mL). Detection rate at 50 IU/mL was 100%. Clinical plasma specimens tested comparing Alinity m BKV IUO to ELITech MGB Alert BKV lab-developed test (LDT) on the Abbott m2000 platform using specimen extraction protocols for DNA or total nucleic acid (TNA) resulted in coefficient of correlation of 0.900 and 0.963, respectively, and mean bias of 0.03 and -0.54 Log IU/mL, respectively. Alinity m BKV IUO compared with Altona RealStar BKV and Roche cobas BKV assays demonstrated coefficient of correlation of 0.941 and 0.980, respectively, and mean bias of -0.47 and -0.31 Log IU/mL, respectively. Urine specimens tested on Alintiy m BKV IUO and ELITech BKV LDT using TNA specimen extraction had a coefficient of correlation of 0.917 and mean bias of 0.29 Log IU/mL. The Alinity m BKV IUO assay was performed with high precision across the dynamic range and correlated well with other available BKV assays. IMPORTANCE BK virus (BKV) in transplant patients can lead to adverse health consequences. Viral load monitoring is important in post-transplant patient care. This study evaluates the Alinity m BKV assay with currently available assays.
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Affiliation(s)
- Julie W. Hirschhorn
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Mark M. Sasaki
- Molecular Diagnostics of Abbott, Des Plaines, Illinois, USA
| | - April Kegl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tanjina Akter
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tanisha Dickerson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Momka Narlieva
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Nhi Nhan
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Tianxi Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Patricia Jim
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Stephen Young
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Erika Orner
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Phyu Thwe
- Department of Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Danijela Lucic
- Molecular Diagnostics of Abbott, Des Plaines, Illinois, USA
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2
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Krishnamurthy K, Chai J, Wang Y, Naeem R, Goldstein DY. Pitfalls of using polymerase chain reaction-based assays for JAK2 and CALR exon 9 variant testing in myeloproliferative neoplasms: Knowing when to go the extra mile! Am J Clin Pathol 2024; 161:155-161. [PMID: 37788380 DOI: 10.1093/ajcp/aqad122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023] Open
Abstract
OBJECTIVES The BCR::ABL1 negative myeloproliferative neoplasms are sequentially tested for JAK2 p.V617F, followed by CALR exon 9 pathogenic variants. Historically, these variants were thought to be mutually exclusive. However, recent reports indicate coexisting JAK2 p.V617F and CALR exon 9 somatic variants. METHODS Analysis of JAK2 p.V617F and CALR exon 9 variant was performed by polymerase chain reaction (PCR)-based assays. Subsequent testing was performed on the Genexus integrated sequencer (ThermoFisher) using the Oncomine myeloid assay GX v2. RESULTS CALR exon 9 variants were positive in 3 cases, while 2 were positive for JAK2 p.V617F on PCR-based assays. Next-generation sequencing confirmed the JAK2 P.V617F status in all cases. CALR variants resulting in in-frame deletions were identified in 2 cases at a variant allele frequency of 52.16% and 50.91%, while the third case had an intronic CALR variant c.-48G>A at a variant allele frequency of 51.1%. Thus, CALR variants in all 3 cases were interpreted as potentially germline. Of the 228 cases that underwent JAK2 p.V617F and CALR cotesting in the past 2 years, only these 2 cases were positive for both JAK2 p.V617F and CALR exon 9 variants. CONCLUSIONS These cases highlight the importance of understanding the pitfalls of molecular techniques in current practice.
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Affiliation(s)
| | - Jiani Chai
- Department of Pathology, Montefiore Medical Center, Bronx, NY, US
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center, Bronx, NY, US
- Albert Einstein College of Medicine, Bronx, NY, US
| | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center, Bronx, NY, US
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, NY, US
- Albert Einstein College of Medicine, Bronx, NY, US
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Kroll MH, Bi C, Salm AE, Szymanski J, Goldstein DY, Wolgast LR, Rosenblatt G, Fox AS, Kapoor H. Risk Estimation of Severe COVID-19 Based on Initial Biomarker Assessment Across Racial and Ethnic Groups. Arch Pathol Lab Med 2023; 147:1109-1118. [PMID: 37338199 DOI: 10.5858/arpa.2023-0039-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
CONTEXT.— Disease courses in COVID-19 patients vary widely. Prediction of disease severity on initial diagnosis would aid appropriate therapy, but few studies include data from initial diagnosis. OBJECTIVE.— To develop predictive models of COVID-19 severity based on demographic, clinical, and laboratory data collected at initial patient contact after diagnosis of COVID-19. DESIGN.— We studied demographic data and clinical laboratory biomarkers at time of diagnosis, using backward logistic regression modeling to determine severe and mild outcomes. We used deidentified data from 14 147 patients who were diagnosed with COVID-19 by polymerase chain reaction SARS-CoV-2 testing at Montefiore Health System, from March 2020 to September 2021. We generated models predicting severe disease (death or more than 90 hospital days) versus mild disease (alive and fewer than 2 hospital days), starting with 58 variables, by backward stepwise logistic regression. RESULTS.— Of the 14 147 patients, including Whites, Blacks, and Hispanics, 2546 (18%) patients had severe outcomes and 3395 (24%) had mild outcomes. The final number of patients per model varied from 445 to 755 because not all patients had all available variables. Four models (inclusive, receiver operating characteristic, specific, and sensitive) were identified as proficient in predicting patient outcomes. The parameters that remained in all models were age, albumin, diastolic blood pressure, ferritin, lactic dehydrogenase, socioeconomic status, procalcitonin, B-type natriuretic peptide, and platelet count. CONCLUSIONS.— These findings suggest that the biomarkers found within the specific and sensitive models would be most useful to health care providers on their initial severity evaluation of COVID-19.
