Background: Next generation targeted resequencing is replacing Sanger sequencing at high pace in routine genetic diagnosis. The need for well validated, high quality enrichment platforms to complement the bench-top next generation sequencing devices is high.Results: We used the WaferGen Smartchip platform to perform highly parallelized PCR based target enrichment for a set of known cancer genes in a well characterized set of cancer cell lines from the NCI60 panel. Optimization of PCR assay design and cycling conditions resulted in a high enrichment efficiency. We provide proof of a high mutation rediscovery rate and have included technical replicates to enable SNP calling validation demonstrating the high reproducibility of our enrichment platform.Conclusions: Here we present our custom developed quantitative PCR based target enrichment platform. Using highly parallel nanoliter singleplex PCR reactions makes this a flexible and efficient platform. The high mutation validation rate shows this platform's promise as a targeted resequencing method for multi-gene routine sequencing diagnostics. © 2014 De Wilde et al.; licensee BioMed Central Ltd.
CITATION STYLE
De Wilde, B., Lefever, S., Dong, W., Dunne, J., Husain, S., Derveaux, S., … Vandesompele, J. (2014). Target enrichment using parallel nanoliter quantitative PCR amplification. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-184
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