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Levy B, Kanagal-Shamanna R, Sahajpal NS, Neveling K, Rack K, Dewaele B, Olde Weghuis D, Stevens-Kroef M, Puiggros A, Mallo M, Clifford B, Mantere T, Hoischen A, Espinet B, Kolhe R, Solé F, Raca G, Smith AC. A framework for the clinical implementation of optical genome mapping in hematologic malignancies. Am J Hematol 2024; 99:642-661. [PMID: 38164980 DOI: 10.1002/ajh.27175] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Haematological Malignancies, Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Puiggros
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Mallo
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Francesc Solé
- MDS Research Group, Microarrays Unit, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Adam C Smith
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Pang AWC, Kosco K, Sahajpal NS, Sridhar A, Hauenstein J, Clifford B, Estabrook J, Chitsazan AD, Sahoo T, Iqbal A, Kolhe R, Raca G, Hastie AR, Chaubey A. Analytic Validation of Optical Genome Mapping in Hematological Malignancies. Biomedicines 2023; 11:3263. [PMID: 38137484 PMCID: PMC10741484 DOI: 10.3390/biomedicines11123263] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.
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Affiliation(s)
| | | | - Nikhil S. Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | | | | | | | | | | | | | - Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
| | - Alex R. Hastie
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
| | - Alka Chaubey
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
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Sahajpal NS, Mondal AK, Fee T, Hilton B, Layman L, Hastie AR, Chaubey A, DuPont BR, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing. J Mol Diagn 2023; 25:234-246. [PMID: 36758723 DOI: 10.1016/j.jmoldx.2023.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.
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Affiliation(s)
- Nikhil S Sahajpal
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Timothy Fee
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Benjamin Hilton
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Lawrence Layman
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | | | - Barbara R DuPont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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Iqbal MA, Broeckel U, Levy B, Skinner S, Sahajpal NS, Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy PL, Kolhe R. Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases. J Mol Diagn 2023; 25:175-188. [PMID: 36828597 PMCID: PMC10851778 DOI: 10.1016/j.jmoldx.2022.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 02/24/2023] Open
Abstract
This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.
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Affiliation(s)
- M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Nikhil S Sahajpal
- Greenwood Genetic Center, Greenwood, South Carolina; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | - Aaron Stence
- Department of Pathology, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Kamel Awayda
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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Vashisht A, Ahluwalia P, Mondal AK, Singh H, Sahajpal NS, Fulzele S, Kota V, Gahlay GK, Kolhe R. Immune Factors Drive Expression of SARS-CoV-2 Receptor Genes Amid Sexual Disparity. Viruses 2023; 15:v15030657. [PMID: 36992366 PMCID: PMC10056434 DOI: 10.3390/v15030657] [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] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The emergence of COVID-19 has led to significant morbidity and mortality, with around seven million deaths worldwide as of February 2023. There are several risk factors such as age and sex that are associated with the development of severe symptoms due to COVID-19. There have been limited studies that have explored the role of sex differences in SARS-CoV-2 infection. As a result, there is an urgent need to identify molecular features associated with sex and COVID-19 pathogenesis to develop more effective interventions to combat the ongoing pandemic. To address this gap, we explored sex-specific molecular factors in both mouse and human datasets. The host immune targets such as TLR7, IRF7, IRF5, and IL6, which are involved in the immune response against viral infections, and the sex-specific targets such as AR and ESSR were taken to investigate any possible link with the SARS-CoV-2 host receptors ACE2 and TMPRSS2. For the mouse analysis, a single-cell RNA sequencing dataset was used, while bulk RNA-Seq datasets were used to analyze the human clinical data. Additional databases such as the Database of Transcription Start Sites (DBTS), STRING-DB, and the Swiss Regulon Portal were used for further analysis. We identified a 6-gene signature that showed differential expression in males and females. Additionally, this gene signature showed potential prognostic utility by differentiating ICU patients from non-ICU patients due to COVID-19. Our study highlights the importance of assessing sex differences in SARS-CoV-2 infection, which can assist in the optimal treatment and better vaccination strategies.
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Affiliation(s)
- Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | | | - Sadanand Fulzele
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Gagandeep K. Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar 143005, India
- Correspondence: (G.K.G.); (R.K.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Correspondence: (G.K.G.); (R.K.)
