Expert Review of Molecular Diagnostics

INTRODUCTION: To date, several emerging biomarkers have gained considerable interest in the field of predictive molecular oncology. The advent of precision medicine has led to the development of innovative drugs targeting rare molecular pathways independently from histology, defined as tissue-agnostic drugs. AREAS COVERED: Although there is a lot of promise for this new tissue-agnostic model in the oncological scenario, crucial issues from both the diagnostic and therapeutic standpoint are emerging...

BACKGROUND: Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants. METHODS: A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels...

INTRODUCTION: Considering the ongoing increase in antibiotic resistance, the importance of judicious use of antibiotics through reduction of exposure is crucial. Adding procalcitonin (PCT) and other biomarkers to pathogen-specific tests may help to further improve antibiotic therapy algorithms and advance antibiotic stewardship programs to achieve these goals. AREAS COVERED: In recent years, several trials have investigated the inclusion of biomarkers such as PCT into clinical decision-making algorithms...

INTRODUCTION: The non-invasive identification of liver fibrosis related to Non-Alcoholic Fatty Liver Disease is crucial for risk-stratification of patients. Currently, the reference standard to stage hepatic fibrosis relies on liver biopsy, but multiple approaches are developed to allow for non-invasive diagnosis and risk stratification. Non-invasive tests, including blood-based scores and vibration-controlled transient elastography, have been widely validated and represent a good surrogate for risk stratification according to recent European and American guidelines...

INTRODUCTION: Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, with localized hypermethylation at promoters of certain genes. AREA COVERED: The present review aims to emphasize on recent investigations on the epigenetic landscape of ocular surface squamous neoplasia, that could be targeted/explored using novel approaches such as personalized medicine...

BACKGROUND: Gene models based on GRCh37 human genome assembly is preferred by many international projects over other updated assemblies (GRCh38 and T2T). Discrepant genes (DGs), those recognized as protein coding in the new but not the old assembly, are ignored by several genomic resources and discarded by variant prioritization tools relying on information based on GRCh37. METHODS: We curated a set of Ensembl genes with discrepant annotations between GRCh37 and GRCh38, additionally matching their RefSeq transcripts...

OBJECTIVES: Urinary activated leukocyte cell adhesion molecule (uALCAM) is emerging as an outstanding biomarker for active lupus nephritis (ALN). This study aims to evaluate the analytic performance of the human ALCAM ELISA as an assay method to quantify uALCAM in patients with lupus nephritis. METHODS: A commercially available human ALCAM ELISA kit was validated for its analytical performance as per Clinical & Laboratory Standards Institute guidelines. RESULTS: Assaying 30 sets of serial dilutions of ALCAM exhibited an average CV of 10% and 97%-105% recovery...

INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED: A literature search was conducted in PubMed and supplemented by citation searching...

INTRODUCTION: Mucormycosis is a highly aggressive angio-invasive disease of humans caused by Mucorales fungi. Prior to the COVID-19 pandemic, mucormycosis was a rare mycosis typically seen in immunocompromised patients with hematological malignancies or in transplant recipients. During the second wave of the pandemic, there was a dramatic increase in the disease, especially in India where a unique set of circumstances led to large numbers of life-threatening and disfiguring rhino-orbital-cerebral mucormycosis (ROCM) infections...

INTRODUCTION: Due to the limited number of studies focusing on the optimal treatment of multiple Krukenberg tumor (KT)-gastric carcinoma (KT - GC), it is necessary to conduct large-scale studies to confirm the definite role of serum tumor markers in the diagnosis and prognosis of KT. Moreover, the clinical significance of variant 6 of CD44 (CD44v6) in transcoelomic metastasis should be considered. AREAS COVERED: This review covers molecular pre-cancer diagnosis, gastric carcinoma metastasis, and anti-cancer treatments...

INTRODUCTION: Breast cancer (BC) is a major public health concern, and identifying new biomarkers and therapeutic targets is critical to improving patient outcomes. MALAT1, a long noncoding RNA, has emerged as a promising candidate due to its overexpression in BC and the associated poor prognosis. Understanding the role of MALAT1 in BC progression is paramount for the development of effective therapeutic strategies. COVERED AREA: This review delves into the structure and function of MALAT1, and examines its expression pattern in breast cancer (BC) and its association with different BC subtypes...

