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Carrillo-Ng H, Arvanitis L, Manoukian S, Arias-Stella JA. Metastatic Testicular Sex Cord Tumor Harboring a EWSR1::ATF1 Gene Fusion-A Case Report of a Novel Neoplasm: "Inflammatory and Nested Testicular Sex Cord Tumor". Int J Surg Pathol 2024; 32:830-837. [PMID: 37715645 DOI: 10.1177/10668969231195043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
We present a case report of a 54-year-old male with a metastatic testicular sex cord tumor harboring a EWSR1::ATF1 gene fusion. The tumor displayed a solid and nested architecture with sclerotic stroma and variable inflammatory infiltrate, and was positive for SF-1, inhibin, EMA, CD30, and WT1 expression. Further genetic analysis identified a EWSR1::ATF1 gene fusion. Overall findings were consistent with an "inflammatory and nested testicular sex cord tumor," a recently described testicular neoplasm characterized by EWSR1::ATF1 gene fusion and aggressive clinical behavior. Due to the aggressive nature of this entity and the limited response to current treatment options available, identification of potential biomarkers for early diagnosis and targeted therapies are critical. This case report provides important insights into the genomic landscape of testicular sex cord-stromal tumors, especially within the CTNNB1-negative subset of patients with an aggressive clinical course, and further supports the distinction of "inflammatory and nested testicular sex cord tumor" as a separate entity from Sertoli cell tumors due to its characteristic morphological, immunohistochemical and molecular, features and clinical behavior.
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Affiliation(s)
- Hugo Carrillo-Ng
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Saro Manoukian
- Department of Diagnostic Radiology, City of Hope National Medical Center, Duarte, CA, USA
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2
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Kunimasa K, Tamiya M, Inoue T, Kawamura T, Miyazaki A, Kojitani Y, Honma K, Nishino K. Clinical application of the Lung Cancer Compact Panel TM using various types of cytological specimens in patients with lung cancer. Lung Cancer 2024; 189:107498. [PMID: 38324922 DOI: 10.1016/j.lungcan.2024.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND The Lung Cancer Compact PanelTM (compact panel) is a gene panel that can detect driver alterations with high sensitivity in liquid samples, including tumor cells. This study examined the ability of a compact panel to detect genetic mutations in liquid specimens used in clinical practice. METHODS Three cohorts, bronchoscopic biopsy forceps washing (washing cohort), pleural effusion (pleural cohort), and spinal fluid (spinal cohort), were analyzed using the compact panel. Liquid samples were added into the GM (Genemetrics) tubes and analyzed. The washing cohort assessed the concordance rate of gene panel analysis outcomes in tissue specimens derived from the primary tumor. Meanwhile, the pleural cohort investigated the impact of storing specimens for 8 weeks and more on nucleic acid and mutation detection rates. RESULTS In the washing cohort (n = 79), the concordance rate with mutations detected in tissues was 75/79 (94.9 %). This rate reached 100 % when focusing solely on driver alterations for treatment. The pleural cohort (n = 8) showed no deterioration in nucleic acid quality or quantity after 8 weeks of storage in GM tubes. Similarly, in the spinal cohort (n = 9), spinal fluid with malignant cells exhibited driver alterations similar to those in the primary tumor. These findings underscore the efficacy of the compact panel in accurately identifying genetic mutations in different liquid specimens. CONCLUSIONS The compact panel is a reliable tool for detecting driver alterations in various cytological specimens. Its consistent performance across diverse sample types emphasizes its potential for guiding targeted therapies for patients with lung cancer and enhancing precision medicine approaches.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan.
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takahisa Kawamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Akito Miyazaki
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yoshiki Kojitani
- Department of Medical Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology & Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
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3
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Kulkarni A, Tanga S, Karmakar A, Hota A, Maji B. CRISPR-Based Precision Molecular Diagnostics for Disease Detection and Surveillance. ACS APPLIED BIO MATERIALS 2023; 6:3927-3945. [PMID: 37788375 DOI: 10.1021/acsabm.3c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Sensitive, rapid, and portable molecular diagnostics is the future of disease surveillance, containment, and therapy. The recent SARS-CoV-2 pandemic has reminded us of the vulnerability of lives from ever-evolving pathogens. At the same time, it has provided opportunities to bridge the gap by translating basic molecular biology into therapeutic tools. One such molecular biology technique is CRISPR (clustered regularly interspaced short palindromic repeat) which has revolutionized the field of molecular diagnostics at the need of the hour. The use of CRISPR-Cas systems has been widespread in biology research due to the ease of performing genetic manipulations. In 2012, CRISPR-Cas systems were, for the first time, shown to be reprogrammable, i.e., capable of performing sequence-specific gene editing. This discovery catapulted the field of CRISPR-Cas research and opened many unexplored avenues in the field of gene editing, from basic research to therapeutics. One such field that benefitted greatly from this discovery was molecular diagnostics, as using CRISPR-Cas technologies enabled existing diagnostic methods to become more sensitive, accurate, and portable, a necessity in disease control. This Review aims to capture some of the trajectories and advances made in this arena and provides a comprehensive understanding of the methods and their potential use as point-of-care diagnostics.
