Next-generation sequencing for the analysis of cancer specimens

Abstract

Massively parallel sequencing (also known as next-generation sequencing, or NGS), which provides genomic data at low cost and high accuracy, is ideally suited for clinical testing of cancer specimens. NGS results may inform the cancer diagnosis or choice of therapy. The genomes of cancer cells carry somatic (often referred to as acquired) alterations, which fall into four general classes: single nucleotide variants (SNVs), small insertions and deletions (indels), copy number variants (CNVs), and structural variants (SVs). The genetic complexity of cancers underscores the importance of NGS to evaluate the full spectrum of sequence variations in dozens to thousands of genes in a single test. Amplification-based as well as hybrid capture-based methods for NGS testing can be used for the analysis of cancer specimens, and assays that target a panel of genes (from several genes, to several hundred genes), the exome, or the genome have been developed. Although each type of assay carries with it specific test design considerations, all NGS assays share a set of preanalytic, analytic, and postanalytic/reporting issues that must be addressed during test validation and routine clinical use. In addition, the analytic portion of an NGS test consists of three individual components (i.e., the sequencing platform; the wet bench procedures; and the bioinformatics pipeline), which creates some unique quality management issues.