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Affiliation(s)
- Martin H Kroll
- From the Department of Medical Operations and Quality (Kroll), Quest Diagnostics, Secaucus, New Jersey
| | - Caixia Bi
- Department of Corporate Medical (Bi), Quest Diagnostics, Secaucus, New Jersey
| | - Ann E Salm
- Department of Infectious Diseases/Immunology (Salm, Kapoor), Quest Diagnostics, Secaucus, New Jersey
| | - James Szymanski
- Department of Pathology, Montefiore Medical Center, Bronx, New York (Szymanski, Goldstein, Wolgast, Fox)
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, New York (Szymanski, Goldstein, Wolgast, Fox)
| | - Lucia R Wolgast
- Department of Pathology, Montefiore Medical Center, Bronx, New York (Szymanski, Goldstein, Wolgast, Fox)
| | - Gregory Rosenblatt
- The Department of Pathology, Albert Einstein College of Medicine, Bronx, New York (Rosenblatt). Kapoor is currently located at HK Healthcare Consultant LLC in Davie, Florida
| | - Amy S Fox
- Department of Pathology, Montefiore Medical Center, Bronx, New York (Szymanski, Goldstein, Wolgast, Fox)
| | - Hema Kapoor
- Department of Infectious Diseases/Immunology (Salm, Kapoor), Quest Diagnostics, Secaucus, New Jersey
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4
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Menezes ME, Silver EJ, Goldstein DY, Collins-Ogle MD, Fox AS, Coupey SM. Prevalence and Factors Associated With Mycoplasma genitalium Infection in At-Risk Female Adolescents in Bronx County, New York. Sex Transm Dis 2023; 50:635-641. [PMID: 37255234 DOI: 10.1097/olq.0000000000001840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Mycoplasma genitalium infection can adversely affect female reproductive health, but data are limited about prevalence and characteristics of the infection in female adolescents. We employed a sensitive assay to detect M. genitalium infection, and we describe its characteristics in a clinical sample of women younger than 21 years. METHODS We recruited females aged 13 to 20 years in children's hospital clinics whose clinicians were testing for chlamydia/gonorrhea. Participants completed a questionnaire providing demographics, sexual history, and current symptoms. Urine/endocervical samples were tested for chlamydia/gonorrhea and partitioned for M. genitalium testing using Aptima M. genitalium assay. We reviewed records for the clinic visit to document examination, diagnosis, and results of sexually transmitted infection (STI) testing. We compared prevalence of M. genitalium infection by demographics, sexual history, symptoms, and signs. RESULTS Of 153 participants mean age 18.07 ± 1.68 years, 58% self-identified as Hispanic, 27% Black, 64% straight/heterosexual, 27% bisexual, 1% gay/lesbian, 29% reported a prior STI diagnosis. Prevalence of M. genitalium was 11.1% (17/153), 13 of 17 were asymptomatic, 2 of 17 had pelvic inflammatory disease (PID), 3 of 17 coinfected with chlamydia or gonorrhea. Prevalence of chlamydia was 6.6% and of gonorrhea 2.6%. A logistic regression model indicated independent associations of bisexual orientation versus all other orientations (adjusted odds ratio [aOR], 4.80; 95% confidence interval [CI], 1.38-16.67), self-reported prior STI (aOR, 3.83; 95% CI, 1.10-13.37), and self-reported prior PID (aOR, 9.12; 95% CI, 1.02-81.72) with higher odds of M. genitalium infection. CONCLUSIONS Findings suggest that in at-risk female populations younger than 21 years, M. genitalium is a prevalent STI and symptomatic adolescents may warrant testing and treatment. Further study of harms and benefits of testing asymptomatic bisexual female adolescents or those with prior STI/PID is needed.
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Fels JM, Khan S, Forster R, Skalina KA, Sirichand S, Fox AS, Bergman A, Mitchell WB, Wolgast LR, Szymczak WA, Bortz RH, Dieterle ME, Florez C, Haslwanter D, Jangra RK, Laudermilch E, Wirchnianski AS, Barnhill J, Goldman DL, Khine H, Goldstein DY, Daily JP, Chandran K, Kelly L. Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006211. [PMID: 35831070 PMCID: PMC9528964 DOI: 10.1101/mcs.a006211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/24/2022] [Indexed: 11/24/2022] Open
Abstract
The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.