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Affiliation(s)
- Akshara Kulkarni
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Sadiya Tanga
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Arkadeep Karmakar
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Arpita Hota
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Basudeb Maji
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
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4
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Lee K, Lee J, Choi J, Sim SH, Kim JE, Kim MH, Park YH, Kim JH, Koh SJ, Park KH, Kang MJ, Ahn MS, Lee KE, Kim HJ, Ahn HK, Kim HJ, Park KU, Park IH. Genomic analysis of plasma circulating tumor DNA in patients with heavily pretreated HER2 + metastatic breast cancer. Sci Rep 2023; 13:9928. [PMID: 37336919 DOI: 10.1038/s41598-023-35925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023] Open
Abstract
We explored accumulated genomic alterations in patients with heavily treated HER2 + metastatic breast cancer enrolled in the KCSG BR18-14/KM10B trial. Targeted sequencing was performed with circulating tumor DNAs (ctDNAs) collected before the treatment of 92 patients. ctDNAs collected at the time of disease progression from seven patients who had a durable response for > 12 months were also analyzed. Sixty-five genes were identified as pathogenic alterations in 99 samples. The most frequently altered genes were TP53 (n = 48), PIKCA (n = 21) and ERBB3 (n = 19). TP53 and PIK3CA mutations were significantly related with shorter progression free survival (PFS), and patients with a higher ctDNA fraction showed a worse PFS. The frequency of homologous recombination deficiency (HRD)-related gene mutations was higher than that in matched tumor tissues, and these mutations tended to be associated with shorter PFS. New pathogenic variants were found at the end of treatment in all seven patients, including BRCA2, VHL, RAD50, RB1, BRIP1, ATM, FANCA, and PIK3CA mutations. In conclusion, TP53 and PIK3CA mutations, as well as a higher ctDNA fraction, were associated with worse PFS with trastuzumab and cytotoxic chemotherapy. The enrichment of HRD-related gene mutations and newly detected variants in ctDNA may be related to resistance to treatment.
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Affiliation(s)
- Kyoungmin Lee
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jongwon Lee
- Brain Korea 21 Plus Project for Biomedical Science, Korea University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sung Hoon Sim
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yeon Hee Park
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Su-Jin Koh
- Department of Hematology and Oncology, Ulsan University Hospital, Ulsan University College of Medicine, Ulsan, Korea
| | - Kyong Hwa Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Myoung Joo Kang
- Division of Oncology, Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Mi Sun Ahn
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Kyoung Eun Lee
- Department of Hematology and Oncology, Ewha Womans University Hospital, Seoul, Korea
| | - Hee-Jun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Chung-Ang University Hospital, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Han Jo Kim
- Division of Oncology and Hematology, Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Keon Uk Park
- Division of Hematology/Oncology, Department of Internal Medicine, Keimyung University Dongsan Hospital, Daegu, Korea
| | - In Hae Park
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea.
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Salik D, Richert B, Smits G. Clinical and molecular diagnosis of genodermatoses: Review and perspectives. J Eur Acad Dermatol Venereol 2023; 37:488-500. [PMID: 36502512 DOI: 10.1111/jdv.18769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
Genodermatoses are a complex and heterogeneous group of genetic skin disorders characterized by variable expression and clinical and genetic heterogeneity, rendering their diagnosis challenging. DNA-based techniques, like whole-exome sequencing, can establish a diagnosis in 50% of cases. RNA-sequencing is emerging as an attractive tool that can obtain information regarding gene expression while integrating functional genomic data with regard to the interpretation of variants. This increases the diagnostic rate by an additional 10-15%. In the present review, we detail the clinical steps involved in the diagnosis of genodermatoses, as well as the current DNA-based technologies available to clinicians. Herein, the intention is to facilitate a better understanding of the possibilities and limitations of these diagnostic technologies. In addition, this review could guide dermatologists through new emerging techniques, such as RNA-sequencing and its applications to familiarizing them with future techniques. Currently, this multi-omics approach is likely the best strategy designed to promote the diagnosis of patients with genodermatoses and discover new skin disease genes that could result in novel targeted therapies.
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Affiliation(s)
- Deborah Salik
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Bertrand Richert
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics Université Libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
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6
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Yu C, Qi X, Yan W, Wu W, Shen B. Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:576-585. [PMID: 35085089 DOI: 10.1109/tcbb.2022.3144170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.
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Polyphenols as Potent Epigenetics Agents for Cancer. Int J Mol Sci 2022; 23:ijms231911712. [PMID: 36233012 PMCID: PMC9570183 DOI: 10.3390/ijms231911712] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 02/06/2023] Open
Abstract
Human diseases such as cancer can be caused by aberrant epigenetic regulation. Polyphenols play a major role in mammalian epigenome regulation through mechanisms and proteins that remodel chromatin. In fruits, seeds, and vegetables, as well as food supplements, polyphenols are found. Compounds such as these ones are powerful anticancer agents and antioxidants. Gallic acid, kaempferol, curcumin, quercetin, and resveratrol, among others, have potent anti-tumor effects by helping reverse epigenetic changes associated with oncogene activation and tumor suppressor gene inactivation. The role dietary polyphenols plays in restoring epigenetic alterations in cancer cells with a particular focus on DNA methylation and histone modifications was summarized. We also discussed how these natural compounds modulate gene expression at the epigenetic level and described their molecular targets in cancer. It highlights the potential of polyphenols as an alternative therapeutic approach in cancer since they modulate epigenetic activity.