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Sahajpal NS, Mondal AK, Tvrdik T, Hauenstein J, Shi H, Deeb KK, Saxe D, Hastie AR, Chaubey A, Savage NM, Kota V, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms. J Mol Diagn 2022; 24:1279-1291. [PMID: 36265723 DOI: 10.1016/j.jmoldx.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/07/2022] Open
Abstract
The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive and time and cost prohibitive, and they often do not reveal the genetic complexity of the tumor, demonstrating the need for alternative technology for better characterization of these tumors. Herein, we report the results from our clinical validation study and demonstrate the utility of optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 hematological neoplasms and 10 controls). The technical performance (quality control metrics) resulted in 100% first-pass rate, with analytical performance (concordance) showing a sensitivity of 98.7%, a specificity of 100%, and an accuracy of 99.2%. OGM demonstrated robust technical, analytical performance, and interrun, intrarun, and interinstrument reproducibility. The limit of detection was determined to be at 5% allele fraction for aneuploidy, translocation, interstitial deletion, and duplication. OGM identified several additional structural variations, revealing the genomic architecture in these neoplasms that provides an opportunity for better tumor classification, prognostication, risk stratification, and therapy selection. Overall, OGM has outperformed the standard-of-care tests in this study and demonstrated its potential as a first-tier cytogenomic test for hematologic malignancies.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Tatiana Tvrdik
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Kristin K Deeb
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Debra Saxe
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | | | - Natasha M Savage
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia.
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Sahajpal NS, Mondal AK, Hastie A, Chaubey A, Kolhe R. Abstract 2933: Utility of optical genome mapping for the chromosomal characterization of cell lines used in preclinical and clinical research. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2933] [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: 11/16/2022]
Abstract
Abstract
Cell lines have revolutionized scientific research as they are employed as primary tools in both basic and clinical research. Cell lines are extensively used to understand disease mechanisms, drug responses, drug metabolism, drug cytotoxicity, antibody production, vaccine development, gene function, generation of artificial tissues, synthesis of biological compounds, and develop transgenic preclinical models. However, the cells acquire additional genetic aberrations from the time the cell lines are established that might significantly impact the research for which the cell line is being used. The current methods to assess structural variants and copy number variants are limited in resolution (Karyotype), targeted (FISH), cannot detect balanced SVs (CMA), and cannot detect SVs in repetitive regions of the genome (NGS). Optical genome mapping (OGM) is an emerging next-generation cytogenenomics technology that can detect SVs including CNVs and complex rearrangements, using Saphyr platform that images ultra-long DNA molecules labelled at unique 6 base-pair motifs that span the entire genome, enabling genome-wide coverage and the ability to detect large SVs throughout the genome. In this study, we analyzed eight different cell lines that included seven cell lines of syndromes such as Fragile X (n=2), FSHD (n=2), DMD1 (n=1), Prader Willi (n=1), deafness (n=1), and one cell line for a transgenic mouse model. We have additionally analyzed 104 lymphoblast cell lines from the 1000 genomes project which do not have known clinical features. Briefly, ultra-high molecular weight DNA (150kb to >1Mb) was isolated from cultured cells using ~1.5 million cells as per manufacturer’s protocol, uniformly labeled at a specific 6-base sequence motif, and loaded into a cartridge, where the molecules were electrophoretically linearized and imaged multiple times using the Bionano Genomics Saphyr® platform. Using the captured images, a de novo genome map indicating the positions of the labels was constructed and compared to a reference genome to detect structural differences in the 2 maps. Chromosomal aberrations were detected by comparing optical maps to a reference and control dataset, and a coverage-based CNV calling was performed. In the present study, all eight cell lines were characterized with the concordance of reported genetic aberration in the syndromic cell lines. However, in the transgenic mouse cell line, several additional clinically pathogenic variants were detected in addition to the know variation. The study demonstrates the strength of OGM technology for detecting SVs and CNVs and its utility in the chromosomal characterization of cell lines that might significantly contribute towards accurate and reproducible research in a particular phenotype.
Citation Format: Nikhil S. Sahajpal, Ashis K. Mondal, Alex Hastie, Alka Chaubey, Ravindra Kolhe. Utility of optical genome mapping for the chromosomal characterization of cell lines used in preclinical and clinical research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2933.
