Application of Next Generation Sequencing in Laboratory Medicine
Yiming Zhong 
, Ph.D, Feng Xu , Ph.D, Jinhua Wu , Ph.D, Jeffrey Schubert , Ph.D, and Marilyn M. Li , M.D
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Review Article2021-01-01
Abstract : The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Review Article2021-03-01
Role of Genetic Variants and Gene Expression in the Susceptibility and Severity of COVID-19
Sarita Choudhary
Ann Lab Med 2021; 41(2): 129-138, M.D., Karli Sreenivasulu , Ph.D., Prasenjit Mitra , M.D., Sanjeev Misra , M.S., M.Ch., and Praveen Sharma , Ph.D.Abstract : Since its first report in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly emerged as a pandemic affecting nearly all countries worldwide. As the COVID-19 pandemic progresses, the need to identify genetic risk factors for susceptibility to this serious illness has emerged. Host genetic factors, along with other risk factors may help determine susceptibility to respiratory tract infections. It is hypothesized that the ACE2 gene, encoding angiotensin-converting enzyme 2 (ACE2), is a genetic risk factor for SARS-CoV-2 infection and is required by the virus to enter cells. Together with ACE2, transmembrane protease serine 2 (TMPRSS2) and dipeptidyl peptidase-4 (DPP4) also play an important role in disease severity. Evaluating the role of genetic variants in determining the direction of respiratory infections will help identify potential drug target candidates for further study in COVID-19 patients. We have summarized the latest reports demonstrating that ACE2 variants, their expression, and epigenetic factors may influence an individual’s susceptibility to SARS-CoV-2 infection and disease outcome.
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Review Article2021-11-01
General Laboratory Medicine
Biomarkers for Prognosis and Treatment Response in COVID-19 Patients
Giulia Bivona
Ann Lab Med 2021; 41(6): 540-548, M.D., Luisa Agnello , Ph.D., and Marcello Ciaccio , M.D., Ph.D.Abstract : During a severe infection such as coronavirus disease 2019 (COVID-19), the level of almost all analytes can change, presenting a correlation with disease severity and survival; however, a biomarker cannot be translated into clinical practice for treatment guidance until it is proven to have a significant impact. Several studies have documented the association between COVID-19 severity and circulating levels of C-reactive protein (CRP) and interleukin-6, and the accuracy of the CRP level in predicting treatment responses has been evaluated. Moreover, promising findings on prothrombin and D-dimer have been reported. However, the clinical usefulness of these biomarkers in COVID-19 is far from proven. The burst of data generation during this pandemic has led to the publication of numerous studies with several notable drawbacks, weakening the strength of their findings. We provide an overview of the key findings of studies on biomarkers for the prognosis and treatment response in COVID-19 patients. We also highlight the main drawbacks of these studies that have limited the clinical use of these biomarkers.
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Brief Communication2021-03-01
Surveillance of Coronavirus Disease 2019 (COVID-19) Testing in Clinical Laboratories in Korea
Hee Jae Huh
Ann Lab Med 2021; 41(2): 225-229, M.D., Ki Ho Hong , M.D., Taek Soo Kim , M.D., Sang Hoon Song , M.D., Kyoung Ho Roh , M.D., Hyukmin Lee , M.D., Gye Cheol Kwon , M.D.Abstract : In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic, an online laboratory surveillance system was established to monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacities and results. SARS-CoV-2 rRT-PCR testing data were collected from 97 clinical laboratories, including 84 medical institutions and 13 independent clinical laboratories in Korea. We assessed the testing capacities to utilize SARS-CoV-2 rRT-PCR based on surveillance data obtained from February 7th to June 4th, 2020 and evaluated positive result characteristics according to the reagents used and sample types. A total of 1,890,319 SARS-CoV-2 rRT-PCR testing were performed, 2.3% of which were positive. Strong correlations were observed between the envelope (E) gene and RNA-dependent RNA polymerase (RdRp)/nucleocapsid (N) genes threshold cycle (Ct) values for each reagent. No statistically significant differences in gene Ct values were observed between the paired upper and lower respiratory tract samples, except in the N gene for nasopharyngeal swab and sputum samples. Our study showed that clinical laboratories in Korea have rapidly expanded their testing capacities in response to the COVID-19 outbreak, with a peak daily capacity of 34,193 tests. Rapid expansion in testing capacity is a critical component of the national response to the ongoing pandemic.