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8
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Ma H, Wang X, Yan H, Liu Q, Yang D, Bian T. Dual intracranial infection with Nocardia farcinica and Cryptococcus neoformans diagnosed by next-generation sequencing in a patient with nephrotic syndrome: A case report. Medicine (Baltimore) 2022; 101:e30325. [PMID: 36107518 PMCID: PMC9439795 DOI: 10.1097/md.0000000000030325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RATIONALE Intracranial infections are associated with high morbidity and mortality in immunocompromised patients, due to delayed diagnosis and treatment. Establishing a rapid, accurate diagnosis and a precise therapeutic regimen is crucial for management of the patients. Our report described a rare intracranial infection of patient with nephrotic syndrome. PATIENT CONCERNS A 66-year-old woman with a history of nephrotic syndrome presented symptoms in central nervous system for 1 month, followed by headache and fever over several days. DIAGNOSIS Neurological examination, brain imaging, and cerebrospinal fluid (CSF) tests exhibited resemblance to intracranial infection. Subsequently, CSF cultures confirmed the presence of Cryptococcus. Fortunately, next-generation sequencing revealed the concomitant infection with Nocardia farcinica in addition to Cryptococcus neoformans. INTERVENTIONS The treatment with intravenous fluconazole combined with amphotericin could not immediately ameliorate her symptoms. The patient's condition improved significantly with minimal deficits after timely administration of antibiotics against N farcinica. OUTCOMES One month later, cranial MRI indicated that basal ganglia lesions ameliorated. The patient has recovered well. LESSONS SUBSECTIONS To our best knowledge, this is the first case report of intracranial infection caused by both N farcinica and C neoformans in a patient with nephrotic syndrome. Remarkably, extensive application of next-generation sequencing can facilitate investigation on the potential role of various pathogenic organisms in infectious diseases.
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Affiliation(s)
- Hongmei Ma
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
- *Correspondence: Hongmei Ma, Department of Neurology, Beijing Fengtai You’anmen Hospital, No. 199 You’anmen Wai Avenue, Fengtai District, Beijing 100069, China (e-mail: )
| | - Xiangbo Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Heli Yan
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Qing Liu
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
| | - Dan Yang
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
| | - Tingting Bian
- Department of Neurology, Beijing Fengtai You’anmen Hospital, BeijingChina
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Dotolo S, Esposito Abate R, Roma C, Guido D, Preziosi A, Tropea B, Palluzzi F, Giacò L, Normanno N. Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice. Biomedicines 2022; 10:biomedicines10092074. [PMID: 36140175 PMCID: PMC9495893 DOI: 10.3390/biomedicines10092074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).
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Affiliation(s)
- Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Davide Guido
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Alessia Preziosi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Beatrice Tropea
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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Pandey SK, Mohanta GC, Kumar V, Gupta K. Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection. Vaccines (Basel) 2022; 10:1200. [PMID: 36016088 PMCID: PMC9414050 DOI: 10.3390/vaccines10081200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.
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Affiliation(s)
- Satish Kumar Pandey
- Department of Biotechnology, School of Life Sciences, Mizoram University (Central University), Aizawl 796004, India
| | - Girish C. Mohanta
- Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh 160030, India;
| | - Vinod Kumar
- Department of Dermatology, Venerology and Leprology, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Kuldeep Gupta
- Russel H. Morgan, Department of Radiology and Radiological Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
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11
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Liu MC, MacKay M, Kase M, Piwowarczyk A, Lo C, Schaeffer J, Finkle JD, Mason CE, Beaubier N, Blackwell KL, Park BH. Longitudinal Shifts of Solid Tumor and Liquid Biopsy Sequencing Concordance in Metastatic Breast Cancer. JCO Precis Oncol 2022; 6:e2100321. [PMID: 35721584 PMCID: PMC9200387 DOI: 10.1200/po.21.00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/17/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue-based next-generation sequencing (NGS) in metastatic breast cancer (mBC) is limited by the inability to noninvasively track tumor evolution. Cell-free DNA (cfDNA) NGS has made sequential testing feasible; however, the relationship between cfDNA and tissue-based testing in mBC is not well understood. Here, we evaluate concordance between tissue and cfDNA NGS relative to cfDNA sampling frequency in a large, clinically annotated mBC data set. METHODS Tempus