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Development of a gene panel for next-generation sequencing of clinically relevant mutations in cell-free DNA from cancer patients.

Abstract：

BACKGROUND:When tumour tissue is unavailable, cell-free DNA (cfDNA)can serve as a surrogate for genetic analyses. Because mutated alleles in cfDNA are usually below 1%, next-generation sequencing (NGS)must be narrowed to target only clinically relevant genes. In this proof-of-concept study, we developed a panel to use in ultra-deep sequencing to identify such mutations in cfDNA. METHODS:Our panel ('SiRe') covers 568 mutations in six genes (EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRα)involved in non-small-cell lung cancer (NSCLC), gastrointestinal stromal tumour, colorectal carcinoma and melanoma. We evaluated the panel performance in three steps. First, we analysed its analytical sensitivity on cell line DNA and by using an artificial reference standard with multiple mutations in different genes. Second, we analysed cfDNA from cancer patients at presentation (n=42), treatment response (n=12) and tumour progression (n=11); all patients had paired tumour tissue and cfDNA previously genotyped with a Taqman-derived assay (TDA). Third, we tested blood samples prospectively collected from NSCLC patients (n=79) to assess the performance of SiRe in clinical practice. RESULTS:SiRe had a high analytical performance and a 0.01% lower limit of detection. In the retrospective series, SiRe detected 40 EGFR, 11 KRAS, 1 NRAS and 5 BRAF mutations (96.8% concordance with TDA). In the baseline samples, SiRe had 100% specificity and 79% sensitivity relative to tumour tissue. Finally, in the prospective series, SiRe detected 8.7% (4/46) of EGFR mutations at baseline and 42.9% (9/21) of EGFR p.T790M in patients at tumour progression. CONCLUSIONS:SiRe is a feasible NGS panel for cfDNA analysis in clinical practice.

journal_name

Br J Cancer

journal_title

British journal of cancer

authors

Malapelle U,Mayo de-Las-Casas C,Rocco D,Garzon M,Pisapia P,Jordana-Ariza N,Russo M,Sgariglia R,De Luca C,Pepe F,Martinez-Bueno A,Morales-Espinosa D,González-Cao M,Karachaliou N,Viteri Ramirez S,Bellevicine C,Molina-Vila M

doi

10.1038/bjc.2017.8

subject

Has Abstract

pub_date

2017-03-14 00:00:00

pages

802-810

issue

eissn

0007-0920

issn

1532-1827

pii

bjc20178

journal_volume

116

pub_type

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Development of a gene panel for next-generation sequencing of clinically relevant mutations in cell-free DNA from cancer patients.