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Review Article2021-03-01
Sustainability in Healthcare: Perspectives and Reflections Regarding Laboratory Medicine
Aroa Molero
Ann Lab Med 2021; 41(2): 139-144, Michele Calabrò , Maguelone Vignes , Ph.D., Bernard Gouget , Ph.D., and Damien Gruson , Ph.D.Abstract : Healthcare structures serve to protect and improve public health; however, they can have negative effects on human well-being and the environment. Thus, sustainability is an important target in a rapidly changing healthcare environment. We analyzed the state of the art in research on healthcare and sustainability by exploring literature on different healthcare systems and their relations with the environment. Our review presents conceptual and practical developments regarding sustainability, as well as an overview of their evolution in the healthcare sector over time. We also discuss how sustainability could be applied to reduce the environmental impact of clinical laboratories by ensuring that resources are used efficiently and responsibly. Finally, we describe how laboratory medicine can contribute to a sustainable healthcare system through integration of innovation and emerging technologies while providing high-quality services to patients and caregivers.
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Review Article2022-01-01
Clinical Chemistry
Hormone Immunoassay Interference: A 2021 Update
Khaldoun Ghazal
Ann Lab Med 2022; 42(1): 3-23, Pharm., Ph.D., Severine Brabant , M.D., Dominique Prie , M.D., Ph.D., and Marie-Liesse Piketty , Pharm., Ph.D.Abstract : Immunoassays are powerful qualitative and quantitative analytical techniques. Since the first description of an immunoassay method in 1959, advances have been made in assay designs and analytical characteristics, opening the door for their widespread implementation in clinical laboratories. Clinical endocrinology is closely linked to laboratory medicine because hormone quantification is important for the diagnosis, treatment, and prognosis of endocrine disorders. Several interferences in immunoassays have been identified through the years; although some are no longer encountered in daily practice, cross-reaction, heterophile antibodies, biotin, and anti-analyte antibodies still cause problems. Newer interferences are also emerging with the development of new therapies. The interfering substance may be exogenous (e.g., a drug or substance absorbed by the patient) or endogenous (e.g., antibodies produced by the patient), and the bias caused by interference can be positive or negative. The consequences of interference can be deleterious when clinicians consider erroneous results to establish a diagnosis, leading to unnecessary explorations or inappropriate treatments. Clinical laboratories and manufacturers continue to investigate methods for the detection, elimination, and prevention of interferences. However, no system is completely devoid of such incidents. In this review, we focus on the analytical interferences encountered in daily practice and possible solutions for their detection or elimination.
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Review Article2021-01-01
Biomarker-Guided Risk Assessment for Acute Kidney Injury: Time for Clinical Implementation?
Christian Albert
Ann Lab Med 2021; 41(1): 1-15 , M.D., Michael Haase , M.D., Annemarie Albert , M.D., Antonia Zapf , Ph.D., Rüdiger Christian Braun-Dullaeus , M.D., and Anja Haase-Fielitz , Pharm.D.Abstract : Acute kidney injury (AKI) is a common and serious complication in hospitalized patients, which continues to pose a clinical challenge for treating physicians. The most recent Kidney Disease Improving Global Outcomes practice guidelines for AKI have restated the importance of earliest possible detection of AKI and adjusting treatment accordingly. Since the emergence of initial studies examining the use of neutrophil gelatinase-associated lipocalin (NGAL) and cycle arrest biomarkers, tissue inhibitor metalloproteinase-2 (TIMP-2) and insulin-like growth factor-binding protein (IGFBP7), for early diagnosis of AKI, a vast number of studies have investigated the accuracy and additional clinical benefits of these biomarkers. As proposed by the Acute Dialysis Quality Initiative, new AKI diagnostic criteria should equally utilize glomerular function and tubular injury markers for AKI diagnosis. In addition to refining our capabilities in kidney risk prediction with kidney injury biomarkers, structural disorder phenotypes referred to as “preclinical-” and “subclinical AKI” have been described and are increasingly recognized. Additionally, positive biomarker test findings were found to provide prognostic information regardless of an acute decline in renal function (positive serum creatinine criteria). We summarize and discuss the recent findings focusing on two of the most promising and clinically available kidney injury biomarkers, NGAL and cell cycle arrest markers, in the context of AKI phenotypes. Finally, we draw conclusions regarding the clinical implications for kidney risk prediction.