LENS was used to analyze deidentified records of mBC cases with Tempus xT (tissue) and xF (cfDNA) sequencing results. Then, various metrics of concordance were assessed within overlapping probe regions of the tissue and cfDNA assays (104 genes), focusing on pathogenic variants. Variant allele frequencies of discordant and concordant pathogenic variants were also compared. Analyses were stratified by mBC subtype and time between tests. RESULTS Records from 300 paired tissue and liquid biopsies were analyzed. Median time between tissue and blood collection was 78.5 days (standard deviation = 642.99). The median number of pathogenic variants/patient was one for cfDNA and two for tissue. Across the cohort, 77.8% of pathogenic tissue variants were found in cfDNA and 75.7% of pathogenic cfDNA variants were found in tissue when tests were ≤ 7 days apart, which decreased to 50.3% and 51.8%, respectively, for > 365 days. Furthermore, the median patient-level variant concordance was 67% when tests were ≤7 days apart and 30%-37% when > 30 days. The median variant allele frequencies of discordant variants were generally lower than those of concordant variants within the same time frame. CONCLUSION We observed high concordances between tissue and cfDNA results that generally decreased with longer durations between tests. Thus, cfDNA NGS reliably measures tissue genomics and is likely beneficial for longitudinal monitoring of molecular changes in mBC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, TN
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12
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Michelini S, Herbst KL, Precone V, Manara E, Marceddu G, Dautaj A, Maltese PE, Paolacci S, Ceccarini MR, Beccari T, Sorrentino E, Aquilanti B, Velluti V, Matera G, Gagliardi L, Miggiano GAD, Bertelli M. A Multi-Gene Panel to Identify Lipedema-Predisposing Genetic Variants by a Next-Generation Sequencing Strategy. J Pers Med 2022; 12:jpm12020268. [PMID: 35207755 PMCID: PMC8877075 DOI: 10.3390/jpm12020268] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/25/2022] Open
Abstract
Lipedema is a disabling disease characterized by symmetric enlargement of the lower and/or upper limbs due to deposits of subcutaneous fat, that is easily misdiagnosed. Lipedema can be primary or syndromic, and can be the main feature of phenotypically overlapping disorders. The aim of this study was to design a next-generation sequencing (NGS) panel to help in the diagnosis of lipedema by identifying genes specific for lipedema but also genes for overlapping diseases, and targets for tailored treatments. We developed an NGS gene panel consisting of 305 genes potentially associated with lipedema and putative overlapping diseases relevant to lipedema. The genomes of 162 Italian and American patients with lipedema were sequenced. Twenty-one deleterious variants, according to 3 out of 5 predictors, were detected in PLIN1, LIPE, ALDH18A1, PPARG, GHR, INSR, RYR1, NPC1, POMC, NR0B2, GCKR, PPARA in 17 patients. This extended NGS-based approach has identified a number of gene variants that may be important in the diagnosis of lipedema, that may affect the phenotypic presentation of lipedema or that may cause disorders that could be confused with lipedema. This tool may be important for the diagnosis and treatment of people with pathologic subcutaneous fat tissue accumulation.
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Affiliation(s)
- Sandro Michelini
- Vascular Diagnostics and Rehabilitation Service, Marino Hospital, ASL Roma 6, 00047 Marino, Italy;
| | - Karen L. Herbst
- Department of Endocrinology and Research, Total Lipedema Care, Los Angeles, CA 90211, USA;
| | - Vincenza Precone
- MAGI EUREGIO, 39100 Bolzano, Italy; (V.P.); (G.M.); (E.S.); (M.B.)
| | - Elena Manara
- MAGI’S LAB, 38068 Rovereto, Italy; (E.M.); (A.D.); (P.E.M.)
| | | | - Astrit Dautaj
- MAGI’S LAB, 38068 Rovereto, Italy; (E.M.); (A.D.); (P.E.M.)
| | | | - Stefano Paolacci
- MAGI’S LAB, 38068 Rovereto, Italy; (E.M.); (A.D.); (P.E.M.)
- Correspondence:
| | - Maria Rachele Ceccarini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy; (M.R.C.); (T.B.)
- C.I.B., Consorzio Interuniversitario per le Biotecnologie, 34148 Trieste, Italy
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy; (M.R.C.); (T.B.)
- C.I.B., Consorzio Interuniversitario per le Biotecnologie, 34148 Trieste, Italy
| | - Elisa Sorrentino
- MAGI EUREGIO, 39100 Bolzano, Italy; (V.P.); (G.M.); (E.S.); (M.B.)
| | - Barbara Aquilanti
- UOC Nutrizione Clinica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (B.A.); (V.V.); (G.M.); (L.G.); (G.A.D.M.)
| | - Valeria Velluti
- UOC Nutrizione Clinica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (B.A.); (V.V.); (G.M.); (L.G.); (G.A.D.M.)
| | - Giuseppina Matera
- UOC Nutrizione Clinica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (B.A.); (V.V.); (G.M.); (L.G.); (G.A.D.M.)
| | - Lucilla Gagliardi
- UOC Nutrizione Clinica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (B.A.); (V.V.); (G.M.); (L.G.); (G.A.D.M.)
| | - Giacinto Abele Donato Miggiano
- UOC Nutrizione Clinica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (B.A.); (V.V.); (G.M.); (L.G.); (G.A.D.M.)
| | - Matteo Bertelli
- MAGI EUREGIO, 39100 Bolzano, Italy; (V.P.); (G.M.); (E.S.); (M.B.)
