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Challenges and opportunities for next-generation sequencing in companion diagnostics
Erick Lin1, Jeremy Chien, Frank S Ong
1Illumina, Inc. 5200 Illumina Way, San Diego, CA 92122, USA.
Expert Review of Molecular Diagnostics
|September 25, 2014
Summary
Next-generation sequencing (NGS) is transitioning from research to molecular diagnostics, offering powerful tools for cancer companion diagnostics. Despite challenges, NGS holds promise for identifying key cancer genes.
Area of Science:
- Genomics
- Molecular Diagnostics
- Cancer Research
Background:
- Next-generation sequencing (NGS) costs have decreased, enabling its use beyond research.
- NGS assays are increasingly relevant for molecular diagnostics, particularly in oncology.
Purpose of the Study:
- To explore the application of NGS in molecular diagnostics.
- To highlight the potential of NGS for developing cancer companion diagnostics.
Main Methods:
- Genotypic assays (DNA sequencing): whole genome, whole exome, and targeted gene sequencing.
- Phenotypic assays: epigenetic modifications (ChIP-seq, bisulfite sequencing) and gene expression (RNA-sequencing).
Main Results:
- The US FDA has cleared 12 DNA-based companion diagnostic tests, all for cancer.
- NGS offers broad capabilities for probing cancer-related genes.
Conclusions:
- NGS presents significant opportunities for developing novel companion diagnostics in oncology.
- Overcoming current challenges will facilitate broader NGS implementation in cancer diagnostics.
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