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Anchored multiplex PCR for targeted next-generation sequencing
Open accessAbstract
We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5–100%) and 100% specificity (95% confidence limit: 99.3–100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.
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Self-citation
Metadata
- Authors
- Zheng, Z., Liebers, M., Zhelyazkova, B., Cao, Y., Panditi, D., Lynch, K. D., Chen, J., Robinson, H. E., Shim, H. S., Chmielecki, J., Pao, W., Engelman, J. A., Iafrate, A. J., & Le, L. P.
- Venue
- Nature Medicine
- Published
- 2014-11-10
- Volume
- 20
- Issue
- 12
- Pages
- 1479-1484
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W2062291041
- Cited by
- 915
- References
- 28
- FWCI
- 16.33
- Type
- journal article
- Language
- en
- Open access
- green
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