- MAGI’S LAB, 38068 Rovereto, Italy; (E.M.); (A.D.); (P.E.M.)
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13
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Piening BD, Dowdell AK, Zhang M, Loza BL, Walls D, Gao H, Mohebnasab M, Li YR, Elftmann E, Wei E, Gandla D, Lad H, Chaib H, Sweitzer NK, Deng M, Pereira AC, Cadeiras M, Shaked A, Snyder MP, Keating BJ. Whole Transcriptome Profiling of Prospective Endomyocardial Biopsies Reveals Prognostic and Diagnostic Signatures of Cardiac Allograft Rejection. J Heart Lung Transplant 2022; 41:840-848. [DOI: 10.1016/j.healun.2022.01.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022] Open
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14
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Cho JH, Charnot-Katsikas A, Segal J, Pytel P. Identification of Molecular Alterations Challenging Initial Pathologic Classification in Cases of Clinician-Initiated Next-Generation Sequencing Testing. Am J Clin Pathol 2021; 156:1007-1018. [PMID: 34180985 DOI: 10.1093/ajcp/aqab062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Large gene panel next-generation sequencing (NGS) is a powerful tool capable of generating predictive data on cancer prognosis and response to specific therapeutic interventions. The utility of large panel NGS data on tumor classification, however, may be underappreciated because of a workflow that often circumvents the surgical pathologist. We sought to describe cases in which NGS data lead to an unanticipated change in tumor classification and to discuss current workflow practices of NGS testing that limit its use as a diagnostic adjunct. METHODS We performed a retrospective review to identify cases in which NGS testing uncovered data that led to a revision of the initial pathologic diagnosis that an outside or in-house pathologist had made. RESULTS Nine cases are presented in which NGS data provided insights that led to a revision of the original pathologic diagnosis. Distinctive molecular signatures, mutational signatures, fusions, or identification of viral sequencing provided the critical evidence on which these tumors were reclassified. CONCLUSIONS The current workflow of NGS testing should always include the surgical pathologist as an active partner to ensure that the molecular results are fully reflected in the final diagnosis. In some instances, active participation by the surgical pathologist may require amendment of previously issued pathology reports.
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Affiliation(s)
- Joseph H Cho
- Medical Sciences Institute, Versiti Blood Center of Wisconsin, Milwaukee, WI, USA
| | | | - Jeremy Segal
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Peter Pytel
- Department of Pathology, University of Chicago, Chicago, IL, USA
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15
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Moura E, Daltro SRT, Sás DM, Engracia Filho JR, Farias MR, Pimpão CT. Genetic analysis of a possible case of canine X-linked ectodermal dysplasia. J Small Anim Pract 2021; 62:1127-1130. [PMID: 34076266 DOI: 10.1111/jsap.13385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/07/2021] [Accepted: 05/16/2021] [Indexed: 11/30/2022]
Abstract
In the present report, we describe targeted next-generation sequencing of the EDA gene of a male poodle with a clinical and histopathological diagnosis of X-linked hypohidrotic ectodermal dysplasia. The result was compared with the reference sequence and with the result of the sequencing of a normal dog's EDA gene. No point variant, small deletion or insertion were found in the exons and splice sites, but a transition and a transversion were found in the intron 6' and 3' UTR, respectively. The cause of the dysplasia of the affected dog in this study is neither a point variant nor a small deletion or insertion in the exons and splice sites of the EDA gene. Therefore, patients with phenotype of XLHED may have other types of variants in the EDA gene or variants in other genes of the EDA signalling pathway.
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Affiliation(s)
- E Moura
- Service of Medical Genetics, Course of Veterinary Medicine, School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - S R T Daltro
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - D M Sás
- Genotyping - Diagnósticos Genéticos, Botucatu, São Paulo, Brazil
| | - J R Engracia Filho
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - M R Farias
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - C T Pimpão
- Graduate Program in Animal Science, School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
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16
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Angerilli V, Galuppini F, Pagni F, Fusco N, Malapelle U, Fassan M. The Role of the Pathologist in the Next-Generation Era of Tumor Molecular Characterization. Diagnostics (Basel) 2021; 11:339. [PMID: 33670699 PMCID: PMC7922586 DOI: 10.3390/diagnostics11020339] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Current pathology practice is being shaped by the increasing complexity of modern medicine, in particular of precision oncology, and major technological advances. In the "next-generation technologies era", the pathologist has become the person responsible for the integration and interpretation of morphologic and molecular information and for the delivery of critical answers to diagnostic, prognostic and predictive queries, acquiring a prominent position in the molecular tumor boards.
