Molecular Identification of Infection Using Nanopore Sequencing: A Case Report and Literature Review.

(previously known as ) infection is not common in Hong Kong. is a fish-borne cestode parasite that infects humans after consuming raw or insufficiently cooked fish containing plerocercoids. We reported a case of infection in a 40-year-old woman who presented with a complaint of epigastric pain and diarrhea.

Comprehensive Review of COVID-19: Epidemiology, Pathogenesis, Advancement in Diagnostic and Detection Techniques, and Post-Pandemic Treatment Strategies.

At present, COVID-19 remains a public health concern due to the ongoing evolution of SARS-CoV-2 and its prevalence in particular countries. This paper provides an updated overview of the epidemiology and pathogenesis of COVID-19, with a focus on the emergence of SARS-CoV-2 variants and the phenomenon known as 'long COVID'. Meanwhile, diagnostic and detection advances will be mentioned.

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.

Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis.

Plasma Circulating mRNA Profile for the Non-Invasive Diagnosis of Colorectal Cancer Using NanoString Technologies.

Colorectal cancer (CRC) is one of the most prevalent cancers and the second leading cause of cancer deaths in developed countries. Early CRC may have no symptoms and symptoms usually appear with more advanced diseases. Regular screening can identify people who are at increased risk of CRC in order to offer earlier treatment.

Cell-free circulating tumor RNAs in plasma as the potential prognostic biomarkers in colorectal cancer.

Background: Cell free RNA (cfRNA) contains transcript fragments from multiple cell types, making it useful for cancer detection in clinical settings. However, the pathophysiological origins of cfRNAs in plasma from colorectal cancer (CRC) patients remain unclear.

Methods: To identify the tissue-specific contributions of cfRNAs transcriptomic profile, we used a published single-cell transcriptomics profile to deconvolute cell type abundance among paired plasma samples from CRC patients who underwent tumor-ablative surgery.

The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis.

Pediatric population was generally less affected clinically by SARS-CoV-2 infection. Few pediatric cases of COVID-19 have been reported compared to those reported in infected adults. However, a rapid increase in the hospitalization rate of SARS-CoV-2 infected pediatric patients was observed during Omicron variant dominated COVID-19 outbreak.

Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.

The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19.

The diagnostic significance of CDH17-positive circulating tumor cells in patients with colorectal cancer.

Background: Colorectal cancer (CRC) is the second leading cause of cancer deaths in Hong Kong. We tested the hypothesis that circulating tumor cell (CTC) analysis by ARB101 antibody could be used as a tool for CRC detection, progression, and therapy response.

Research Methods: ARB101 antibody was used for investigation of CDH17 expression in formalin-fixed, paraffin-embedded (FFPE) tissue sections and circulating tumor cells (CTCs) of CRC patients.

The non-invasive diagnosis of colorectal cancer via a SOX9-based gene panel.

Colorectal cancer (CRC) threatens human health seriously. Early diagnosis of CRC is critical to improving patient survival. Meanwhile, non-invasive detection through tumor-circulating markers can be an important auxiliary diagnosis.

The clinical application of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid: case reports and literature review.

Introduction: Clinical metagenomic next-generation sequencing (mNGS) allows a comprehensive genetic analysis of microbial materials. Different from other traditional target-driven molecular diagnostic tests, such as PCR, mNGS is a hypothesis-free diagnostic approach that allows a comprehensive genetic analysis of the clinical specimens that cover nearly any common, rare, and new pathogens ranging broadly from viruses, bacteria, fungi to parasites.

Areas Covered: In this article, we discussed the clinical application of the mNGS using two clinical cases as examples and described the use of mNGS to assist the diagnosis of parasitic pulmonary infection.

Whole genome amplicon sequencing and phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from lineage B.1.36.27 isolated in Hong Kong.

Background: The import of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.36.

The current and future applications of hybridization technologies in anatomical pathology.

Introduction: hybridization (ISH) plays an important role in the field of molecular diagnostics, especially in an anatomical pathology laboratory. ISH is a technique that can detect the targeted DNA or RNA sequences in tissue sections from frozen or fixed materials with labeled DNA or RNA probes. Radioactive and non-radioactive probes are the two major probes that can be used to label the targeted nucleic acids.

Performance comparison of the Cobas® Liat® and Cepheid® GeneXpert® systems on SARS-CoV-2 detection in nasopharyngeal swab and posterior oropharyngeal saliva.

