Anchored Multiplex PCR for Targeted Next-generation Sequencing

Overview

Journal Nat Med

Specialties General Medicine
Molecular Biology

Date 2014 Nov 11

PMID 25384085

Citations 411

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

Affiliations

Soon will be listed here.

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.

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