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Diagnostics
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Emerging Biomarkers of Clinical Diagnosis
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Emerging Biomarkers of Clinical Diagnosis

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 20461

Special Issue Editor

Dr. Ji Hyun Park

E-Mail Website
Guest Editor
Department of Hemato-Oncololgy, Konkuk University Medical Center, Seolu, Republic of Korea
Interests: hemato-oncololgy; biomarkers; personalized medicine; molecular signatures; prognosis; predictive diagnosis; blood analysis

Special Issue Information

Dear Colleagues,

Biomarkers are essential components in diagnosing a disease or pathogenic process, monitoring patients, and providing a prognosis for patients. Any biological indicator that can be tested can be used as a biomarker, including DNA, RNA, proteins, metabolites, blood, urine, and so on. Other physiological and morphological biomarkers may also be measured or used for clinical or diagnostic imaging.

Biomarkers are of significant therapeutic value in the early diagnosis of disease when the clinical symptoms are not yet obvious and will prolong patients' lives or enhance their quality of life.

This Special Issue investigates the rapidly developing area of emerging biomarkers in clinical diagnosis and their applications, which offer a novel approach to the clinical care of patients.

Dr. Ji Hyun Park
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarkers
  • personalized medicine
  • molecular signatures
  • prognosis
  • predictive diagnostics
  • prognostic diagnostics
  • genetic biomarkers
  • blood analysis
  • liquid biopsy
  • tumor marker

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (6 papers)

