title: Target enrichment using parallel nanoliter quantitative PCR amplification.
abstract: 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.
authors.forename: Bram
authors.initials: B
authors.lastname: De Wilde
authors.forename: Steve
authors.initials: S
authors.lastname: Lefever
authors.forename: Wes
authors.initials: W
authors.lastname: Dong
authors.forename: Jude
authors.initials: J
authors.lastname: Dunne
authors.forename: Syed
authors.initials: S
authors.lastname: Husain
authors.forename: Stefaan
authors.initials: S
authors.lastname: Derveaux
authors.forename: Jan
authors.initials: J
authors.lastname: Hellemans
authors.affiliation: Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium. Joke.Vandesompele@ugent.be.
authors.forename: Jo
authors.initials: J
authors.lastname: Vandesompele
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000032:analysis / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA