Challenges and opportunities for next-generation sequencing in companion diagnostics

Erick Lin, Jeremy Chien, Frank S. Ong, Jian Bing Fan

Research output: Contribution to journalReview article

9 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)193-209
Number of pages17
JournalExpert Review of Molecular Diagnostics
Volume15
Issue number2
DOIs
StatePublished - Feb 1 2015
Externally publishedYes

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Exome
RNA Sequence Analysis
Gene Expression
Molecular Pathology
Neoplasm Genes
Deoxyribonuclease I
DNA
Tumor Suppressor Genes
DNA Sequence Analysis
Oncogenes
Routine Diagnostic Tests
Epigenomics
Formaldehyde
Hypersensitivity
Genome
Costs and Cost Analysis
Research
Genes
Neoplasms
hydrogen sulfite

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

Cite this

Challenges and opportunities for next-generation sequencing in companion diagnostics. / Lin, Erick; Chien, Jeremy; Ong, Frank S.; Fan, Jian Bing.

In: Expert Review of Molecular Diagnostics, Vol. 15, No. 2, 01.02.2015, p. 193-209.

Research output: Contribution to journalReview article

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