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Affiliation(s)
| | | | | | - Karin A Skalina
- Montefiore Medical Center/Albert Einstein College of Medicine
| | | | - Amy S Fox
- Montefiore Medical Center/Albert Einstein College of Medicine
| | | | | | - Lucia R Wolgast
- Montefiore Medical Center/Albert Einstein College of Medicine
| | | | | | | | - Catalina Florez
- Albert Einstein College of Medicine and United States Military Academy at West Point
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6
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Bijur PE, Friedman BW, Baron SW, Ramasahayam A, Nerenberg R, Sharpe S, Goldstein DY, Esses D. Should COVID-19 symptoms be used to cohort patients in the emergency department? A retrospective analysis. Am J Emerg Med 2022; 54:274-278. [PMID: 35220142 PMCID: PMC8818126 DOI: 10.1016/j.ajem.2022.01.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022] Open
Abstract
Objective Methods Results Conclusion
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Affiliation(s)
- Polly E Bijur
- Albert Einstein College of Medicine, Department of Emergency Medicine, Rose F. Kennedy Center, 1410 Pelham Parkway South, Bronx, NY 10461, USA.
| | - Benjamin W Friedman
- Montefiore Medical Center, Department of Emergency Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
| | - Sarah W Baron
- Montefiore Medical Center, Department of Medicine, Division of Hospital Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
| | - Abhiram Ramasahayam
- Montefiore Medical Center, Department of Emergency Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
| | - Rebecca Nerenberg
- Montefiore Medical Center, Department of Emergency Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
| | - Shellyann Sharpe
- Jacobi Medical Center, 1400 Pelham Parkway South, Bronx, NY 10461, USA.
| | - D Yitzchak Goldstein
- Montefiore Medical Center, Department of Emergency Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
| | - David Esses
- Montefiore Medical Center, Department of Emergency Medicine, 111 East 210(th) Street, Bronx, NY 10467, USA.
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7
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Lee E, Goldstein DY, Naeem R. Identifying unnecessary duplicate genetic testing in a large medical center. Am J Clin Pathol 2021. [DOI: 10.1093/ajcp/aqab189.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Introduction
Genetic testing has become ubiquitous in clinical medicine and plays an important role in making diagnoses and guiding treatment plans. Indiscriminate use of these tests can cause duplicate testing, which is typically not indicated because results from repeated constitutional molecular genetic testing should not change over time. Thus, duplicate genetic testing often represents inappropriate test utilization that can contribute an unnecessary burden on the laboratory and health care system.
Objective
The purpose of our study is to determine the incidence of duplicate testing of in-house genetic testing offered at a large medical center, which includes cystic fibrosis, factor V Leiden, prothrombin G20210A, methylenetetrahydrofolate reductase (MTHFR) C677T, and MTHFR A1298C, and to develop a tool to identify and block duplicate testing.
Methods
We retrospectively analyzed internal laboratory databases of all cystic fibrosis (n = 36164), factor V Leiden (n = 3264), prothrombin G20210A (n = 2890), MTHFR C667T (n = 1451), and MTHFR A1293C (n = 1290) testing performed at the molecular pathology laboratory at a large medical center from either January 2010 or January 2014 to July 2019. We analyzed and cleaned the databases with the R programming language, and we developed a prototype web-based app to proactively identify duplicate test requests with the Shiny R package.
Results
From January 2010 to July 2019, 3535 (9.8%) of the 36164 cystic fibrosis tests performed were duplicate tests for 3257 unique patients. Of these duplicate cystic fibrosis tests, 2997 were repeated once in the same patient, 244 were repeated twice in the same patient, 14 were repeated three times in the same patient, and 2 were repeated four times in the same patient. From January 2014 to July 2019, 99 (3.0%) of the 3264 factor V Leiden tests, 86 (3.0%) of the 2890 prothrombin G20210A tests, 49 (3.4%) of the 1451 MTHFR C667T, and 46 (3.6%) of the 1290 MTHFR A1298C tests performed were duplicate tests.
We developed a proof-of-concept Shiny web-browser app that provides a user-friendly interface to determine if a patient has been previously tested in the molecular pathology lab. This app operates locally on a laboratory computer and uses spreadsheets automatically exported from the electronic medical record. These features allow for the app to be deployed quickly without needing to be integrated into the electronic medical record.
Conclusions
The results of this study indicate that unnecessary duplicate testing represents a small but significant proportion of genetic testing performed by the molecular pathology laboratory. Duplicate testing occurred more frequently with cystic fibrosis testing, which reflects its high volume at the medical center. Deployment of web-based apps using Shiny can provide straightforward and efficient tools for reducing duplicate tests.
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Affiliation(s)
| | | | - Rizwan Naeem
- Yale School of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine
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8
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Chekuri S, Szymczak WA, Goldstein DY, Nori P, Marrero Rolon R, Spund B, Singh-Tan S, Mohrmann L, Assa A, Southern WN, Baron SW. SARS-CoV-2 coinfection with additional respiratory virus does not predict severe disease: a retrospective cohort study. J Antimicrob Chemother 2021; 76:iii12-iii19. [PMID: 34555160 PMCID: PMC8460099 DOI: 10.1093/jac/dkab244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) claimed over 4 million lives by July 2021 and continues to pose a serious public health threat. Objectives Our retrospective study utilized respiratory pathogen panel (RPP) results in patients with SARS-CoV-2 to determine if coinfection (i.e. SARS-CoV-2 positivity with an additional respiratory virus) was associated with more severe presentation and outcomes. Methods All patients with negative influenza/respiratory syncytial virus testing who underwent RPP testing within 7 days of a positive SARS-CoV-2 test at a large, academic medical centre in New York were examined. Patients positive for SARS-CoV-2 with a negative RPP were compared with patients positive for SARS-CoV-2 and positive for a virus by RPP in terms of biomarkers, oxygen requirements and severe COVID-19 outcome, as defined by mechanical ventilation or death within 30 days. Results Of the 306 SARS-CoV-2-positive patients with RPP testing, 14 (4.6%) were positive for a non-influenza virus (coinfected). Compared with the coinfected group, patients positive for SARS-CoV-2 with a negative RPP had higher inflammatory markers and were significantly more likely to be admitted (P = 0.01). Severe COVID-19 outcome occurred in 111 (36.3%) patients in the SARS-CoV-2-only group and 3 (21.4%) patients in the coinfected group (P = 0.24). Conclusions Patients infected with SARS-CoV-2 along with a non-influenza respiratory virus had less severe disease on presentation and were more likely to be admitted—but did not have more severe outcomes—than those infected with SARS-CoV-2 alone.
