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BMC Cancer
Published in: BMC Cancer 1/2015

Open Access 01-12-2015 | Research article

Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium

Authors: Bastiaan BJ Tops, Nicola Normanno, Henriette Kurth, Eliana Amato, Andrea Mafficini, Nora Rieber, Delphine Le Corre, Anna Maria Rachiglio, Anne Reiman, Orla Sheils, Christoph Noppen, Ludovic Lacroix, Ian A Cree, Aldo Scarpa, Marjolijn JL Ligtenberg, Pierre Laurent-Puig

Published in: BMC Cancer | Issue 1/2015

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Abstract

Background

The number of predictive biomarkers that will be necessary to assess in clinical practice will increase with the availability of drugs that target specific molecular alterations. Therefore, diagnostic laboratories are confronted with new challenges: costs, turn-around-time and the amount of material required for testing will increase with the number of tests performed on a sample. Our consortium of European clinical research laboratories set out to test if semi-conductor sequencing provides a solution for these challenges.

Methods

We designed a multiplex PCR targeting 87 hotspot regions in 22 genes that are of clinical interest for lung and/or colorectal cancer. The gene-panel was tested by 7 different labs in their own clinical setting using ion-semiconductor sequencing.

Results

We analyzed 155 samples containing 112 previously identified mutations in the KRAS, EGFR en BRAF genes. Only 1 sample failed analysis due to poor quality of the DNA. All other samples were correctly genotyped for the known mutations, even as low as 2%, but also revealed other mutations. Optimization of the primers used in the multiplex PCR resulted in a uniform coverage distribution over the amplicons that allows for efficient pooling of samples in a sequencing run.

Conclusions

We show that a semi-conductor based sequencing approach to stratify colon and lung cancer patients is feasible in a clinical setting.
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Metadata
Title
Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
Authors
Bastiaan BJ Tops
Nicola Normanno
Henriette Kurth
Eliana Amato
Andrea Mafficini
Nora Rieber
Delphine Le Corre
Anna Maria Rachiglio
Anne Reiman
Orla Sheils
Christoph Noppen
Ludovic Lacroix
Ian A Cree
Aldo Scarpa
Marjolijn JL Ligtenberg
Pierre Laurent-Puig
Publication date
01-12-2015
Publisher
BioMed Central
Published in
BMC Cancer / Issue 1/2015
Electronic ISSN: 1471-2407
DOI
https://doi.org/10.1186/s12885-015-1015-5

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