Dutch genome diagnostic centers (GDC) use next-generation sequencing (NGS)-based diagnostic applications for the diagnosis of primary immunodeficiencies (PIDs). The interpretation of genetic variants in many PIDs is complicated because of the phenotypic and genetic heterogeneity. To analyze uniformity of variant filtering, interpretation, and reporting in NGS-based diagnostics for PID, an external quality assessment was performed. Four main Dutch GDCs participated in the quality assessment. Unannotated variant call format (VCF) files of two PID patient analyses per laboratory were distributed among the four GDCs, analyzed, and interpreted (eight analyses in total). Variants that would be reported to the clinician and/or advised for further investigation were compared between the centers. A survey measuring the experiences of clinical laboratory geneticists was part of the study. Analysis of samples with confirmed diagnoses showed that all centers reported at least the variants classified as likely pathogenic (LP) or pathogenic (P) variants in all samples, except for variants in two genes (PSTPIP1 and BTK). The absence of clinical information complicated correct classification of variants. In this external quality assessment, the final interpretation and conclusions of the genetic analyses were uniform among the four participating genetic centers. Clinical and immunological data provided by a medical specialist are required to be able to draw proper conclusions from genetic data.

荷兰基因组诊断中心 (GDC) 使用基于下一代测序 (NGS) 的诊断应用程序来诊断原发性免疫缺陷 (PID)。由于表型和遗传异质性，许多 PID 中遗传变异的解释很复杂。为了分析基于 NGS 的 PID 诊断中变异过滤、解释和报告的一致性，进行了外部质量评估。四个主要的荷兰 GDC 参与了质量评估。每个实验室的两个 PID 患者分析的未注释变异调用格式 (VCF) 文件在四个 GDC 中分发、分析和解释（总共八个分析）。将向临床医生报告和/或建议进一步研究的变异在各中心之间进行比较。该研究的一部分是一项衡量临床实验室遗传学家经验的调查。对确诊样本的分析显示，所有中心至少报告了所有样本中被归类为可能致病（LP）或致病（P）变异的变异，但两个基因（PSTPIP1和BTK）的变异除外。缺乏临床信息使变异的正确分类变得复杂。在本次外部质量评估中，四个参与的遗传中心对遗传分析的最终解释和结论是一致的。需要医学专家提供的临床和免疫学数据才能从遗传数据中得出正确的结论。