Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Abstract

Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.

Keywords: cancer somatic mutation; diagnostics; gene-panel; genetic modifiers; inherited cancer syndrome; next-generation sequencing; theranostics; whole-exome-sequencing; whole-genome-sequencing.

Figure 1

Pipeline illustrating the four major blocks in next-generation sequencing (NGS) studies. ¹ Illumina^®; ² Agilent Technology^®; ³ Nimblegen^®; ⁴ MIP: Molecular Inversion Probe. This method is normally in house developed using specific tools (SciTools^®, Integrated DNA Technologies, Coralville, Iowa, U.S.) assisting in probe design; ⁵ ThermoFisher^®; ⁶ Roche^®; ⁷ PacBio^®. Because of their recent development, information about the Qiagen GeneReader^® and 10x Genomics^® technology are not included in this figure. ^$ Users have reported up to 200,000 pb; * To detect low expressed transcripts, >2000× coverage is needed.

Figure 2

Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for Illumina^®. ¹ This steps removes duplicate sequences using the Picard program; ² GATK: Genome Analysis ToolKit.