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Affiliation(s)
- Sweta Chekuri
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Wendy A Szymczak
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - D Yitzchak Goldstein
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Priya Nori
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Infectious Disease, Montefiore Medical Center, Bronx, NY, USA
| | - Rebecca Marrero Rolon
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Brian Spund
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sumeet Singh-Tan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Laurel Mohrmann
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Andrei Assa
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - William N Southern
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sarah W Baron
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
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9
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Malik P, Asiry S, Goldstein DY, Khader SN. Educational Case: Diagnostic Approach to Salivary Gland Neoplasms. Acad Pathol 2021; 8:23742895211015342. [PMID: 34104713 PMCID: PMC8155761 DOI: 10.1177/23742895211015342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 04/06/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology
Competencies for Medical Education (PCME), a set of national standards for teaching
pathology. These are divided into three basic competencies: Disease Mechanisms and
Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology.
For additional information, and a full list of learning objectives for all three
competencies, seehttp://journals.sagepub.com/doi/10.1177/2374289517715040. 1
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Affiliation(s)
- Preeti Malik
- Division of Pediatrics, The Children's Hospital at Montefiore, NY, USA
| | - Saeed Asiry
- Department of Pathology, Albert Einstein College of Medicine, NY, USA
| | | | - Samer N Khader
- Department of Pathology, Albert Einstein College of Medicine, NY, USA
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10
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Bortz RH, Florez C, Laudermilch E, Wirchnianski AS, Lasso G, Malonis RJ, Georgiev GI, Vergnolle O, Herrera NG, Morano NC, Campbell ST, Orner EP, Mengotto A, Dieterle ME, Fels JM, Haslwanter D, Jangra RK, Celikgil A, Kimmel D, Lee JH, Mariano MC, Nakouzi A, Quiroz J, Rivera J, Szymczak WA, Tong K, Barnhill J, Forsell MNE, Ahlm C, Stein DT, Pirofski LA, Goldstein DY, Garforth SJ, Almo SC, Daily JP, Prystowsky MB, Faix JD, Fox AS, Weiss LM, Lai JR, Chandran K. Single-Dilution COVID-19 Antibody Test with Qualitative and Quantitative Readouts. mSphere 2021; 6:e00224-21. [PMID: 33883259 PMCID: PMC8546701 DOI: 10.1128/msphere.00224-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to place an immense burden on societies and health care systems. A key component of COVID-19 control efforts is serological testing to determine the community prevalence of SARS-CoV-2 exposure and quantify individual immune responses to prior SARS-CoV-2 infection or vaccination. Here, we describe a laboratory-developed antibody test that uses readily available research-grade reagents to detect SARS-CoV-2 exposure in patient blood samples with high sensitivity and specificity. We further show that this sensitive test affords the estimation of viral spike-specific IgG titers from a single sample measurement, thereby providing a simple and scalable method to measure the strength of an individual's immune response. The accuracy, adaptability, and cost-effectiveness of this test make it an excellent option for clinical deployment in the ongoing COVID-19 pandemic.IMPORTANCE Serological surveillance has become an important public health tool during the COVID-19 pandemic. Detection of protective antibodies and seroconversion after SARS-CoV-2 infection or vaccination can help guide patient care plans and public health policies. Serology tests can detect antibodies against past infections; consequently, they can help overcome the shortcomings of molecular tests, which can detect only active infections. This is important, especially when considering that many COVID-19 patients are asymptomatic. In this study, we describe an enzyme-linked immunosorbent assay (ELISA)-based qualitative and quantitative serology test developed to measure IgG and IgA antibodies against the SARS-CoV-2 spike glycoprotein. The test can be deployed using commonly available laboratory reagents and equipment and displays high specificity and sensitivity. Furthermore, we demonstrate that IgG titers in patient samples can be estimated from a single measurement, enabling the assay's use in high-throughput clinical environments.
