Application Progress of High-Throughput Sequencing in Ocular Diseases

Abstract

Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS has not only identified several normal ocular surface microorganisms but has also discovered many pathogenic bacteria, fungi, parasites, and viruses associated with eye diseases, including rare pathogens that were previously difficult to identify. At present, HTS can directly sequence RNA, which will promote research on the occurrence, development, and underlying mechanism of eye diseases. Although HTS has certain limitations, including low effectiveness, contamination, and high cost, it is still superior to traditional diagnostic methods for its efficient and comprehensive diagnosis of ocular diseases. This review summarizes the progress of the application of HTS in ocular diseases, intending to explore the pathogenesis of eye diseases and improve their diagnosis.

Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review

“…HTS technology is also called the next-generation sequencing (NGS) technologies, which are specifically divided into second and third-generation sequencing technologies [5] . As an application for HTS, metagenomic NGs (mNGS) is a powerful technology that can simultaneously achieve the qualitative and quantitative identification of pathogens in endophthalmitis, which is more accurate and has revealed wide prospects for identifying pathogens that have not been previously identified, compared with traditional pathogen culture [6][7] . There has been much discussion of the advantages and disadvantages of metagenomic techniques, the lack of corresponding reference gene sequence databases, technical difficulties of metagenome assembly, and phasing in heterogeneous environmental samples being some of its disadvantages.…”

Emerging contaminants: A One Health perspective

“… 197 One of the significant benefits of sequencing methods is their ability to identify a wide range of pathogens or ARGs across diverse microorganisms present in samples. 198 Despite their high-throughput nature, the sensitivity of these methods relies heavily on the effectiveness of the analysis pipelines. 199 In recent years, computational tools have played a pivotal role in enhancing pathogen surveillance.…”

Small data machine learning in materials science

“…The concept of high-throughput stems from gene sequencing. The first-generation sequencing can only measure one sequence of one sample at a time to generate relatively small data, while high-throughput sequencing can measure a large number of samples at a time, resulting in data in the dozens of gigabytes even hundreds of gigabytes 70,71 . One of the characteristics of high-throughput lies in the ability of processing a lot of samples in a short time to obtain more data.…”