Targeted-capture Massively-parallel Sequencing Enables Robust Detection of Clinically Informative Mutations from Formalin-fixed Tumours

Overview

Journal Sci Rep

Specialty Science

Date 2013 Dec 17

PMID 24336498

Citations 29

Authors

Stephen Q Wong

Jason Li

Renato Salemi

Karen E Sheppard

Hongdo Do

Richard W Tothill

Grant A McArthur

Alexander Dobrovic

Affiliations

Soon will be listed here.

Abstract

Massively parallel sequencing offers the ability to interrogate a tumour biopsy for multiple mutational changes. For clinical samples, methodologies must enable maximal extraction of available sequence information from formalin-fixed and paraffin-embedded (FFPE) material. We assessed the use of targeted capture for mutation detection in FFPE DNA. The capture probes targeted the coding region of all known kinase genes and selected oncogenes and tumour suppressor genes. Seven melanoma cell lines and matching FFPE xenograft DNAs were sequenced. An informatics pipeline was developed to identify variants and contaminating mouse reads. Concordance of 100% was observed between unfixed and formalin-fixed for reported COSMIC variants including BRAF V600E. mutations in genes not conventionally screened including ERBB4, ATM, STK11 and CDKN2A were readily detected. All regions were adequately covered with independent reads regardless of GC content. This study indicates that hybridisation capture is a robust approach for massively parallel sequencing of FFPE samples.

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