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Affiliation(s)
- Robert H Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, New York, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Gorka Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ryan J Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - George I Georgiev
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Natalia G Herrera
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nicholas C Morano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sean T Campbell
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Erika P Orner
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Amanda Mengotto
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - M Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alev Celikgil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Duncan Kimmel
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - James H Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Margarette C Mariano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antonio Nakouzi
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Jose Quiroz
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Johanna Rivera
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Wendy A Szymczak
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jason Barnhill
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, New York, USA
| | | | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Daniel T Stein
- Montefiore Medical Center, Bronx, New York, USA
- Division of Endocrinology and Diabetes, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Liise-Anne Pirofski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - D Yitzchak Goldstein
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Scott J Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Johanna P Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Michael B Prystowsky
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - James D Faix
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Amy S Fox
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
- Montefiore Medical Center, Bronx, New York, USA
| | - Jonathan R Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
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11
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Forest SK, Orner EP, Goldstein DY, Wirchnianski AS, Bortz RH, Laudermilch E, Florez C, Malonis RJ, Georgiev GI, Vergnolle O, Lo Y, Campbell ST, Barnhill J, Cadoff EM, Lai JR, Chandran K, Weiss LM, Fox AS, Prystowsky MB, Wolgast LR. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Qualitative IgG Assays: The Value of Numeric Reporting. Arch Pathol Lab Med 2021; 145:929-936. [PMID: 33821952 DOI: 10.5858/arpa.2020-0851-sa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG testing is used for serosurveillance and will be important to evaluate vaccination status. Given the urgency to release coronavirus disease 2019 (COVID-19) serology tests, most manufacturers have developed qualitative tests. OBJECTIVE To evaluate clinical performance of six different SARS-CoV-2 IgG assays and their quantitative results to better elucidate the clinical role of serology testing in COVID-19. DESIGN Six SARS-CoV-2 IgG assays were tested using remnant specimens from 190 patients. Sensitivity and specificity were evaluated for each assay with the current manufacturer's cutoff and a lower cutoff. A numeric result analysis and discrepancy analysis were performed Results: The specificity was >93% for all assays, and sensitivity was >80% for all assays (≥ 7 days post-polymerase chain reaction [PCR] testing). Inpatients with more severe disease had higher numeric values compared to health care workers with mild or moderate disease. Several discrepant serology results were those just below the manufacturers cutoff. CONCLUSIONS SARS-CoV-2 IgG antibody testing can aid in the diagnosis of COVID-19 especially with negative PCR. Quantitative COVID-19 IgG results are important to better understand the immunological response and disease course of this novel virus and to assess immunity as part of future vaccination programs.
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Affiliation(s)
- Stefanie K Forest
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Erika P Orner
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - D Yitzchak Goldstein
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Ariel S Wirchnianski
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Robert H Bortz
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Ethan Laudermilch
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Catalina Florez
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Ryan J Malonis
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - George I Georgiev
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Olivia Vergnolle
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Yungtai Lo
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Sean T Campbell
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Jason Barnhill
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Evan M Cadoff
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Jonathan R Lai
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Kartik Chandran
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Louis M Weiss
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Amy S Fox
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Michael B Prystowsky
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
| | - Lucia R Wolgast
- Department of Pathology (Forest, Orner, Goldstein, Campbell, Cadoff, Weiss, Fox, Prystowsky, Wolgast), Department of Microbiology and Immunology (Wirchnianski, Bortz III, Laudermilch, Florez, Chandran), Department of Biochemistry (Malonis, Georgiev, Vergnolle, Lai), and the Department of Epidemiology and Population Medicine (Lo), at Albert Einstein College of Medicine, Bronx, NY; Department of Chemistry and Life Sciences, United States Military Academy, West Point, NY (Florez, Barnhill); Department of Radiology, Uniformed Services University of Health Science, Bethesda, MD (Barnhill)
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12
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Ikemura K, Bellin E, Yagi Y, Billett H, Saada M, Simone K, Stahl L, Szymanski J, Goldstein DY, Reyes Gil M. Using Automated Machine Learning to Predict the Mortality of Patients With COVID-19: Prediction Model Development Study. J Med Internet Res 2021; 23:e23458. [PMID: 33539308 PMCID: PMC7919846 DOI: 10.2196/23458] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND During a pandemic, it is important for clinicians to stratify patients and decide who receives limited medical resources. Machine learning models have been proposed to accurately predict COVID-19 disease severity. Previous studies have typically tested only one machine learning algorithm and limited performance evaluation to area under the curve analysis. To obtain the best results possible, it may be important to test different machine learning algorithms to find the best prediction model. OBJECTIVE In this study, we aimed to use automated machine learning (autoML) to train various machine learning algorithms. We selected the model that best predicted patients' chances of surviving a SARS-CoV-2 infection. In addition, we identified which variables (ie, vital signs, biomarkers, comorbidities, etc) were the most influential in generating an accurate model. METHODS Data were retrospectively collected from all patients who tested positive for COVID-19 at our institution between March 1 and July 3, 2020. We collected 48 variables from each patient within 36 hours before or after the index time (ie, real-time polymerase chain reaction positivity). Patients were followed for 30 days or until death. Patients' data were used to build 20 machine learning models with various algorithms via autoML. The performance of machine learning models was measured by analyzing the area under the precision-recall curve (AUPCR). Subsequently, we established model interpretability via Shapley additive explanation and partial dependence plots to identify and rank variables that drove model predictions. Afterward, we conducted dimensionality reduction to extract the 10 most influential variables. AutoML models were retrained by only using these 10 variables, and the output models were evaluated against the model that used 48 variables. RESULTS Data from 4313 patients were used to develop the models. The best model that was generated by using autoML and 48 variables was the stacked ensemble model (AUPRC=0.807). The two best independent models were the gradient boost machine and extreme gradient boost models, which had an AUPRC of 0.803 and 0.793, respectively. The deep learning model (AUPRC=0.73) was substantially inferior to the other models. The 10 most influential variables for generating high-performing models were systolic and diastolic blood pressure, age, pulse oximetry level, blood urea nitrogen level, lactate dehydrogenase level, D-dimer level, troponin level, respiratory rate, and Charlson comorbidity score. After the autoML models were retrained with these 10 variables, the stacked ensemble model still had the best performance (AUPRC=0.791). CONCLUSIONS We used autoML to develop high-performing models that predicted the survival of patients with COVID-19. In addition, we identified important variables that correlated with mortality. This is proof of concept that autoML is an efficient, effective, and informative method for generating machine learning-based clinical decision support tools.
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Affiliation(s)
- Kenji Ikemura
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States.,Tsubomi Technology, The Bronx, NY, United States
| | - Eran Bellin
- Department of Epidemiology and Population Health and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Henny Billett
- Department of Oncology and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | | | | | - Lindsay Stahl
- Department of Epidemiology and Population Health and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - James Szymanski
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - D Y Goldstein
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - Morayma Reyes Gil
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
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13
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Fels JM, Khan S, Forster R, Skalina KA, Sirichand S, Fox AS, Bergman A, Mitchell WB, Wolgast LR, Szymczak WA, Bortz RH, Dieterle ME, Florez C, Haslwanter D, Jangra RK, Laudermilch E, Wirchnianski AS, Barnhill J, Goldman DL, Khine H, Goldstein DY, Daily JP, Chandran K, Kelly L. Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference. medRxiv 2021. [PMID: 33594384 PMCID: PMC7885943 DOI: 10.1101/2021.02.08.21250641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of variants, we found that while some became ‘endemic’ to the Bronx, other, novel variants rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic. Temporally and geographically resolved sequencing of SARS-CoV-2 genotypes enabled surveillance of novel genotypes, identification of endemic viral variants, and clinical inferences, in the first wave of the COVID-19 pandemic in the Bronx.
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14
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Campbell ST, Orner EP, Reyes Gil M, Fox AS, Goldstein DY, Wolgast LR, Cadoff EM, Freedman VH, Akabas MH, Prystowsky MB, Szymczak WA. Mater Artium Necessitas: The Birth of a COVID-19 Command Center. Acad Pathol 2021; 8:23742895211015347. [PMID: 34046523 PMCID: PMC8138285 DOI: 10.1177/23742895211015347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 04/16/2021] [Indexed: 01/29/2023] Open
Abstract
In February of 2020, New York City was unprepared for the COVID-19 pandemic. Cases of SARS-CoV-2 infection appeared and spread rapidly. Hospitals had to repurpose staff and establish diagnostic testing for this new viral infection. In the background of the usual respiratory pathogen testing performed in the clinical laboratory, SARS-CoV-2 testing at the Montefiore Medical System grew exponentially, from none to hundreds per day within the first week of testing. The job of appropriately routing SARS-CoV-2 viral specimens became overwhelming. Additional staff was required to triage these specimens to multiple in-house testing platforms as well as external reference laboratories. Since medical school classes and many research laboratories shut down at the Albert Einstein College of Medicine and students were eager to help fight the pandemic, we seized the opportunity to engage and train senior MD-PhD students to assist in triaging specimens. This volunteer force enabled us to establish the "Pathology Command Center," staffed by these students as well as residents and furloughed dental associates. The Pathology Command Center staff were tasked with the accessioning and routing of specimens, answering questions from clinical teams, and updating ever evolving protocols developed in collaboration with a team of Infectious Disease clinicians. Many lessons were learned during this process, including how best to restructure an accessioning department and how to properly onboard students and repurpose staff while establishing safeguards for their well-being during these unprecedented times. In this article, we share some of our challenges, successes, and what we ultimately learned as an organization.
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Affiliation(s)
- Sean T. Campbell
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Erika P. Orner
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | | | - Amy S. Fox
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | | | - Lucia R. Wolgast
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Evan M. Cadoff
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Victoria H. Freedman
- Graduate Division of Biomedical Sciences, Department of Microbiology
and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Myles H. Akabas
- Departments of Physiology & Biophysics, Neuroscience, and
Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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15
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Skalina KA, Goldstein DY, Sulail J, Hahm E, Narlieva M, Szymczak W, Fox AS. Extended storage of SARS-CoV-2 nasopharyngeal swabs does not negatively impact results of molecular-based testing across three clinical platforms. J Clin Pathol 2020; 75:61-64. [PMID: 33144357 PMCID: PMC8685649 DOI: 10.1136/jclinpath-2020-206738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/19/2023]
Abstract
With the global outbreak of COVID-19, the demand for testing rapidly increased and quickly exceeded the testing capacities of many laboratories. Clinical tests which receive CE (Conformité Européenne) and Food and Drug Administration (FDA) authorisations cannot always be tested thoroughly in a real-world environment. Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the US FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time reverse transcriptase-PCR testing.