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Sahajpal NS, Mondal AK, Ananth S, Njau A, Jones K, Ahluwalia P, Oza E, Ross TM, Kota V, Kothandaraman A, Fulzele S, Hegde M, Chaubey A, Rojiani AM, Kolhe R. Clinical validation of a multiplex PCR-based detection assay using saliva or nasopharyngeal samples for SARS-Cov-2, influenza A and B. Sci Rep 2022; 12:3480. [PMID: 35241679 PMCID: PMC8894395 DOI: 10.1038/s41598-022-07152-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Received: 06/03/2021] [Accepted: 01/19/2022] [Indexed: 01/05/2023] Open
Abstract
The COVID-19 pandemic has resulted in significant diversion of human and material resources to COVID-19 diagnostics, to the extent that influenza viruses and co-infection in COVID-19 patients remains undocumented and pose serious public-health consequences. We optimized and validated a highly sensitive RT-PCR based multiplex-assay for the detection of SARS-CoV-2, influenza A and B viruses in a single-test. This study evaluated clinical specimens (n = 1411), 1019 saliva and 392 nasopharyngeal swab (NPS), tested using two-assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp-RT-PCR based assay that targets SARS-CoV-2, influenza viruses A and B. Of the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. This study presents clinical validation of a multiplex-PCR assay for testing SARS-CoV-2, influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Allan Njau
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Eesha Oza
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | | | - Sadanand Fulzele
- Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Madhuri Hegde
- Global Laboratory Services, Perkin Elmer, Waltham, USA
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA.,Bionano Genomics Inc., San Diego, CA, USA
| | - Amyn M Rojiani
- Department of Pathology, Penn State College of Medicine, Hershey, PA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA, 30912, USA.
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Ahluwalia P, Mondal AK, Ahluwalia M, Sahajpal NS, Jones K, Jilani Y, Gahlay GK, Barrett A, Kota V, Rojiani AM, Kolhe R. Clinical and molecular assessment of an onco-immune signature with prognostic significance in patients with colorectal cancer. Cancer Med 2022; 11:1573-1586. [PMID: 35137551 PMCID: PMC8921909 DOI: 10.1002/cam4.4568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/18/2021] [Revised: 11/24/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the complex tumor microenvironment is key to the development of personalized therapies for the treatment of cancer including colorectal cancer (CRC). In the past decade, significant advances in the field of immunotherapy have changed the paradigm of cancer treatment. Despite significant improvements, tumor heterogeneity and lack of appropriate classification tools for CRC have prevented accurate risk stratification and identification of a wider patient population that may potentially benefit from targeted therapies. To identify novel signatures for accurate prognostication of CRC, we quantified gene expression of 12 immune‐related genes using a medium‐throughput NanoString quantification platform in 93 CRC patients. Multivariate prognostic analysis identified a combined four‐gene prognostic signature (TGFB1, PTK2, RORC, and SOCS1) (HR: 1.76, 95% CI: 1.05–2.95, *p < 0.02). The survival trend was captured in an independent gene expression data set: GSE17536 (177 patients; HR: 3.31, 95% CI: 1.99–5.55, *p < 0.01) and GSE14333 (226 patients; HR: 2.47, 95% CI: 1.35–4.53, *p < 0.01). Further, gene set enrichment analysis of the TCGA data set associated higher prognostic scores with epithelial–mesenchymal transition (EMT) and inflammatory pathways. Comparatively, a lower prognostic score was correlated with oxidative phosphorylation and MYC and E2F targets. Analysis of immune parameters identified infiltration of T‐reg cells, CD8+ T cells, M2 macrophages, and B cells in high‐risk patient groups along with upregulation of immune exhaustion genes. This molecular study has identified a novel prognostic gene signature with clinical utility in CRC. Therefore, along with prognostic features, characterization of immune cell infiltrates and immunosuppression provides actionable information that should be considered while employing personalized medicine.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | | | - Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Kimya Jones
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Yasmeen Jilani
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Amanda Barrett
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Amyn M Rojiani
- Department of Pathology, Penn State College of Medicine, Hershey, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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10