: Nucleic acid amplification tests (NAATs) based methods such as real-time reverse transcription polymerase-chain reaction (real-time RT-PCR) are the gold standard for diagnosis of current infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The cobas® Liat® and cepheid® GeneXpert® systems are two rapid real-time RT-PCR platforms offering rapid, specimen-to-answer detection of SARS-CoV-2.: In this study, we compared the performance of these two systems on SARS-CoV-2 detection in 9 nasopharyngeal swab (NPS) and 70 posterior oropharyngeal saliva specimens collected from 79 patients suspected of SARS-CoV-2 infection between August 2020 and March 2021.

An update on COVID-19 pandemic: the epidemiology, pathogenesis, prevention and treatment strategies.

Introduction: To date, the transmission of Coronavirus Disease-2019 (COVID-19) is still uncontrollable with the fact that the numbers of confirmed and death cases are still increasing. Up to 1st October 2020, 33,842,281 confirmed cases and 1,010,634 confirmed deaths have been reported to the World Health Organization from 216 different countries, areas and territories. Despite the urgent demand for effective treatment strategies, there is still no specific antiviral treatment for COVID-19 and the treatment guidelines for COVID-19 vary between countries.

The diagnostic methods in the COVID-19 pandemic, today and in the future.

Introduction: The emergence of anovel coronavirus identified in patients with unknown cause of acute respiratory disease in Wuhan, China at the end of 2019 has caused aglobal outbreak. The causative coronavirus was later named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease caused by SARS-CoV-2 was named as Coronavirus Disease-2019 (COVID-19). As of 10 August 2020, more than 19,718,030 confirmed cases and 728,013 deaths have been reported.

The potential of circulating exosomal RNA biomarkers in cancer.

Introduction: There are great potentials of using exosomal RNAs (exoRNA) as biomarkers in cancers. The isolation of exoRNA requires the use of ultracentrifugation to isolate cell-free RNA followed by detection using real-time PCR, microarray, next-generation sequencing, or Nanostring nCounter system. The use of exoRNA enrichment panels has largely increased the detection sensitivity and specificity when compared to traditional diagnostic tests.

Current and future molecular diagnostics of gastric cancer.

: Gastric cancer (GC) is the fifth most common cancer and confers the second-highest mortality among other cancers. Improving the survival rates of GC patients requires prompt and accurate diagnosis and effective treatment which is often preceded by the poorly understood pathogenic mechanisms. : This literature review aims to summarize current understanding of genetic and molecular alterations that promote carcinogenesis including (1) activation of oncogenes, (2) overexpression of growth factors, receptors and matrix metalloproteinases, (3) inactivation of tumor suppressor genes, DNA repair genes, and cell adhesion molecules and (4) alterations of cell-cycle regulators that regulate biological characteristics of cancer cells.

The applications of big data in molecular diagnostics.

: Big Data technologies instilled an informational perspective to our understanding of the world. However, fundamental issues such as the management and storage of data can create privacy concerns. Heterogeneous types of data pose challenges in reproducibility and standardization.

The applications of metabolomics in the molecular diagnostics of cancer.

: Metabolomics, the study of metabolites, is a promising research field for cancers. The metabolic pathway in a tumor cell is different from a normal tissue cell. There are two approaches to study the metabolism, targeted and untargeted.

The potential of circulating cell free RNA as a biomarker in cancer.

: It is now clear that circulating cell-free ribonucleic acids (ccfRNAs), including messenger RNA (mRNA) and miRNA, are potential cancer biomarkers. As ccfmiRNA is relatively more stable than ccfmRNA, research should concentrate on developing novel methods to preserve the stability of ccfmRNA and standardization of the protocol which includes extraction, detection, and multicenter validation. : This literature review concentrates on the potential of ccfRNA being used as a biomarker in cancer, with special focus on mRNAs and microRNAs (miRNAs).

Menstrual Blood Human Papillomavirus DNA and TAP1 Gene Polymorphisms as Potential Biomarkers for Screening and Monitoring of Cervical Squamous Intraepithelial Lesion.

Background: Human papillomavirus (HPV) is a known causative factor in the etiology of cervical cancer.

Methods: HPV DNA genotyping was performed in menstrual blood (MB) collected in napkins from patients with cervical intraepithelial neoplasia (CIN), HPV infection and sexually active apparently normal subjects. In the same patient cohort, MB TAP1 I333V and TAP1 D637G gene polymorphisms were examined.

Implementation and new insights in molecular diagnostics for HIV infection.

Acquired immunodeficiency syndrome (AIDS) is a kind of acquired disease that breaks down the immune system. Human immunodeficiency virus (HIV) is the causative agent of AIDS. By the end of 2016, there were 36.

NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics.

Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges.