Anchored multiplex PCR for targeted next-generation sequencing

Nat Med. 2014 Dec;20(12):1479-84. doi: 10.1038/nm.3729. Epub 2014 Nov 10.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bile Duct Neoplasms / genetics*
  • Cholangiocarcinoma / genetics*
  • Gene Fusion / genetics*
  • Gene Rearrangement / genetics*
  • Glioblastoma / genetics*
  • Humans
  • Lung Neoplasms / genetics*
  • Multiplex Polymerase Chain Reaction / methods*
  • Paraffin Embedding
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA / methods*
  • Thyroid Neoplasms / genetics*