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Have you already read below article about NextGENe? Aim of the study that Dacheva et. al. described in this paper is to evaluate the sensitivity and specificity of the Ion PGM for diagnostic mutation screening of BRCA1/2 genes. By comparing different library prep methods and analysis software packages they prove that NGS can be used to detect all variants discovered by Sanger Sequencing. NextGENe, used as part of their analysis pipeline, proofs to be a reliable tool to detect the variants and to filter out sequence artifacts.
Acheva et. al. - Validation of an NGS Approach for Diagnostic BRCA1/BRCA2 Mutation Testing with NextGENe