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Affiliation(s)
- Karin A Skalina
- Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - D Y Goldstein
- Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Jaffar Sulail
- Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Eunkyu Hahm
- Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Momka Narlieva
- Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Wendy Szymczak
- Pathology, Montefiore Medical Center, Bronx, New York, USA
| | - Amy S Fox
- Pathology, Montefiore Medical Center, Bronx, New York, USA
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16
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Pham J, Meyer S, Nguyen C, Williams A, Hunsicker M, McHardy I, Gendlina I, Goldstein DY, Fox AS, Hudson A, Darby P, Hovey P, Morales J, Mitchell J, Harrington K, Majlessi M, Moberly J, Shah A, Worlock A, Walcher M, Eaton B, Getman D, Clark C. Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection. J Clin Microbiol 2020; 58:e01669-20. [PMID: 32727828 PMCID: PMC7512162 DOI: 10.1128/jcm.01669-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID50)/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | - Ian McHardy
- Scripps Health, Microbiology Laboratory, San Diego California, USA
| | - Inessa Gendlina
- Montefiore Medical Center, Department of Pathology, Bronx, New York, USA
| | | | - Amy S Fox
- Montefiore Medical Center, Department of Pathology, Bronx, New York, USA
| | | | - Paul Darby
- Hologic, Inc., San Diego California, USA
| | - Paul Hovey
- Hologic, Inc., San Diego California, USA
| | | | | | | | | | | | - Ankur Shah
- Hologic, Inc., San Diego California, USA
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17
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Bortz RH, Florez C, Laudermilch E, Wirchnianski AS, Lasso G, Malonis RJ, Georgiev GI, Vergnolle O, Herrera NG, Morano NC, Campbell ST, Orner EP, Mengotto A, Dieterle ME, Fels JM, Haslwanter D, Jangra RK, Celikgil A, Kimmel D, Lee JH, Mariano M, Antonio N, Jose Q, Rivera J, Szymczak WA, Tong K, Barnhill J, Forsell MNE, Ahlm C, Stein DT, Pirofski LA, Goldstein DY, Garforth SJ, Almo SC, Daily JP, Prystowsky MB, Faix JD, Fox AS, Weiss LM, Lai JR, Chandran K. Development, clinical translation, and utility of a COVID-19 antibody test with qualitative and quantitative readouts. medRxiv 2020:2020.09.10.20192187. [PMID: 32935116 PMCID: PMC7491531 DOI: 10.1101/2020.09.10.20192187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The COVID-19 global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to place an immense burden on societies and healthcare systems. A key component of COVID-19 control efforts is serologic testing to determine the community prevalence of SARS-CoV-2 exposure and quantify individual immune responses to prior infection or vaccination. Here, we describe a laboratory-developed antibody test that uses readily available research-grade reagents to detect SARS-CoV-2 exposure in patient blood samples with high sensitivity and specificity. We further show that this test affords the estimation of viral spike-specific IgG titers from a single sample measurement, thereby providing a simple and scalable method to measure the strength of an individual's immune response. The accuracy, adaptability, and cost-effectiveness of this test makes it an excellent option for clinical deployment in the ongoing COVID-19 pandemic.
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Affiliation(s)
- Robert H. Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, NY 10996, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ariel S. Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gorka Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - George I. Georgiev
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Natalia G. Herrera
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nicholas C. Morano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sean T. Campbell
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika P. Orner
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amanda Mengotto
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - M. Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alev Celikgil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Duncan Kimmel
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - James H. Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Margarette Mariano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nakouzi Antonio
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Quiroz Jose
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Johanna Rivera
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Wendy A. Szymczak
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jason Barnhill
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, NY 10996, USA
| | | | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Daniel T. Stein
- Division of Endocrinology & Diabetes, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Liise-anne Pirofski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | | | - Scott J. Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna P. Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | | | - James D. Faix
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amy S. Fox
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Louis M. Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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18
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Zhang X, Goldstein DY, Khader SN. Educational Case: Non-Small Cell Lung Cancer: Pathologic Diagnosis and Molecular Understanding. Acad Pathol 2019; 6:2374289519881951. [PMID: 31696153 PMCID: PMC6822184 DOI: 10.1177/2374289519881951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/06/2019] [Accepted: 08/17/2019] [Indexed: 11/15/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040.
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Affiliation(s)
- Xi Zhang
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | | | - Samer N Khader
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
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19
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Marks E, Wang Y, Shi Y, Susa J, Jacobson M, Goldstein DY. Specific TCR gene rearrangements in mycosis fungoides: does advanced clinical stage show a preference? J Clin Pathol 2018; 71:1072-1077. [PMID: 30171087 DOI: 10.1136/jclinpath-2018-205324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 11/04/2022]
Abstract
AIMS The relationship between the presence of specific T-cell receptor (TCR) gene rearrangements and clinical stage in mycosis fungoides (MF) has not been studied. We analysed a cohort of patients with a diagnosis of MF to determine the different types of specific TCR gene rearrangements present and their relationship to disease stage. METHODS A retrospective chart review was used to select patients with a diagnosis of MF who had a skin biopsy and a positive TCR gene rearrangement study in either blood or tissue and at least 2 years of clinical follow-up. RESULTS 43 patients were identified and divided into two groups. The first group consisted of 23 patients with early stage disease (IA-IIA) that was either stable or went into partial or complete remission with minimal intervention. None of these patients advanced to late stage disease. The second group consisted of 20 patients who had either late stage disease at diagnosis or progressed to late stage disease at some point in time. In the first group, only 4/23 (17%) patients had a single TCR gene rearrangement in the Vɣ1-8 region. In contrast, the second group had 13/20 (65%) patients with a single TCR gene rearrangement in the Vɣ1-8 region (p=0.002). CONCLUSION The presence of a single TCR gene rearrangement in the Vɣ1-8 region could possibly be related to a more advanced stage of MF. However, more comprehensive studies, such as next generation sequencing, with a larger cohort is necessary for a more definitive conclusion.
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Affiliation(s)
- Etan Marks
- Department of Pathology, NYU Langone Medical Center, New York, USA
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yang Shi
- Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joseph Susa
- Division of Dermatopathology, Cockerell Dermatopathology, Dallas, Texas, USA
| | - Mark Jacobson
- Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York, USA
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York, USA
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20
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Kim T, Khader SN, Goldstein DY. Educational Case: Cervical Neoplasia: HPV and Its Link to Cancer. Acad Pathol 2018; 5:2374289518770651. [PMID: 29978016 PMCID: PMC6024286 DOI: 10.1177/2374289518770651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/12/2018] [Accepted: 03/22/2018] [Indexed: 11/23/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040.