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Research

Jump to: Review, Other

14 pages, 935 KiB  
Article
Enhancing Precision in HIV Treatment: Validation of a Robust Next-Generation Sequencing System for Drug Resistance Mutation Analysis
by Ashutosh Vashisht, Ashis K. Mondal, Vishakha Vashisht, Sudha Ananth, Ahmet Alptekin, Kimya Jones, Jaspreet K. Farmaha and Ravindra Kolhe
Diagnostics 2024, 14(16), 1766; https://doi.org/10.3390/diagnostics14161766 - 14 Aug 2024
Cited by 1 | Viewed by 1546
Abstract
Background: Multidrug-resistant HIV strains challenge treatment efficacy and increase mortality rates. Next-generation sequencing (NGS) technology swiftly detects variants, facilitating personalized antiretroviral therapy. Aim: This study aimed to validate the Vela Diagnostics NGS platform for HIV drug resistance mutation analysis, rigorously assessed with clinical [...] Read more.
Background: Multidrug-resistant HIV strains challenge treatment efficacy and increase mortality rates. Next-generation sequencing (NGS) technology swiftly detects variants, facilitating personalized antiretroviral therapy. Aim: This study aimed to validate the Vela Diagnostics NGS platform for HIV drug resistance mutation analysis, rigorously assessed with clinical samples and CAP proficiency testing controls previously analyzed by Sanger sequencing. Method: The experimental approach involved the following: RNA extraction from clinical specimens, reverse transcription polymerase chain reaction (RT-PCR) utilizing the Sentosa SX 101 platform, library preparation with the Sentosa SQ HIV Genotyping Assay, template preparation, sequencing using the Sentosa SQ301 instrument, and subsequent data analysis employing the Sentosa SQ Suite and SQ Reporter software. Drug resistance profiles were interpreted using the Stanford HIV Drug Resistance Database (HIVdb) with the HXB2 reference sequence. Results: The Vela NGS system successfully identified a comprehensive array of drug resistance mutations across the tested samples: 28 nucleoside reverse transcriptase inhibitors (NRTI), 25 non-nucleoside reverse transcriptase inhibitors (NNRTI), 25 protease inhibitors (PI), and 10 integrase gene-specific variants. Dilution experiments further validated the system’s sensitivity, detecting drug resistance mutations even at viral loads lower than the recommended threshold (1000 copies/mL) set by Vela Diagnostics. Scope: This study underscores the validation and clinical applicability of the Vela NGS system, and its implementation may offer clinicians enhanced precision in therapeutic decision-making for individuals living with HIV. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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9 pages, 1055 KiB  
Communication
Advancing Evidence Generation for Circulating Tumor DNA: Lessons Learned from A Multi-Assay Study of Baseline Circulating Tumor DNA Levels across Cancer Types and Stages
by Brittany A. McKelvey, Hillary S. Andrews, Frederick L. Baehner, James Chen, Carin R. Espenschied, David Fabrizio, Vanessa Gorton, Claire Gould, Justin Guinney, Greg Jones, Xiangyang Lv, Michael S. Nahorski, Melanie R. Palomares, Gary A. Pestano, Mark Sausen, Alain Silk, Nicole Zhang, Zhihong Zhang, Mark D. Stewart and Jeff D. Allen
Diagnostics 2024, 14(9), 912; https://doi.org/10.3390/diagnostics14090912 - 27 Apr 2024
Cited by 1 | Viewed by 9155
Abstract
Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across [...] Read more.
Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across ctDNA assays has not been widely studied. Friends of Cancer Research formed a collaboration across multiple commercial ctDNA assay developers to assess baseline ctDNA levels across five cancer types in early- and late-stage disease. This retrospective study included eight commercial ctDNA assay developers providing summary-level de-identified data for patients with non-small cell lung cancer (NSCLC), bladder, breast, prostate, and head and neck squamous cell carcinoma following a common analysis protocol. Baseline ctDNA levels across late-stage cancer types were similarly detected, highlighting the potential use of ctDNA as a biomarker in these cancer types. Variability was observed in ctDNA levels across assays in early-stage NSCLC, indicative of the contribution of assay analytical performance and methodology on variability. We identified key data elements, including assay characteristics and clinicopathological metadata, that need to be standardized for future meta-analyses across multiple assays. This work facilitates evidence generation opportunities to support the use of ctDNA as a biomarker for clinical response. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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17 pages, 5082 KiB  
Article
Validation and Implementation of OptiView and EnVision FLEX Detection Systems for Immunocytochemical Staining Protocols of the Ten Most Commonly Used Diagnostic Markers in Routine Cytopathological Practice
by Anja Dremelj, Simona Miceska, Anamarija Kuhar, Natasa Nolde and Veronika Kloboves-Prevodnik
Diagnostics 2024, 14(6), 657; https://doi.org/10.3390/diagnostics14060657 - 21 Mar 2024
Cited by 1 | Viewed by 1775
Abstract
The withdrawal of the iView detection system (iV) forced many cytopathology laboratories, including ours, to substitute immunocytochemical (ICC) staining protocols for routine practice with other detection systems. Our objective was to optimize, validate, and implement ICC protocols using OptiView (OV) and EnVision FLEX [...] Read more.
The withdrawal of the iView detection system (iV) forced many cytopathology laboratories, including ours, to substitute immunocytochemical (ICC) staining protocols for routine practice with other detection systems. Our objective was to optimize, validate, and implement ICC protocols using OptiView (OV) and EnVision FLEX (EnV) detection systems, comparing the results with those obtained using iV. Residual cytologic samples with known diagnoses were used, testing antibodies for the ten most common markers in routine cytopathology diagnostics (calretinin, Ber-EP4, MOC-31, CKAE1/AE3, CK5/6, CD68, LCA, desmin, HBME-1, and WT1). Different staining parameters were tested using OV on BenchMark ULTRA and EnV on Dako Omnis immunostainer, respectively. Optimal staining protocols were then selected and validated on 10 positive and 10 negative cases. The staining results were compared with iV protocols through evaluation of UK NEQAS and internal scores. The optimal staining protocols with OV and EnV demonstrated similar or superior results compared to the existing iV protocols, with slightly stronger intensity regarding positive cells. We have successfully established and validated optimal ICC staining protocols for commonly used markers in routine cytopathology practice. These protocols may benefit other laboratories using similar staining platforms. However, the challenge regarding standardizing ICC protocols across different cytopathology laboratories remains unresolved. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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Review

