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Validation of an NGS mutation detection panel for melanoma
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Reiman, Anne, Kikuchi, Hugh, Scocchia, Daniela, Smith, Peter, Tsang, Yee-Wah, Snead, David and Cree, Ian A. (2017) Validation of an NGS mutation detection panel for melanoma. BMC Cancer, 17 (1). 3149. doi:10.1186/s12885-017-3149-0 ISSN 1471-2407.
An open access version can be found in:
Official URL: http://dx.doi.org/10.1186/s12885-017-3149-0
Abstract
Background: Knowledge of the genotype of melanoma is important to guide patient management. Identification
of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver
oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as
immunotherapy.
Methods: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation
sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential
advantages in turnaround time. We describe here an Ampliseq hotspot panel for melanoma for use with the
IonTorrent Personal Genome Machine (PGM) which covers the mutations currently of most clinical interest.
Results: We have validated this in 151 cases of skin and uveal melanoma from our files, and correlated the data with
PCR based assessment of BRAF status. There was excellent agreement, with few discrepancies, though NGS does have
greater coverage and picks up some mutations that would be missed by PCR. However, these are often rare and of
unknown significance for treatment.
Conclusions: PCR methods are rapid, less time-consuming and less expensive than NGS, and could be used as triage
for patients requiring more extensive diagnostic workup. The NGS panel described here is suitable for clinical use with
formalin-fixed paraffin-embedded (FFPE) samples.
| Item Type: | Journal Article | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine > Reproductive Health ( - until July 2016) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Journal or Publication Title: | BMC Cancer | ||||||||
| Publisher: | BioMed Central Ltd. | ||||||||
| ISSN: | 1471-2407 | ||||||||
| Official Date: | 22 February 2017 | ||||||||
| Dates: |
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| Volume: | 17 | ||||||||
| Number: | 1 | ||||||||
| Article Number: | 3149 | ||||||||
| DOI: | 10.1186/s12885-017-3149-0 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Open Access Version: |
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