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Ahluwalia P, Mondal AK, Sahajpal NS, Rojiani MV, Kolhe R. Gene signatures with therapeutic value: emerging perspective for personalized immunotherapy in renal cancer. Immunotherapy 2021; 13:1535-1547. [PMID: 34753298 DOI: 10.2217/imt-2021-0187] [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] [Indexed: 11/21/2022] Open
Abstract
Renal cancer is one of the deadliest urogenital diseases. In recent years, the advent of immunotherapy has led to significant improvement in the management of patients with renal cancer. Although cancer immunotherapy and its combinations had benefited numerous patients, several challenges need to be addressed. Apart from the high costs of treatment, the lack of predictive biomarkers and toxic side-effects have impeded its wider applicability. To address these issues, new biomarkers are required to predict responsiveness and design personalized treatment strategies. Recent advances in the field of single-cell sequencing and multi-dimensional spatial transcriptomics have identified clinically relevant subtypes of renal cancer. Furthermore, there is emerging potential for gene signatures based on immune cells, non-coding RNAs, and pathways such as metabolism and RNA modification. In this review article, we have discussed recent progress in the identification of gene signatures with predictive and prognostic potential in renal cancer.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Mumtaz V Rojiani
- Department of Pharmacology, Penn State University College of Medicine, PA 17033, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
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11
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Sahajpal NS, Mondal AK, Njau A, Petty Z, Chen J, Ananth S, Ahluwalia P, Williams C, Ross TM, Chaubey A, DeSantis G, Schroth GP, Bahl J, Kolhe R. High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses. Viruses 2021; 13:v13102063. [PMID: 34696495 PMCID: PMC8540770 DOI: 10.3390/v13102063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/31/2022] Open
Abstract
Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.
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Affiliation(s)
- Nikhil S. Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
| | - Allan Njau
- Department of Pathology, Aga Khan University Hospital, Nairobi 30270-00100, Kenya;
| | - Zachary Petty
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; (Z.P.); (J.C.); (J.B.)
| | - Jiani Chen
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; (Z.P.); (J.C.); (J.B.)
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
| | - Colin Williams
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA;
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
- Bioano Genomics Inc., San Diego, CA 92121, USA
| | - Grace DeSantis
- Research and Development, Illumina Inc., San Diego, CA 92122, USA; (G.D.); (G.P.S.)
| | - Gary P. Schroth
- Research and Development, Illumina Inc., San Diego, CA 92122, USA; (G.D.); (G.P.S.)
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; (Z.P.); (J.C.); (J.B.)
- Department of Infectious Disease, University of Georgia, Athens, GA 30602, USA
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA 30602, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (A.K.M.); (S.A.); (P.A.); (C.W.); (A.C.)
- Correspondence: ; Tel.: +1-(706)-721-2771; Fax: +1-(706)-434-6053
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12
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Mahant S, Sahajpal NS, Nanda S. Insights into the mechanism of Cymbopogan martinii essential oil in topical therapy of acne vulgaris. Future Microbiol 2021; 16:1181-1193. [PMID: 34615379 DOI: 10.2217/fmb-2021-0039] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aim: The present study investigated the essential oil of Cymbopogan martinii (palmarosa oil; PRO) as a potential topical therapy in acne vulgaris. Materials & methods: GC-MS profiling and biocompatibility studies of PRO were undertaken. The antimicrobial potential was assessed against Cutibacterium acnes. anti-inflammatory, antityrosinase activity and lipid peroxidation were also evaluated. Results: Geraniol was identified as the major phytoconstituent, and the oil was found to be safe for topical application. The minimum inhibitory concentration and minimum bactericidal concentration values were noted as 16 μl/ml. PRO reduced the cytokine levels of TNF-α, IL-12 and IL-8 and inhibited tyrosinase. A low concentration of the oil (up to 0.5 μl/ml) produced malondialdehyde levels equivalent to that of untreated cells. Conclusion: PRO may prove useful as a natural topical agent in the management of acne.