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Review Article2021-11-01
General Laboratory Medicine
Application of Single-Domain Antibodies (“Nanobodies”) to Laboratory Diagnosis
Tahir S. Pillay
Ann Lab Med 2021; 41(6): 549-558, MBChB., Ph.D. and Serge Muyldermans , Ph.D.Abstract : Antibodies have proven to be central in the development of diagnostic methods over decades, moving from polyclonal antibodies to the milestone development of monoclonal antibodies. Although monoclonal antibodies play a valuable role in diagnosis, their production is technically demanding and can be expensive. The large size of monoclonal antibodies (150 kDa) makes their re-engineering using recombinant methods a challenge. Single-domain antibodies, such as “nanobodies,” are a relatively new class of diagnostic probes that originated serendipitously during the assay of camel serum. The immune system of the camelid family (camels, llamas, and alpacas) has evolved uniquely to produce heavy-chain antibodies that contain a single monomeric variable antibody domain in a smaller functional unit of 12–15 kDa. Interestingly, the same biological phenomenon is observed in sharks. Since a single-domain antibody molecule is smaller than a conventional mammalian antibody, recombinant engineering and protein expression in vitro using bacterial production systems are much simpler. The entire gene encoding such an antibody can be cloned and expressed in vitro. Single-domain antibodies are very stable and heat-resistant, and hence do not require cold storage, especially when incorporated into a diagnostic kit. Their simple genetic structure allows easy re-engineering of the protein to introduce new antigen-binding characteristics or attach labels. Here, we review the applications of single-domain antibodies in laboratory diagnosis and discuss the future potential in this area.
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Original Article2021-11-01
Comparison of SARS-CoV-2 Antibody Responses and Seroconversion in COVID-19 Patients Using Twelve Commercial Immunoassays
Sojeong Yun
Ann Lab Med 2021; 41(6): 577-587, B.S., Ji Hyeong Ryu , M.S., Joo Hee Jang , B.S., Hyunjoo Bae , M.S., Seung-Hyo Yoo , M.T., Ae-Ran Choi , M.T., Sung Jin Jo , M.D., Jihyang Lim , M.D., Jehoon Lee , M.D., Hyejin Ryu , M.D., Sung-Yeon Cho , M.D., Dong-Gun Lee , M.D., Jongmin Lee , M.D., Seok Chan Kim , M.D., Yeon-Joon Park , M.D., Hyeyoung Lee , M.D., and Eun-Jee Oh , M.D.Abstract : Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays have high clinical utility in managing the pandemic. We compared antibody responses and seroconversion of coronavirus disease 2019 (COVID-19) patients using different immunoassays. Methods: We evaluated 12 commercial immunoassays, including three automated chemiluminescent immunoassays (Abbott, Roche, and Siemens), three enzyme immunoassays (Bio-Rad, Euroimmun, and Vircell), five lateral flow immunoassays (Boditech Med, SD biosensor, PCL, Sugentech, and Rapigen), and one surrogate neutralizing antibody assay (GenScript) in sequential samples from 49 COVID-19 patients and 10 seroconversion panels. Results: The positive percent agreement (PPA) of assays for a COVID-19 diagnosis ranged from 84.0% to 98.5% for all samples (>14 days after symptom onset), with IgM or IgA assays showing higher PPAs. Seroconversion responses varied across the assay type and disease severity. Assays targeting the spike or receptor-binding domain protein showed a tendency for early seroconversion detection and higher index values in patients with severe disease. Index values from SARS-CoV-2 binding antibody assays (three automated assays, one LFIA, and three EIAs) showed moderate to strong correlations with the neutralizing antibody percentage (r=0.517–0.874), and stronger correlations in patients with severe disease and in assays targeting spike protein. Agreement among the 12 assays was good (74.3%–96.4%) for detecting IgG or total antibodies. Conclusions: Positivity rates and seroconversion of SARS-CoV-2 antibodies vary depending on the assay kits, disease severity, and antigen target. This study contributes to a better understanding of antibody response in symptomatic COVID-19 patients using currently available assays.
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Review Article2021-01-01
Diagnostic Immunology
Clinical Utility of Mac-2 Binding Protein Glycosylation Isomer in Chronic Liver Diseases
Nobuharu Tamaki
Ann Lab Med 2021; 41(1): 16-24, M.D., Ph.D., Masayuki Kurosaki , M.D., Ph.D., Rohit Loomba , M.D., M.H.S., and Namiki Izumi , M.D., Ph.D.Abstract : An accurate evaluation of liver fibrosis is clinically important in chronic liver diseases. Mac-2 binding protein glycosylation isomer (M2BPGi) is a novel serum marker for liver fibrosis. In this review, we discuss the role of M2BPGi in diagnosing liver fibrosis in chronic hepatitis B and C, chronic hepatitis C after sustained virologic response (SVR), and nonalcoholic fatty liver disease (NAFLD). M2BPGi predicts not only liver fibrosis but also the hepatocellular carcinoma (HCC) development and prognosis in patients with chronic hepatitis B and C, chronic hepatitis C after SVR, NAFLD, and other chronic liver diseases. M2BPGi can also be used to evaluate liver function and prognosis in patients with cirrhosis. M2BPGi levels vary depending on the etiology and the presence or absence of treatment. Therefore, the threshold of M2BPGi for diagnosing liver fibrosis and predicting HCC development has to be adjusted according to the background and treatment status.
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