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Affiliation(s)
- Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Francesca Galuppini
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20122 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138 Naples, Italy;
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
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17
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Clinical phenotype associated with TANGO2 gene mutation. Arch Pediatr 2020; 28:80-86. [PMID: 33342685 DOI: 10.1016/j.arcped.2020.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/12/2020] [Accepted: 11/15/2020] [Indexed: 01/04/2023]
Abstract
The clinical picture associated with a Transport and Golgi Organization 2 (TANGO2) gene bi-allelic mutation is represented by encephalopathy and rhabdomyolysis marked by cardiac rhythm disorders and neurological regression. The presentation of encephalopathy is diverse and can range from isolated language delay and cognitive impairment in a child to multiple disabilities and spastic quadriparesis. Hypothyroidism has also been frequently reported. This article presents the clinical phenotype of seven children with a TANGO2 bi-allelic mutation. The mutation was found by sequencing a panel of genes associated with rhabdomyolysis. While the clinical picture represents generalized cases, there is phenotypic variability in, for example, the degree of disability for each patient. A TANGO2 gene mutation, nevertheless, represents a serious illness with a limited life expectancy due to an unpredictable risk of cardiac rhythm disorder and death, particularly during rhabdomyolysis. Although the natural history of the disease presents an evolution of rhabdomyolysis triggered by infections or effort, an early diagnosis is difficult due in part to the fact that there is a lack of specific biochemical marker or identifying symptoms in the early presentation of the disease. Clinicians must therefore consider the TANGO2 gene when confronted with rhabdomyolysis in a patient suffering from an early developmental disorder. In the meantime, management of the disease remains purely symptomatic.
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18
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De Cario R, Kura A, Suraci S, Magi A, Volta A, Marcucci R, Gori AM, Pepe G, Giusti B, Sticchi E. Sanger Validation of High-Throughput Sequencing in Genetic Diagnosis: Still the Best Practice? Front Genet 2020; 11:592588. [PMID: 33343633 PMCID: PMC7738558 DOI: 10.3389/fgene.2020.592588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS)'s crucial role in supporting genetic diagnosis and personalized medicine leads to the definition of Guidelines for Diagnostic NGS by the European Society of Human Genetics. Factors of different nature producing false-positive/negative NGS data together with the paucity of internationally accepted guidelines providing specified NGS quality metrics to be followed for diagnostics purpose made the Sanger validation of NGS variants still mandatory. We reported the analysis of three cases of discrepancy between NGS and Sanger sequencing in a cohort of 218 patients. NGS was performed by Illumina MiSeq® and Haloplex/SureSelect protocols targeting 97 or 57 or 10 gene panels usually applied for diagnostics. Variants called following guidelines suggested by the Broad Institute and identified according to MAF <0.01 and allele balance >0.2 were Sanger validated. Three out of 945 validated variants showed a discrepancy between NGS and Sanger. In all three cases, a deep evaluation of the discrepant gene variant results and methodological approach allowed to confirm the NGS datum. Allelic dropout (ADO) occurrence during polymerase chain or sequencing reaction was observed, mainly related to incorrect variant zygosity. Our study extends literature data in which almost 100% "high quality" NGS variants are confirmed by Sanger; moreover, it demonstrates that in case of discrepancy between a high-quality NGS variant and Sanger validation, NGS call should not be a priori assumed to represent the source of the error. Actually, difficulties (i.e., ADO, unpredictable presence of private variants on primer-binding regions) of the so-called gold standard direct sequencing should be considered especially in light of the constantly implemented and accurate high-throughput technologies. Our data along with literature raise a discussion on the opportunity to establish a standardized quality threshold by International Guidelines for clinical NGS in order to limit Sanger confirmation to borderline conditions of variant quality parameters and verification of correct gene variant call/patient coupling on a different blood sample aliquot.
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Affiliation(s)
- Rosina De Cario
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Andrea Volta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Florence, Italy
| | - Anna Maria Gori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Florence, Italy
| | - Guglielmina Pepe
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Florence, Italy
| | - Elena Sticchi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Atherothrombotic Diseases Center, Careggi University Hospital, Florence, Italy
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19
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Wang S, You H, Yu S. Long non-coding RNA HOXA-AS2 promotes the expression levels of hypoxia-inducible factor-1α and programmed death-ligand 1, and regulates nasopharyngeal carcinoma progression via miR-519. Oncol Lett 2020; 20:245. [PMID: 32973958 PMCID: PMC7509505 DOI: 10.3892/ol.2020.12107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy arising from the nasopharyngeal epithelium and belongs to the group of head and neck cancer types, which are usually associated with viral and/or environmental influences, as well as heredity causes. A recent study reported that the long non-coding RNA (lncRNA) HOXA cluster antisense RNA 2 (HOXA-AS2) may be a prognostic biomarker in NPC; however, the specific mechanisms underlying NCP progression are yet to be determined. The aim of the present study was to investigate the biological role of HOXA-AS2 in NPC. In the present study, the gene expression levels of HOXA-AS2, miR-519, hypoxia-inducible factor (HIF-1α) and programmed death-ligand 1 (PD-L1) were detected using reverse transcription-quantitative PCR (RT-qPCR) analysis and western blotting. Bioinformatics analysis and a dual luciferase reporter assay were performed to predict and confirm the direct interactions between HOXA-AS2 and microRNA (miR)-519, as well as between miR-519 and HIF-1α. A MTT assay was used to detect the cell viability, while cell migratory and invasive abilities were assessed using wound healing and Transwell assays. HOXA-AS2 and HIF-1α were found to be significantly upregulated in NPC tumor tissues, as well as in NPC cell lines. The overexpression of HOXA-AS2 significantly enhanced NPC progression, including the cell proliferative, migratory and invasive abilities. HOXA-AS2 was identified to directly bind to miR-519, whereas a miR-519 inhibitor significantly rescued the HOXA-AS2 knockdown-attenuated progression of NPC. Moreover, miR-519 could bind to HIF-1α and PD-L1. Overexpression of HIF-1α and PD-L1 significantly promoted NPC progression and partially recovered the phenotype of NPC cells attenuated by HOXA-AS2 knockdown. In conclusion, the present study demonstrated that HOXA-AS2/miR-519/HIF-1α and/or HOXA-AS2/miR-519/PD-L1 may be a novel mechanism regulating the progression of NPC, which may facilitate the development of targeted clinical therapy.
