Next-Generation Sequencing

The first commercialised method of DNA sequencing was Sanger sequencing. Next-generation sequencing (NGS), also known as high-throughput sequencing, is the catch-all term used to describe a number of different modern sequencing technologies.

Next generation sequencing is a common and versatile tool for biological and medical research. We describe the basic steps for analyzing next generation sequencing data, including quality checking and mapping to a reference genome. We also explain the further data analysis for three common applications of next generation sequencing: variant detection, RNA-seq, and ChIP-seq ¹⁾.

The purpose of a study by Vivancos Sánchez et al. was to assess the clinical impact of next-generation sequencing (NGS), as an increasingly available and advantageous tool, for glioblastoma patients. Adult patients aged less than 65, and surgically treated for glioblastoma between 2010-2021, were included. Tumor samples were analyzed with NGS using the Oncomine Comprehensive v3 (OCA) panel and Ion Reporter Genexus v5.9.1 (Thermo Fisher Scientific). Thirty-two patients were included, with a median age of 47.7 years and a median overall survival of 25 months. Identification of mutations by NGS resulted in a change in diagnosis in two cases. In all patients but one, at least one genetic alteration was detected (median of three per patient), most commonly EGFR amplification. In 93.7% of patients, biomarkers that make them potentially eligible for a clinical trial were found. No survival differences were seen regarding genetic alterations, although a trend towards better survival for those patients without CDK4 mutation was observed (p = 0.088). The use of NGS provides useful information for diagnosis, especially in young patients, and it will probably become valuable for clinical decision-making as more therapeutic targets and treatments emerge. For the moment, it is crucial for scientific progress to happen ²⁾.