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) |
|---|---|
| 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 |
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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 journal › Review article
}
TY - JOUR
T1 - Challenges and opportunities for next-generation sequencing in companion diagnostics
AU - Lin, Erick
AU - Chien, Jeremy
AU - Ong, Frank S.
AU - Fan, Jian Bing
PY - 2015/2/1
Y1 - 2015/2/1
N2 - 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.
AB - 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.
KW - bioinformatics
KW - companion diagnostics
KW - CTC
KW - ctDNA
KW - next-generation sequencing
KW - NGS
KW - precision medicine
KW - precision oncology
KW - tumor heterogeneity
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UR - http://www.scopus.com/inward/citedby.url?scp=84921390202&partnerID=8YFLogxK
U2 - 10.1586/14737159.2015.961916
DO - 10.1586/14737159.2015.961916
M3 - Review article
C2 - 25249308
AN - SCOPUS:84921390202
VL - 15
SP - 193
EP - 209
JO - Expert Review of Anticancer Therapy
JF - Expert Review of Anticancer Therapy
SN - 1473-7140
IS - 2
ER -