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Affiliation(s)
- Sheefali Mahant
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA
| | - Sanju Nanda
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
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13
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Ahluwalia P, Ahluwalia M, Mondal AK, Sahajpal NS, Kota V, Rojiani MV, Kolhe R. Natural Killer Cells and Dendritic Cells: Expanding Clinical Relevance in the Non-Small Cell Lung Cancer (NSCLC) Tumor Microenvironment. Cancers (Basel) 2021; 13:cancers13164037. [PMID: 34439191 PMCID: PMC8394984 DOI: 10.3390/cancers13164037] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major subtype of lung cancer that accounts for almost 85% of lung cancer cases worldwide. Although recent advances in chemotherapy, radiotherapy, and immunotherapy have helped in the clinical management of these patients, the survival rate in advanced stages remains dismal. Furthermore, there is a critical lack of accurate prognostic and stratification markers for emerging immunotherapies. To harness immune response modalities for therapeutic benefits, a detailed understanding of the immune cells in the complex tumor microenvironment (TME) is required. Among the diverse immune cells, natural killer (NK cells) and dendritic cells (DCs) have generated tremendous interest in the scientific community. NK cells play a critical role in tumor immunosurveillance by directly killing malignant cells. DCs link innate and adaptive immune systems by cross-presenting the antigens to T cells. The presence of an immunosuppressive milieu in tumors can lead to inactivation and poor functioning of NK cells and DCs, which results in an adverse outcome for many cancer patients, including those with NSCLC. Recently, clinical intervention using modified NK cells and DCs have shown encouraging response in advanced NSCLC patients. Herein, we will discuss prognostic and predictive aspects of NK cells and DC cells with an emphasis on NSCLC. Additionally, the discussion will extend to potential strategies that seek to enhance the anti-tumor functionality of NK cells and DCs.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (A.K.M.); (N.S.S.)
| | - Meenakshi Ahluwalia
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (A.K.M.); (N.S.S.)
| | - Nikhil S. Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (A.K.M.); (N.S.S.)
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Mumtaz V. Rojiani
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (A.K.M.); (N.S.S.)
- Correspondence: ; Tel.: +1-706-721-2771; Fax: +1-706-434-6053
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14
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Sahajpal NS, Mondal AK, Ananth S, Njau A, Fulzele S, Ahaluwalia P, Chaubey A, Hegde M, Rojiani AM, Kolhe R. Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic. Acad Pathol 2021; 8:23742895211023948. [PMID: 34263025 PMCID: PMC8246561 DOI: 10.1177/23742895211023948] [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: 12/23/2020] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 11/30/2022] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, led to unprecedented demands assigned to clinical diagnostic laboratories worldwide, forcing them to make significant changes to their regular workflow as they adapted to new diagnostic tests and sample volumes. Herein, we summarize the modifications/adaptation the laboratory had to exercise to cope with rapidly evolving situations in the current pandemic. In the first phase of the pandemic, the laboratory validated 2 reverse transcription polymerase chain reaction–based assays to test ∼1000 samples/day and rapidly modified procedures and validated various preanalytical and analytical steps to overcome the supply chain constraints that would have otherwise derailed testing efforts. Further, the pooling strategy was validated for wide-scale population screening using nasopharyngeal swab samples and saliva samples. The translational research arm of the laboratory pursued several initiatives to understand the variable clinical manifestations that this virus presented in the population. The phylogenetic evolution of the virus was investigated using next-generation sequencing technology. The laboratory has initiated the formation of a consortium that includes groups investigating genomes at the level of large structural variants, using genome optical mapping via this collaborative global effort. This article summarizes our journey as the laboratory has sought to adapt and continue to positively contribute to the unprecedented demands and challenges of this rapidly evolving pandemic.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Allan Njau
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Sadanand Fulzele
- Center for Healthy Aging, Medical College of Georgia, Augusta University, GA, USA
| | - Pankaj Ahaluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Madhuri Hegde
- Global Laboratory Services, PerkinElmer Inc, Waltham, GA, USA
| | - Amyn M Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
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15
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Sahajpal NS, Mondal AK, Ananth S, Njau A, Ahluwalia P, Kota V, Caspary K, Ross TM, Farrell M, Shannon MP, Fulzele S, Chaubey A, Hegde M, Rojiani AM, Kolhe R. Clinical Validation of a Sensitive Test for Saliva Collected in Healthcare and Community Settings with Pooling Utility for Severe Acute Respiratory Syndrome Coronavirus 2 Mass Surveillance. J Mol Diagn 2021; 23:788-795. [PMID: 33957320 PMCID: PMC8129802 DOI: 10.1016/j.jmoldx.2021.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 10/14/2020] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 12/28/2022] Open
