Beyens Matthias, Boeckx Nele, Van Camp Guy, Op de Beeck Ken, Vandeweyer Geert
Center of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43, 2650, Antwerp, Belgium.
Center of Oncological Research, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
BMC Bioinformatics. 2017 Dec 14;18(1):554. doi: 10.1186/s12859-017-1985-1.
Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge.
We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data.
pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.
Haloplex靶向重测序是一种用于分析基因面板中种系和体细胞变异的常用方法。然而，相关的湿实验程序可能会引入假阳性结果，这在后续数据分析中需要加以考虑。据我们所知，目前尚无一个一体化的软件包能够提供针对与扩增子富集相关的系统误差的变异过滤原理。
我们展示了pyAmpli，这是一个独立于平台的并行化Python软件包，它为Haloplex数据实现了基于扩增子的种系和体细胞变异过滤策略。pyAmpli可以根据用户预先定义的标准过滤变异的系统误差。我们表明，pyAmpli在不降低灵敏度的情况下显著提高了特异性，这对于报告基因面板数据中真正的阳性临床相关突变至关重要。
pyAmpli是一个易于使用的软件工具，它提高了靶向重测序数据中真正的阳性变异检出率。它特别减少了与基于PCR的靶向区域富集相关的误差。
