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Anchored multiplex PCR for targeted next-generation sequencing.

Authors
 Zongli Zheng  ;  Matthew Liebers  ;  Boryana Zhelyazkova  ;  Yi Cao  ;  Divya Panditi  ;  Kerry D Lynch  ;  Juxiang Chen  ;  Hayley E Robinson  ;  Hyo Sup Shim  ;  Juliann Chmielecki  ;  William Pao  ;  Jeffrey A Engelman  ;  A John Iafrate  ;  Long Phi Le 
Citation
 Nature Medicine, Vol.20(12) : 1479-1484, 2014 
Journal Title
 Nature Medicine 
ISSN
 1078-8956 
Issue Date
2014
Abstract
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.
Full Text
http://www.nature.com/nm/journal/v20/n12/full/nm.3729.html
DOI
10.1038/nm.3729
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers
Yonsei Authors
Shim, Hyo Sup(심효섭) ORCID logo https://orcid.org/0000-0002-5718-3624
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/138607
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