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Affiliation(s)
- Shuyong Wang
- Department of Otolaryngology, Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong 261041, P.R. China
| | - Huizeng You
- Department of Otolaryngology, Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong 261041, P.R. China
| | - Sa Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhuji People's Hospital of Zhejiang Province, Zhuji, Zhejiang 311800, P.R. China
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20
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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21
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Jing C, Wang T, Ma R, Cao H, Wang Z, Liu S, Chen D, Zhang J, Wu Y, Zhang Y, Wu J, Feng J. New genetic variations discovered in KRAS wild-type cetuximab resistant chinese colorectal cancer patients. Mol Carcinog 2020; 59:478-491. [PMID: 32141150 DOI: 10.1002/mc.23172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
To perform a comprehensive genomic analysis of colorectal cancer (CRC) tumor to detect genetic variants and identify novel resistant mutations associated with cetuximab-resistance in CRC patients. A retrospective study was performed using whole exome sequencing (WES) to identify common genetic factors from 22 cetuximab-sensitive and 10 cetuximab-resistant patients. In all 10 cetuximab-resistant patients, we discovered there are 37 significantly mutated genes (SMGs). CYP4A11 was the most frequently mutated gene in cetuximab-resistant patients. BCAS1 and GOLGA6L1 were found to be among the second group of frequently mutated genes with a frequency of 60%. After cosine similarity analysis, three mutational signatures (signature a, b, and c) were found in all CRC tumors, similar to signature 1, 5, and 6 in COSMIC, respectively. Gene ontology analysis was performed on SMGs and found 12 enriched GO terms. Four genes are enriched in six specific Kyoto Encyclopedia of Genes and Genomes pathway groups, including the metabolism of xenobiotics by cytochrome P450, steroid hormone biosynthesis, retinol metabolism, and drug metabolism. Our data supports a network composed of SMGs and cellular signaling pathways that have been positively linked to the mechanisms of cetuximab resistance. These involve DNA damage repair, angiogenesis, invasion, drug metabolism, and the CRC tumor microenvironment. There is a SMG, OR9G1 correlated with survival rates of KRAS wild-type colon adenocarcinoma patients. These findings support further investigation using WES in a prospective clinical study of cetuximab resistance CRC, to further identify, confirm, and extend the clinical significance of these and other potentially important new candidate predictive biomarkers of cetuximab response.
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Affiliation(s)
- Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Cell Biology, Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Siwen Liu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dan Chen
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Junying Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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22
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Molnár C, Bádon ES, Mokánszki A, Mónus A, Beke L, Győry F, Nagy E, Méhes G. High Genetic Diversity and No Evidence of Clonal Relation in Synchronous Thyroid Carcinomas Associated with Hashimoto's Thyroiditis: A Next-Generation Sequencing Analysis. Diagnostics (Basel) 2020; 10:diagnostics10010048. [PMID: 31963551 PMCID: PMC7167801 DOI: 10.3390/diagnostics10010048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 12/17/2022] Open
Abstract
The close association between pre-existing Hashimoto’s thyroiditis and thyroid cancer is well established. The simultaneous occurrence of multiple neoplastic foci within the same organ suggests a common genotoxic effect potentially contributing to carcinogenesis, the nature of which is still not clear. Next-generation sequencing (NGS) provides a potent tool to demonstrate and compare the mutational profile of the independent neoplastic foci. Our collection of 47 cases with thyroid carcinoma and Hashimoto’s thyroiditis included 14 with at least two tumorous foci. Detailed histological analysis highlighted differences in histomorphology, immunoprofile, and biological characteristics. Further, a 67-gene NGS panel was applied to demonstrate the mutational diversity of the synchronic tumors. Significant differences could be detected with a wide spectrum of pathogenic gene variants involved (ranging between 5 and 18, cutoff >5.0 variant allele frequencies (VAF)). Identical gene variants represented in both synchronous tumors of the same thyroid gland were found in only two cases (BRAF and JAK3 genes). An additional set of major driver mutations was identified at variable allele frequencies in a highly individual setup suggesting a clear clonal independence. The different BRAF statuses in coincident thyroid carcinoma foci within the same organ outline a special challenge for molecular follow-up and therapeutic decision-making.
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Affiliation(s)
- Csaba Molnár
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
| | - Lívia Beke
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
| | - Ferenc Győry
- Department of Surgery, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Endre Nagy
- Division of Endocrinology, Department of Internal Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (C.M.); (E.S.B.); (A.M.); (A.M.); (L.B.)
