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Article ; Online: Meta-analysis of the robustness of COVID-19 diagnostic kit performance during the early pandemic

George J Netto / Chandrakumar Shanmugam / Michael Behring / Vishwas Luthra / Sixto M Leal / Sooryanarayana Varambally / Upender Manne

BMJ Open, Vol 12, Iss

2022 Volume 4

Keywords	Medicine ; R
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Immunophenotypic profiles and prognosis for colorectal mucinous adenocarcinomas are dependent on anatomic location.

Patel, Chirag / Behring, Michael / Al Diffalha, Sameer / Dhall, Deepti / Lee, Goo / Shanmugam, Chandrakumar / Grizzle, William E / Manne, Upender

Cancer medicine

2023 Volume 12, Issue 8, Page(s) 9637–9643

Abstract: Background: The prognostic value of mucinous adenocarcinomas (MCAs, exhibiting >50% extracellular mucin) of the colorectum, in relation to their anatomic location is not well studied.: Materials and methods: We compared MCAs (n = 175) with non-MCAs ( ... ...

Abstract	Background: The prognostic value of mucinous adenocarcinomas (MCAs, exhibiting >50% extracellular mucin) of the colorectum, in relation to their anatomic location is not well studied. Materials and methods: We compared MCAs (n = 175) with non-MCAs (NMCAs, n = 1015) and the cancer-specific survival rates were evaluated, based on their anatomic site, by univariate Kaplan-Meier and multivariate Cox methods. Subsets of these tumors were immunostained for MUC1, MUC2, Bcl-2, and p53. Results: MCAs were more commonly found in the right colon, were of high-grade, and were more prevalent in younger patients (<40 years). They exhibited strong expression of MUC2 and Bcl-2 and showed less p53 nuclear staining. In contrast, most NMCAs were low-grade with high expression of MUC1. MCAs of the rectum were associated with poorer outcomes relative to NMCAs (HR 1.85, CI 95% 1.15-2.97), even though the distributions of advanced-stage tumors were similar. Conclusion: Late-stage disease and age were poor independent prognostic indicators of cancer-specific deaths across all tumor locations. In summary, rectal MCAs have a poor prognosis.
MeSH term(s)	Humans ; Tumor Suppressor Protein p53/metabolism ; Colorectal Neoplasms/pathology ; Adenocarcinoma, Mucinous/pathology ; Prognosis ; Mucins/metabolism
Chemical Substances	Tumor Suppressor Protein p53 ; Mucins
Language	English
Publishing date	2023-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.5803
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Meta-analysis of the robustness of COVID-19 diagnostic kit performance during the early pandemic.

Shanmugam, Chandrakumar / Behring, Michael / Luthra, Vishwas / Leal, Sixto M / Varambally, Sooryanarayana / Netto, George J / Manne, Upender

BMJ open

2022 Volume 12, Issue 4, Page(s) e053912

Abstract: Background: Accurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19.: Methods: We reviewed 85 studies (21 530 ... ...

Abstract	Background: Accurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19. Methods: We reviewed 85 studies (21 530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic. All relevant articles, published up to 31 May 2020, in PubMed, BioRiXv, MedRiXv and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10 355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5538 patients) between test performance in meta-analyses. Synthesis of results was done using random effects modelling and bias was evaluated according to QUADAS-2 guidelines. Results: The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1957 positive RT-PCR COVID-19 participants, 1585 had positive serum antibody (IgM±IgG) tests (sensitivity 0.81, 95% CI 0.66 to 0.90). While 3509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95% CI 0.94 to 0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory approval than for real-world reporting data. Discussion: The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimise false negative RT-PCR results. Lack of standardised assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.
MeSH term(s)	Antibodies, Viral ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Testing ; Humans ; Pandemics ; SARS-CoV-2 ; Sensitivity and Specificity
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2022-04-21
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2021-053912
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Article ; Online: COVID-2019 - A comprehensive pathology insight.

Shanmugam, Chandrakumar / Mohammed, Abdul Rafi / Ravuri, Swarupa / Luthra, Vishwas / Rajagopal, Narasimhamurthy / Karre, Saritha

Pathology, research and practice

2020 Volume 216, Issue 10, Page(s) 153222

Abstract: Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. The lungs are the main organs affected leading to pneumonia and ... ...

Abstract	Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. The lungs are the main organs affected leading to pneumonia and respiratory failure in severe cases that may need mechanical ventilation. Occasionally patient may present with gastro-intestinal, cardiac and neurologic symptoms with or without lung involvement. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. Other organs like liver and kidneys may be involved secondarily. Currently the treatment is principally symptomatic and prevention by proper use of personal protective equipment and other measures is crucial to limit the spread. In the midst of pandemic there is paucity of literature on pathological features including pathogenesis, hence in this review we provide the current pathology centered understanding of COVID-19. Furthermore, the pathogenetic pathway is pivotal in the development of therapeutic targets.
MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections/pathology ; Humans ; Pandemics ; Pneumonia, Viral/pathology ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-18
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2020.153222
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Article: Meta-Analysis of Robustness of COVID-19 Diagnostic Kits During Early Pandemic.