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Affiliation(s)
- Teresa Kim
- Albert Einstein College of Medicine, Bronx, NY, USA
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21
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Naeem RC, Goldstein DY, Einstein MH, Ramos Rivera G, Schlesinger K, Khader SN, Suhrland M, Fox AS. SurePath Specimens Versus ThinPrep Specimen Types on the COBAS 4800 Platform: High-Risk HPV Status and Cytology Correlation in an Ethnically Diverse Bronx Population. Lab Med 2018; 48:207-213. [PMID: 28379422 DOI: 10.1093/labmed/lmx019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective To compare the cytologic preparations of 130 cervical specimens (from women of various ethnicities at high risk for human papillomavirus [HPV] infection) using the SurePath (SP) collection system with specimens gathered using the ThinPrep (TP) system, as processed on the Cobas 4800 analyzer, to determine which collection method more accurately identifies HPV infection. Methods In our prospective study, specimens were collected from 130 women of various ethnicities residing in or near Bronx County, NY. The SP-collected specimen was first processed for cytologic findings; if clinical HPV testing was requested on that specimen, it was tested using Hybrid Capture II (HC2) methodology. We tested the remnant SP-collected cell concentrate using the Cobas analyzer. Then, the TP-collected and SP-collected specimens were tested in the same run on that analyzer, and the results were compared. We also compared the results with the concurrent cytologic findings. Results The results were concordant for overall HR-HPV status in 93.8% of cases. Also, a statistically significant lower cycle threshold value was observed with Cobas testing of specimen concentrates tested via the BD SurePath Pap Test (P = .001), suggesting higher sensitivity compared with specimens tested via the ThinPrep Pap Test. Conclusion Cobas 4800 HPV testing of SP-collected specimen concentrates yields comparable results to TP-collected specimen concentrates. Based on the limited data that we derived, SP collection may be a more favorable methodology than TP collection for HPV testing of individuals at high risk in our ethnically diverse, urban patient population.
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Affiliation(s)
- R C Naeem
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - D Y Goldstein
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - Mark H Einstein
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - G Ramos Rivera
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - K Schlesinger
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - S N Khader
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - M Suhrland
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | - A S Fox
- Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
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22
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Goldstein DY, Prystowsky M. Autosomal Recessive Inheritance: Cystic Fibrosis. Acad Pathol 2017; 4:2374289517691769. [PMID: 28815197 PMCID: PMC5528909 DOI: 10.1177/2374289517691769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/25/2016] [Accepted: 01/09/2017] [Indexed: 01/20/2023] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040.
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Affiliation(s)
| | - Michael Prystowsky
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
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23
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Castellucci E, He T, Goldstein DY, Halmos B, Chuy J. DNA Polymerase ɛ Deficiency Leading to an Ultramutator Phenotype: A Novel Clinically Relevant Entity. Oncologist 2017; 22:497-502. [PMID: 28465371 PMCID: PMC5423519 DOI: 10.1634/theoncologist.2017-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 11/17/2022] Open
Abstract
Two cases of metastatic colorectal cancer with a POLE mutation, both of which were ultramutated and microsatellite stable, are presented and discussed from the standpoint of the basic biochemical mechanisms leading to a unique phenotype in POLE deficiency, the challenges faced with interpreting the genomic profiling of tumors in this important subset of patients, and the potential clinical implications. Deficiencies in DNA repair due to mutations in the exonuclease domain of DNA polymerase ɛ have recently been described in a subset of cancers characterized by an ultramutated and microsatellite stable (MSS) phenotype. This alteration in DNA repair is distinct from the better‐known mismatch repair deficiencies which lead to microsatellite instability (MSI) and an increased tumor mutation burden. Instead, mutations in POLE lead to impaired proofreading intrinsic to Pol ɛ during DNA replication resulting in a dramatically increased mutation rate. Somatic mutations of Pol ɛ have been found most frequently in endometrial and colorectal cancers (CRC) and can lead to a unique familial syndrome in the case of germline mutations. While other key genomic abnormalities, such as MSI, have known prognostic and treatment implications, in this case it is less clear. As molecular genotyping of tumors becomes routine in the care of cancer patients, less common, but potentially actionable findings such as these POLE mutations could be overlooked unless appropriate algorithms are in place. We present two cases of metastatic CRC with a POLE mutation, both of which are ultramutated and MSS. The basic biochemical mechanisms leading to a unique phenotype in POLE deficiency as well as challenges faced with interpreting the genomic profiling of tumors in this important subset of patients and the potential clinical implications will be discussed here. The Oncologist 2017;22:497–502 Key Points. Clinicians should recognize that tumors with high tumor mutation burden and that are microsatellite stable may harbor a POLE mutation, which is associated with an ultramutated phenotype. Work‐up for POLE deficiency should indeed become part of the routine molecular testing paradigm for patients with colorectal cancer. This subset of patients may benefit from clinical trials where the higher number of mutation‐associated neoantigens and defect in DNA repair may be exploited therapeutically.
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Affiliation(s)
- Enrico Castellucci
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tianfang He
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Balazs Halmos
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jennifer Chuy
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
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