Sequencing of Nucleic Acids: from the First Human Genome to Next Generation Sequencing in COVID-19 Pandemic

Abstract

Despite being around for more than 40 years, DNA sequencing is regarded as young technology in clinical medicine. As sequencing is becoming cheaper, faster and more accurate, it is rapidly being incorporated into clinical laboratories. In 2003, the completion of the first human genome opened the door to personalized medicine. Ever since it has been expected for genomics to widely impact clinical care and public health. However, many years can pass for genomic discoveries to reflect back and benefit the patients. DNA sequencing represents a less biased approach to diagnostics. It is not only a diagnostic tool, but can also influence clinical management and therapy. As new technologies rapidly emerge it is important for researchers and health professionals to have basic knowledge about the capabilities and drawbacks of the existing sequencing methods, and their use in clinical setting and research. This review provides an overview of nucleic acid sequencing technologies from historical perspective and later focuses on clinical utilization of sequencing. Some of the most promising areas are presented with selected examples from Slovenian researchers.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

“…Unlike Sanger sequencing, which is designed to generate consistent sequences for a single target amplicon, NGS technology allows the sequencing of millions to billions of DNA strands in parallel during a single run. 185,186 EUA has licensed four kits for the targeted testing of SARS-CoV-2 RNA based on Illumina's sequencing by synthesis technology. 161 The details of these kits are summarized in Table 3.…”

Optimal sequencing depth for measuring the concentrations of molecular barcodes

“…Since its commercialisation in the early 2000s, next generation sequencing (NGS) allows to sequence millions of DNA molecules in parallel [1, 2], revolutionizing nucleic acid research. Since then, NGS cost has constantly dropped [3], and today it represents a powerful and accessible tool for many research investigations. In protein engineering, NGS has radically changed experimental approaches to study the fitness landscape of mutant proteins, as in deep mutational scanning experiments (DMS) [4, 5, 6, 7, 8].…”

CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

“…Since the Human Genome Project was completed in 2003 [ 1 ], Whole-Genome Sequencing (WGS) costs are substantially decreasing over time, which has led to the emergence of new sequencing technologies that empower Next-Generation Sequencing (NGS) based on Sequencing by Synthesis (SBS), Sequencing by Oligo Ligation Detection (SOLiD), Single-Molecule Real-Time (SMRT) sequencing and nanopore-based DNA sequencing [ 2 , 3 ]. Among them, Illumina sequencing remains one of the most prevalent sequencing technologies providing high accuracy and coverage with low error rates (< 1%), compared to Pacific Biosciences or Oxford Nanopore technologies, that can afford much longer read lengths but with higher error rates and lower accuracy [ 4 , 5 ].…”