Shanmugam, Chandrakumar / Behring, Michael / Luthra, Vishwas / Leal, Sixto M / Diffalha, Sameer Al / Varambally, Sooryanarayana / Netto, George J / Manne, Upender

medRxiv : the preprint server for health sciences

2021

Abstract: Background: Accurate detection of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is necessary to mitigate the coronavirus disease-19 (COVID-19) pandemic. However, the test reagents and assay platforms are varied and may not be ... ...

Abstract	Background: Accurate detection of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is necessary to mitigate the coronavirus disease-19 (COVID-19) pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19. Methods: We reviewed 85 studies (21,530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic, following the standards outlined in the PRISMA statement. All relevant articles, published up to May 31, 2020, in PubMed, BioRiXv, MedRiXv, and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10,355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5,538 patients) between methods in meta-analyses. Results: The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1,957 positive RT-PCR COVID-19 participants, 1,585 had positive serum antibody (IgM +/- IgG) tests (sensitivity 0.81, 95%CI 0.66-.90). While 3,509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95%CI 0.94-0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory-approval than for real-world reporting data. Conclusions: The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimize false negative RT-PCR results. Lack of standardized assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.01.16.21249937
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: COVID-2019 - A comprehensive pathology insight

Shanmugam, Chandrakumar / Mohammed, Abdul Rafi / Ravuri, Swarupa / Luthra, Vishwas / Rajagopal, Narasimhamurthy / Karre, Saritha

Pathol Res Pract

Abstract	Corona virus disease-2019 (COVID-19) caused by severe acute respiratory syndrome corona virus-2 (SARS CoV-2), a highly contagious single stranded RNA virus genetically related to SARS CoV. The lungs are the main organs affected leading to pneumonia and respiratory failure in severe cases that may need mechanical ventilation. Occasionally patient may present with gastro-intestinal, cardiac and neurologic symptoms with or without lung involvement. Pathologically, the lungs show either mild congestion and alveolar exudation or acute respiratory distress syndrome (ARDS) with hyaline membrane or histopathology of acute fibrinous organizing pneumonia (AFOP) that parallels disease severity. Other organs like liver and kidneys may be involved secondarily. Currently the treatment is principally symptomatic and prevention by proper use of personal protective equipment and other measures is crucial to limit the spread. In the midst of pandemic there is paucity of literature on pathological features including pathogenesis, hence in this review we provide the current pathology centered understanding of COVID-19. Furthermore, the pathogenetic pathway is pivotal in the development of therapeutic targets.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #779553
Database	COVID19

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Article ; Online: Meta-Analysis of Robustness of COVID-19 Diagnostic Kits During Early Pandemic

Shanmugam, Chandrakumar / Behring, Michael / Luthra, Vishwas / Leal, Sixto M. / Varambally, Sooryanarayana / Netto, George J. / Manne, Upender

medRxiv

Abstract: Background Accurate detection of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is necessary to mitigate the coronavirus disease-19 (COVID-19) pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently ... ...

Abstract	Background Accurate detection of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is necessary to mitigate the coronavirus disease-19 (COVID-19) pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19. Methods We reviewed 85 studies (21,530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic, following the standards outlined in the PRISMA statement. All relevant articles, published up to May 31, 2020, in PubMed, BioRiXv, MedRiXv, and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10,355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5,538 patients) between methods in meta-analyses. Results The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1,957 positive RT-PCR COVID-19 participants, 1,585 had positive serum antibody (IgM +/- IgG) tests (sensitivity 0.81, 95%CI 0.66-.90). While 3,509 of 3581 participants RT-PCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95%CI 0.94-0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory-approval than for real-world reporting data. Conclusions The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimize false negative RT-PCR results. Lack of standardized assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.
Keywords	covid19
Language	English
Publishing date	2021-01-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.01.16.21249937
Database	COVID19

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Article ; Online: The combined survival effect of codon 72 polymorphisms and p53 somatic mutations in breast cancer depends on race and molecular subtype.

Hebert-Magee, Shantel / Yu, Han / Behring, Michael / Jadhav, Trafina / Shanmugam, Chandrakumar / Frost, Andra / Eltoum, Isam-Eldin / Varambally, Sooryanarayana / Manne, Upender

PloS one

2019 Volume 14, Issue 2, Page(s) e0211734

Abstract: Background: The codon 72 polymorphism in the p53 gene relates to the risk of breast cancer (BC), but this relationship in racially diverse populations is not known. The present study examined the prognostic value of this polymorphism for African ... ...

Abstract	Background: The codon 72 polymorphism in the p53 gene relates to the risk of breast cancer (BC), but this relationship in racially diverse populations is not known. The present study examined the prognostic value of this polymorphism for African American (AA) and Caucasian (CA) BC patients separately and considered the confounding variables of molecular subtypes and somatic mutations in p53. Methods: Tissue sections of BCs from 116 AAs and 160 CAs were evaluated for p53 mutations and genotyped for the codon 72 polymorphism. The relationships of phenotypes to clinicopathologic features were determined by χ2 analyses; patient survival was estimated by Kaplan-Meier univariate and Cox regression multivariate models in a retrospective cohort study design. Results: The proportion of single nucleotide polymorphism (SNP) 72 alleles differed for races. Many cancers of AAs were Pro/Pro, but most for CAs were Arg/Arg. A higher frequency of missense p53 mutations was evident for AAs. There was an interaction between the SNP allele and p53 mutations for AA women only. The proportion of women with both the Pro/Pro allele and a p53 somatic mutation was higher for AA than CA women. The interaction between missense p53 mutations and Pro/Pro had a negative effect on survival, particularly for AAs with luminal cancers. Conclusions: For BCs, the survival effect of SNP72 combined with a p53 missense mutation is dependent on race and molecular subtype. Although such a mutation is a marker of poor prognosis, it is relevant to identify the variant Pro/Pro in the case of AAs, especially those with luminal subtypes of BC.
MeSH term(s)	African Americans/genetics ; Aged ; Alleles ; Breast Neoplasms/genetics ; Codon/genetics ; Female ; Genotype ; Humans ; Middle Aged ; Mutation/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Prognosis ; Proportional Hazards Models ; Receptor, ErbB-2/genetics ; Retrospective Studies ; Tumor Suppressor Protein p53/genetics
Chemical Substances	Codon ; TP53 protein, human ; Tumor Suppressor Protein p53 ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2019-02-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0211734
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The combined survival effect of codon 72 polymorphisms and p53 somatic mutations in breast cancer depends on race and molecular subtype.

Shantel Hebert-Magee / Han Yu / Michael Behring / Trafina Jadhav / Chandrakumar Shanmugam / Andra Frost / Isam-Eldin Eltoum / Sooryanarayana Varambally / Upender Manne

PLoS ONE, Vol 14, Iss 2, p e

2019 Volume 0211734

Abstract: Background The codon 72 polymorphism in the p53 gene relates to the risk of breast cancer (BC), but this relationship in racially diverse populations is not known. The present study examined the prognostic value of this polymorphism for African American ( ...

Abstract	Background The codon 72 polymorphism in the p53 gene relates to the risk of breast cancer (BC), but this relationship in racially diverse populations is not known. The present study examined the prognostic value of this polymorphism for African American (AA) and Caucasian (CA) BC patients separately and considered the confounding variables of molecular subtypes and somatic mutations in p53. Methods Tissue sections of BCs from 116 AAs and 160 CAs were evaluated for p53 mutations and genotyped for the codon 72 polymorphism. The relationships of phenotypes to clinicopathologic features were determined by χ2 analyses; patient survival was estimated by Kaplan-Meier univariate and Cox regression multivariate models in a retrospective cohort study design. Results The proportion of single nucleotide polymorphism (SNP) 72 alleles differed for races. Many cancers of AAs were Pro/Pro, but most for CAs were Arg/Arg. A higher frequency of missense p53 mutations was evident for AAs. There was an interaction between the SNP allele and p53 mutations for AA women only. The proportion of women with both the Pro/Pro allele and a p53 somatic mutation was higher for AA than CA women. The interaction between missense p53 mutations and Pro/Pro had a negative effect on survival, particularly for AAs with luminal cancers. Conclusions For BCs, the survival effect of SNP72 combined with a p53 missense mutation is dependent on race and molecular subtype. Although such a mutation is a marker of poor prognosis, it is relevant to identify the variant Pro/Pro in the case of AAs, especially those with luminal subtypes of BC.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Molecular Biomarkers of Colorectal Cancer and Cancer Disparities: Current Status and Perspective.

Manne, Upender / Jadhav, Trafina / Putcha, Balananda-Dhurjati Kumar / Samuel, Temesgen / Soni, Shivani / Shanmugam, Chandrakumar / Suswam, Esther A

Current colorectal cancer reports

2016 Volume 12, Issue 6, Page(s) 332–344

Abstract: This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient ... ...

Abstract	This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient race and ethnicity, the usefulness of these molecular alterations as biomarkers needs to be evaluated in different racial/ethnic groups. To accomplish personalized patient care, a combined analysis of multiple molecular alterations in DNA, RNA, microRNAs (miRNAs), metabolites, and proteins in a single test is required to assess disease status in a precise way. Therefore, a special emphasis is placed on issues related to utility of recently identified genetic and molecular alterations in genes, miRNAs, and various "-omes" (e.g., proteomes, kinomes, metabolomes, exomes, methylomes) as candidate molecular markers to determine cancer progression (disease recurrence/relapse and metastasis) and to assess the efficacy of therapy in colorectal cancer in relation to patient race and ethnicity. This review will be useful for oncologists, pathologists, and basic and translational researchers.
Language	English
Publishing date	2016-09-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2214717-2
ISSN	1556-3804 ; 1556-3790
ISSN (online)	1556-3804
ISSN	1556-3790
DOI	10.1007/s11888-016-0338-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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