OBJECTIVE: To assess the diagnostic accuracy of noninvasive prenatal screening (NIPS) in screening for copy number variations (CNVs). METHODS: We conducted a systematic review and meta-analysis by combining our study results with those reported in other articles. We retrospectively collected the data of pregnant women with NIPS testing in the Hangzhou Women's Hospital from December 2019 to February 2022. Simultaneously, a systematic search of PubMed, EMBASE and Web of Science was carried out to identify all relevant peer-reviewed publications...

INTRODUCTION: Gastric cancer (GC) is the fifth most common cancer and the fourth leading cause of cancer-related death worldwide, thus representing a significant global health burden. Early detection and monitoring of GC are essential to improve patient outcomes. While traditional cancer biomarkers such as carcinoembryonic antigen, carbohydrate antigen (CA) 19-9, and CA 72-4 are widely used, their limited sensitivity and specificity necessitate the exploration of alternative biomarkers...

INTRODUCTION: Exportin 1 (XPO1) is overexpressed in several solid tumors, and is associated with poor prognosis. Here, we aimed to evaluate the implication of XPO1 expression in solid tumors through a meta-analysis. METHODS: PubMed, Web of Science, and Embase databases were searched for articles published until February 2023. Statistical data of the patients, odds ratios and hazard ratios (HRs), together with their corresponding 95% confidence intervals (CIs) were pooled to assess clinicopathological features and survival outcomes...

INTRODUCTION: Bladder cancer (BCa) is the most frequent cancer of the urinary tract, with more than 500,000 reported cases and nearly 200,000 related deaths yearly. Cystoscopy is the standard examination used for the initial diagnosis and follow-up of BCa in the noninvasive stage. However, the American Cancer Society does not include BCa screening in its list of recommended cancer screenings. AREAS COVERED: Recently, several urine-based bladder tumor markers (UBBTMs) that identify genomic, transcriptomic, epigenetic, or protein alterations have been introduced, some of which have been approved by the Food and Drug Administration (FDA) to improve its diagnosis and surveillance...

INTRODUCTION: Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS 6110 , IS 1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R)...

INTRODUCTION: Lung cancer is a leading cause of death in patients with cancer. Early diagnosis is crucial to improve the prognosis of patients with lung cancer. Plasma circulating cell-free DNA (cfDNA) contains comprehensive genetic and epigenetic information from tissues throughout the body, suggesting that early detection of lung cancer can be done non-invasively, conveniently, and cost-effectively using high-sensitivity techniques such as sequencing. AREAS COVERED: In this review, we summarize the latest technological innovations, coupled with next-generation sequencing (NGS), regarding genomic alterations, methylation, and fragmentomic features of cfDNA for the early detection of lung cancer, as well as their clinical advances...

INTRODUCTION: Currently available platelet function assays largely ignore the important characteristics of in vivo thrombus generation, such as flow conditions and shear. The AggreGuide A-100 ADP Assay detects platelet aggregation in whole blood using light scattering under flow conditions. AREAS COVERED: In this review article, we discuss the limitations of currently available platelet function assays and the technology underlying the AggreGuide A-100 ADP assay...

OBJECTIVE: To evaluate whether the fetal fraction of cell-free DNA at the first and second trimesters is associated with spontaneous preterm birth. METHODS: This was a retrospective cohort study with singleton pregnancies who underwent noninvasive prenatal testing. According to pregnancy outcome, eligible patients were divided into a delivery group ≥37 weeks of pregnancy (term group) and <37 weeks of pregnancy (spontaneous preterm group)...

BACKGROUND: An important factor in tumor development and progression is the tumor microenvironment (TME), which is heterogeneous. Previous studies have mainly investigated the expression profile and prognostic values of genes in gastric cancer (GC) at the cell population level but neglected the interactions and heterogeneity between cells. METHODS: The pattern of ligand-receptor (LR) interactions was delineated in a scRNA-seq dataset containing 44953 cells from nine GC patients and fourth bulk RNA-seq datasets including data from 1159 GC patients...