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.
Original language | English (US) |
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Pages (from-to) | 193-209 |
Number of pages | 17 |
Journal | Expert Review of Molecular Diagnostics |
Volume | 15 |
Issue number | 2 |
DOIs | |
State | Published - Feb 1 2015 |
Externally published | Yes |
Keywords
- bioinformatics
- companion diagnostics
- CTC
- ctDNA
- next-generation sequencing
- NGS
- precision medicine
- precision oncology
- tumor heterogeneity
ASJC Scopus subject areas
- Pathology and Forensic Medicine
- Molecular Medicine
- Molecular Biology
- Genetics