Anchored multiplex PCR for targeted next-generation sequencing

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review

252 Scopus Citations
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Author(s)

  • 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

Detail(s)

Original languageEnglish
Pages (from-to)1479-1484
Journal / PublicationNature Medicine
Volume20
Issue number12
Early online date10 Nov 2014
Publication statusPublished - Dec 2014
Externally publishedYes

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.

Citation Format(s)

Anchored multiplex PCR for targeted next-generation sequencing. / Zheng, Zongli; Liebers, Matthew; Zhelyazkova, Boryana; Cao, Yi; Panditi, Divya; Lynch, Kerry D.; Chen, Juxiang; Robinson, Hayley E.; Shim, Hyo Sup; Chmielecki, Juliann; Pao, William; Engelman, Jeffrey A.; Iafrate, A. John; Le, Long Phi.

In: Nature Medicine, Vol. 20, No. 12, 12.2014, p. 1479-1484.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review