- Correspondence:
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23
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Paredes SR, Chan C, Rickard MJFX. Immunohistochemistry in screening for heritable colorectal cancer: what to do with an abnormal result. ANZ J Surg 2019; 90:702-707. [PMID: 31828933 DOI: 10.1111/ans.15586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 02/06/2023]
Abstract
Recent developments in our understanding of molecular genetics have transformed screening and diagnostic practices for Lynch syndrome. The current standard involves universal tumour analysis of resected colorectal cancer (and ideally polypectomy) specimens using immunohistochemistry and molecular techniques. Patients with abnormal immunohistochemical findings are subsequently referred for definitive mutational testing. This review relates the molecular pathogenesis of Lynch syndrome to current immunohistochemistry-based screening strategies and discusses the interpretation and clinical implications of screening results.
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Affiliation(s)
- Steven R Paredes
- Discipline of Surgery, School of Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Concord Clinical School, School of Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | - Charles Chan
- Concord Clinical School, School of Medicine, The University of Sydney, Sydney, New South Wales, Australia.,Anatomical Pathology Department, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
| | - Matthew J F X Rickard
- Discipline of Surgery, School of Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Division of Colorectal Surgery, Department of Surgery, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.,Division of Colorectal Surgery, Department of Surgery, Macquarie University Hospital, Macquarie University, Sydney, New South Wales, Australia
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24
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Nakayama T, Katagiri S, Kikkawa T, Obara T, Mori T, Kiriu T. Multiple atypical thymic carcinoids with paraneoplastic giant cell arteritis. Gen Thorac Cardiovasc Surg 2019; 68:1212-1215. [PMID: 31625085 DOI: 10.1007/s11748-019-01230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/10/2019] [Indexed: 11/25/2022]
Abstract
Multiple thymic carcinoids are rare, and giant cell arteritis (GCA) is one of the less recognized paraneoplastic diseases. The co-occurrence of these two diseases is therefore extremely rare. We report herein a patient with multiple atypical thymic carcinoids and asymptomatic paraneoplastic GCA. All the thymic carcinoids were diagnosed histopathologically as atypical thymic carcinoids with an intrathymic metastasis. Treatment consisted of a complete tumor resection followed by observation of the GCA without any adjuvant therapy. Subsequent positron emission tomography revealed a decrease in F-fludeoxyglucose accumulation in the systemic arteries. Based on these findings, paraneoplastic GCA was diagnosed. Thymic carcinoids rarely involve intrathymic metastasis or cause neopleonastic GCA. However, when they do, a complete tumor resection is the best option for management.
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Affiliation(s)
- Takashi Nakayama
- Department of General Thoracic Surgery, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashidai, Fuchu, Tokyo, 183-8524, Japan.
| | - Sayaka Katagiri
- Department of General Thoracic Surgery, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashidai, Fuchu, Tokyo, 183-8524, Japan
| | - Takuma Kikkawa
- Department of General Thoracic Surgery, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashidai, Fuchu, Tokyo, 183-8524, Japan
| | - Tetsuya Obara
- Department of General Thoracic Surgery, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashidai, Fuchu, Tokyo, 183-8524, Japan
| | - Tatsuo Mori
- Department of Intermedicine of Rheumatism, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
| | - Takahiro Kiriu
- Department of Pathology, Tokyo Metropolitan Tama Medical Center, Tokyo, Japan
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25
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Kiavash K, Bluth MH, Thompson AD. An Update Regarding the Molecular Genetics of Melanocytic Neoplasms and the Current Applications of Molecular Genetic Technologies in Their Diagnosis and Treatment. Clin Lab Med 2019; 38:385-399. [PMID: 29776637 DOI: 10.1016/j.cll.2018.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular genetic technologies are used to aid in diagnosis and treatment of borderline melanocytic tumors as an adjuvant to the gold standard histopathologic evaluation. A specific set of fluorescence in situ hybridization probes is widely used to aid in diagnosing challenging melanocytic lesions. New melanoma probe cocktails have revealed increased sensitivity and specificity in ambiguous melanocytic cases. Array comparative genomic hybridization is a more complex technology used for the work-up of diagnostically problematic Spitzoid melanocytic proliferations. Cutting-edge technologies, including next-generation sequencing and cell-free nucleic acid analysis, are promising biomarker applications for mutation detection towards personalized patient management.
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Affiliation(s)
- Katrin Kiavash
- Department of Pathology, Wayne State University, 4160 John R Street, Detroit, MI 48201, USA; Department of Pathology and Laboratory Medicine, Detroit Medical Center University Laboratories, 4160 John R Street, Detroit, MI 48201, USA
| | - Martin H Bluth
- Department of Pathology, Wayne State University, 4160 John R Street, Detroit, MI 48201, USA; Department of Pathology, Wayne State University, School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Andrew David Thompson
- Department of Pathology, Wayne State University, 4160 John R Street, Detroit, MI 48201, USA; Department of Pathology and Laboratory Medicine, Detroit Medical Center University Laboratories, 4160 John R Street, Detroit, MI 48201, USA.
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