Next Generation Sequencing (NGS), and specifically targeted panel sequencing is the state-of-the-art in clinical genetic diagnosis of Mendelian diseases. However, the bioinformatics analysis and interpretation of the generated data can be challenging. A spotlight on the default transcript selection of a user-friendly, commercially available software that is widely used by genetics professionals, i.e. Illumina® VariantStudio®, is presented. For the sake of comparison, we employed Ensembl VEP, an open-source command-line tool, as it provides flexibility regarding transcript selection. The analysis of NGS data deriving from sequencing of 857 germline DNA samples of cancer patients indicated a concordance of 82.82% between the two software programs. Significantly, using the default transcript configuration of VariantStudio®, we failed to annotate correctly 11.45% of the identified loss-of-function variants. Our results underline the importance of cautious software and transcript selection and the need for reliable, white-box data analysis, along with bioinformatics expertise in clinical diagnostics.

下一代测序 (NGS) 和专门靶向 panel 测序是孟德尔疾病临床基因诊断的最新技术。然而，生成数据的生物信息学分析和解释可能具有挑战性。重点介绍了遗传学专业人士广泛使用的用户友好型商用软件（即 Illumina® VariantStudio®）的默认转录本选择。为了比较，我们使用了 Ensembl VEP，一个开源命令行工具，因为它提供了关于转录选择的灵活性。对来自癌症患者的 857 个生殖系 DNA 样本测序的 NGS 数据的分析表明，两个软件程序之间的一致性为 82.82%。值得注意的是，使用 VariantStudio® 的默认脚本配置，我们未能正确注释 11.45% 的已识别功能丧失变体。我们的结果强调了谨慎的软件和转录本选择的重要性，以及对可靠的白盒数据分析以及临床诊断中的生物信息学专业知识的需求。