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32 pages, 5949 KiB  
Review
Genetics, Pathophysiology, and Current Challenges in Von Hippel–Lindau Disease Therapeutics
by Laura Gómez-Virgilio, Mireya Velazquez-Paniagua, Lucero Cuazozon-Ferrer, Maria-del-Carmen Silva-Lucero, Andres-Ivan Gutierrez-Malacara, Juan-Ramón Padilla-Mendoza, Jessica Borbolla-Vázquez, Job-Alí Díaz-Hernández, Fausto-Alejandro Jiménez-Orozco and Maria-del-Carmen Cardenas-Aguayo
Diagnostics 2024, 14(17), 1909; https://doi.org/10.3390/diagnostics14171909 - 29 Aug 2024
Cited by 4 | Viewed by 3212
Abstract
This review article focuses on von Hippel–Lindau (VHL) disease, a rare genetic disorder characterized by the development of tumors and cysts throughout the body. It discusses the following aspects of the disease. Genetics: VHL disease is caused by mutations in the VHL tumor [...] Read more.
This review article focuses on von Hippel–Lindau (VHL) disease, a rare genetic disorder characterized by the development of tumors and cysts throughout the body. It discusses the following aspects of the disease. Genetics: VHL disease is caused by mutations in the VHL tumor suppressor gene located on chromosome 3. These mutations can be inherited or occur spontaneously. This article details the different types of mutations and their associated clinical features. Pathophysiology: The underlying cause of VHL disease is the loss of function of the VHL protein (pVHL). This protein normally regulates hypoxia-inducible factors (HIFs), which are involved in cell growth and survival. When pVHL is dysfunctional, HIF levels become elevated, leading to uncontrolled cell growth and tumor formation. Clinical Manifestations: VHL disease can affect various organs, including the brain, spinal cord, retina, kidneys, pancreas, and adrenal glands. Symptoms depend on the location and size of the tumors. Diagnosis: Diagnosis of VHL disease involves a combination of clinical criteria, imaging studies, and genetic testing. Treatment: Treatment options for VHL disease depend on the type and location of the tumors. Surgery is the mainstay of treatment, but other options like radiation therapy may also be used. Challenges: This article highlights the challenges in VHL disease management, including the lack of effective therapies for some tumor types and the need for better methods to monitor disease progression. In conclusion, we emphasize the importance of ongoing research to develop new and improved treatments for VHL disease. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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Other

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20 pages, 4192 KiB  
Systematic Review
Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis
by Ana María Rodríguez-Ces, Óscar Rapado-González, Ángel Salgado-Barreira, María Arminda Santos, Carlos Aroso, Ana Sofia Vinhas, Rafael López-López and María Mercedes Suárez-Cunqueiro
Diagnostics 2024, 14(14), 1465; https://doi.org/10.3390/diagnostics14141465 - 9 Jul 2024
Cited by 2 | Viewed by 2129
Abstract
Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane [...] Read more.
Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290). Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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17 pages, 679 KiB  
Systematic Review
The Efficiency of Serum Biomarkers in Predicting the Clinical Outcome of Patients with Mesenteric Ischemia during Follow-Up: A Systematic Review
by Florin Vasile Mihaileanu, Stefan Lucian Popa, Simona Grad, Dinu Iuliu Dumitrascu, Abdulrahman Ismaiel, Eliza Rus, Vlad Dumitru Brata, Alexandru Marius Padureanu, Miruna Oana Dita, Daria Claudia Turtoi, Traian Adrian Duse, Andrei Vlad Badulescu, Paolo Bottalico, Giuseppe Chiarioni, Cristina Pop, Cristina Mogosan, Maria Barsan, Claudia Diana Gherman, Bogdan Stancu and Liliana David
Diagnostics 2024, 14(7), 670; https://doi.org/10.3390/diagnostics14070670 - 22 Mar 2024
Cited by 3 | Viewed by 1813
Abstract
The initial clinical manifestation of acute mesenteric ischemia poses a diagnostic challenge, often leading to delays in identification and subsequent surgical intervention, contributing to adverse outcomes. Serum biomarkers, offering insights into the underlying pathophysiology, hold promise as prognostic indicators for acute mesenteric ischemia. [...] Read more.
The initial clinical manifestation of acute mesenteric ischemia poses a diagnostic challenge, often leading to delays in identification and subsequent surgical intervention, contributing to adverse outcomes. Serum biomarkers, offering insights into the underlying pathophysiology, hold promise as prognostic indicators for acute mesenteric ischemia. This systematic review comprehensively explores the role of blood biomarkers in predicting clinical outcomes during follow-up for patients with mesenteric ischemia. A thorough literature search across the PubMed, Cochrane Library, and EMBASE databases yielded 33 relevant publications investigating the efficacy of serum biomarkers in predicting outcomes for mesenteric ischemia. Numerous studies underscore the utility of blood biomarkers in swiftly and accurately differentiating between causes of mesenteric ischemia, facilitating a prompt diagnosis. Elevated levels of specific biomarkers, particularly D-dimers, consistently correlate with heightened mortality risk and poorer clinical outcomes. While certain serum indicators exhibit substantial potential in associating with mesenteric ischemia, further research through rigorous human trials is imperative to enhance their consistent predictive ability during the follow-up period. This study underscores the diagnostic and prognostic significance of specific biomarkers for mesenteric ischemia, emphasizing the necessity for standardized procedures in future investigations. Full article
(This article belongs to the Special Issue Emerging Biomarkers of Clinical Diagnosis)
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