title: Challenges and opportunities for next-generation sequencing in companion diagnostics.
abstract: The rapid decline in sequencing costs has allowed next-generation sequencing (NGS) assays, previously ubiquitous only in research laboratories, to begin making inroads into molecular diagnostics. Genotypic assays - DNA sequencing - include whole genome sequencing, whole exome sequencing, focused assays that target only a handful of genes. Phenotypic assays comprise a broader spectrum of options and can query a variety of epigenetic modifications of DNA (such as ChIP-seq, bisulfite sequencing, DNase-I hypersensitivity site-sequencing, Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing, etc.) that regulate gene expression-related processes or gene expression (RNA-sequencing) itself. To date, the US FDA has only cleared 12 DNA-based companion diagnostic tests, all in cancer. Although challenges exist for NGS in companion diagnostics, the wide-ranging capabilities of NGS offer extraordinary opportunities for the development and implementation of NGS-based companion diagnostics to probe oncogenes, tumor suppressor genes and cancer-enabling genes.
authors.affiliation: Illumina, Inc. 5200 Illumina Way, San Diego, CA 92122, USA.
authors.forename: Erick
authors.initials: E
authors.lastname: Lin
authors.forename: Jeremy
authors.initials: J
authors.lastname: Chien
authors.forename: Frank S
authors.initials: FS
authors.lastname: Ong
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
mesh_terms: D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics*; D006801:Humans; D051188:Knowledge Bases; D025202:Molecular Diagnostic Techniques / Q000191:economics*; D057285:Precision Medicine; D017422:Sequence Analysis, DNA
keywords: CTC; NGS; bioinformatics; companion diagnostics; ctDNA; next-generation sequencing; precision medicine; precision oncology; tumor heterogeneity