Abstract
The clinical performance of saliva compared with nasopharyngeal swabs (NPSs) has shown conflicting results in healthcare and community settings. In the present study, a total of 429 matched NPS and saliva sample pairs, collected in either healthcare or community setting, were evaluated. Phase-1 (protocol U) tested 240 matched NPS and saliva sample pairs; phase 2 (SalivaAll protocol) tested 189 matched NPS and saliva sample pairs, with an additional sample homogenization step before RNA extraction. A total of 85 saliva samples were evaluated with both protocols. In phase-1, 28.3% (68/240) samples tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from saliva, NPS, or both. The detection rate from saliva was lower compared with that from NPS samples (50.0% versus 89.7%). In phase-2, 50.2% (95/189) samples tested positive for SARS-CoV-2 from saliva, NPS, or both. The detection rate from saliva was higher compared with that from NPS samples (97.8% versus 78.9%). Of the 85 saliva samples evaluated with both protocols, the detection rate was 100% for samples tested with SalivaAll, and 36.7% with protocol U. The limit of detection with SalivaAll protocol was 20 to 60 copies/mL. The pooled testing approach demonstrated a 95% positive and 100% negative percentage agreement. This protocol for saliva samples results in higher sensitivity compared with NPS samples and breaks the barrier to using pooled saliva for SARS-CoV-2 testing.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Allan Njau
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Kevin Caspary
- 4th Weapons of Mass Destruction Civil Support Team, Georgia Army National Guard, Marietta, Georgia
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia
| | - Michael Farrell
- Institute for Internet Security and Privacy, Georgia Institute of Technology, Atlanta, Georgia
| | - Michael P Shannon
- Advanced Warfighting Technologies Division, Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, Georgia
| | - Sadanand Fulzele
- Center for Healthy Aging, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Madhuri Hegde
- Global Laboratory Services, PerkinElmer Inc., Waltham, Massachusetts
| | - Amyn M Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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16
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S Sahajpal N, Mondal AK, Njau A, Ananth S, Jones K, Ahluwalia PK, Ahluwalia M, Jilani Y, Chaubey A, Hegde M, Kota V, Rojiani A, Kolhe R. Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints. Future Microbiol 2020; 15:1483-1487. [PMID: 33179525 DOI: 10.2217/fmb-2020-0094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Allan Njau
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Pankaj K Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Meenakshi Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Yasmeen Jilani
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Alka Chaubey
- Global Laboratory Services, PerkinElmer, Waltham, MA 02451, USA
| | - Madhuri Hegde
- Global Laboratory Services, PerkinElmer, Waltham, MA 02451, USA
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Amyn Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, GA 30912, USA
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17
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Sahajpal NS, Jain SK. Molecular Remodeling of the Insulin Receptor Pathway by Thiazolidinediones in Type 2 Diabetes Mellitus: A Brief Review. Protein Pept Lett 2016; 23:836-47. [PMID: 27397605 DOI: 10.2174/0929866523666160703183541] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 11/22/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by abnormalities in carbohydrate, lipoprotein and lipid metabolism, leading to hyperglycemia and several other complications. Insulin is the major hormone regulating these facets by eliciting various biological responses through its receptor. Insulin exerts diverse effects on cells by targeting distinct functions such as gene expression, fatty acid synthesis, glucose transport and receptor translocation. Insulin mediates these effects through signaling pathways utilizing adapter molecules like small Gproteins, lipid and tyrosine kinases. The anomalous cell response in diabetic condition is due to altered expression/function of these molecules. Thiazolidinediones (TZD's), a class of oral hypoglycemic drugs, have shown to modify these responses, leading to insulin sensitizing effect(s). The TZD's are not only PPARγ agonists, but substantial insulin sensitizing activity is observed through its direct and indirect targets of the insulin receptor pathway, which contributes to its overall performance. TZD's alter(s) cell response via downstream players, primarily IRS, Akt/PKB, PKC, GLUT4, MEK, ERK and transcription factor PGC1α. Thus, this review will focus on the alteration(s) of these molecules in various cell types in diabetic condition and their regulation by TZD's. The physiological changes that occur at the molecular level in T2DM and their modulation by TZD's will provide insights into the key players involved and the potential drug targets for future drug development. The review further highlights the key markers to be evaluated in screening of any potential anti-diabetic agent, and to standardize therapy for T2DM based upon its modulation of the various signaling pathways.
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Affiliation(s)
| | - Subheet K Jain
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, (A University with potential for excellence status by UGC, New Delhi), Amritsar [Punjab] 143 005 INDIA.
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