Fattahi Zohreh, Shokouhian Ebrahim, Peymani Fatemeh, Babanejad Mojgan, Beheshtian Maryam, Edizadeh Masoud, Molaei Negar, Alagha Parnian, Ghodratpour Fatemeh, Keshavarzi Fatemeh, Moghadam Masoumeh Goleyjani, Arzhangi Sanaz, Kahrizi Kimia, Najmabadi Hossein
Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Department of Bioinformatics, Genoks Genetic Diagnosis Center, Ankara, Turkey.
Clin Genet. 2025 Jun;107(6):612-619. doi: 10.1111/cge.14692. Epub 2025 Jan 2.
Recent advances in next generation sequencing (NGS) have positioned whole exome sequencing (WES) as an efficient first-tier method in genetic diagnosis. However, despite the diagnostic yield of 35%-50% in intellectual disability (ID) many patients still remain undiagnosed due to inherent limitations and bioinformatic short-comings. In this study, we reanalyzed WES data from 159 Iranian families showing recessively inherited ID. The reanalysis was conducted with an initial clinical re-evaluation of the patients and their families, followed by data reanalysis using two updated bioinformatic pipelines. In the first phase, the BWA-GATK pipeline was utilized for alignment and variant calling, with subsequent variant annotation by the ANNOVAR tool. This approach yielded causative variants in 17 families (10.6%). Among these, six genes (MAZ, ACTR5, AKTIP, MIX23, SERPINB12, and CDC25B) were identified as novel candidates potentially associated with ID, supported by bioinformatics functional annotation and segregation analysis. In the second phase, families with negative results were reassessed using the Illumina DRAGEN Bio-IT platform for variant-calling, and Ilyome, a newly developed web-based tool, for annotation. The second phase identified likely pathogenic variants in two additional families, increasing the total diagnostic yield to 11.9% which is consistent with other studies conducted on cohorts of patients with ID. In conclusion, identification of co-segregating variants in six novel candidate genes in this study, emphasizes once more on the potential of WES reanalysis to uncover previously unknown gene-disease associations. Notably, it demonstrates that systematic reanalysis of WES data using updated bioinformatic tools and a thorough review of the literature for new gene-disease associations while performing phenotypic re-evaluation, can improve diagnostic outcome of WES in recessively inherited ID. Consequently, if performed within a 1-3 year period, it can reduce the number of cases that may require other costly diagnostic methods such as whole genome sequencing.
新一代测序（NGS）技术的最新进展已使全外显子组测序（WES）成为基因诊断中一种高效的一线方法。然而，尽管智力障碍（ID）患者的诊断率为35%-50%，但由于其固有的局限性和生物信息学缺陷，许多患者仍未得到诊断。在本研究中，我们重新分析了来自159个表现为隐性遗传ID的伊朗家庭的WES数据。重新分析首先对患者及其家庭进行了初步临床重新评估，随后使用两个更新的生物信息学流程对数据进行重新分析。在第一阶段，使用BWA-GATK流程进行比对和变异检测，随后通过ANNOVAR工具进行变异注释。这种方法在17个家庭（10.6%）中发现了致病变异。其中，六个基因（MAZ、ACTR5、AKTIP、MIX23、SERPINB12和CDC25B）被确定为可能与ID相关的新候选基因，这得到了生物信息学功能注释和分离分析的支持。在第二阶段，对结果为阴性的家庭使用Illumina DRAGEN生物信息技术平台进行变异检测，并使用新开发的基于网络的工具Ilyome进行注释。第二阶段在另外两个家庭中发现了可能的致病变异，使总诊断率提高到11.9%，这与其他针对ID患者队列的研究结果一致。总之，本研究中在六个新候选基因中鉴定出共分离变异，再次强调了WES重新分析在揭示先前未知的基因-疾病关联方面的潜力。值得注意的是，它表明在进行表型重新评估时，使用更新的生物信息学工具对WES数据进行系统重新分析，并对新的基因-疾病关联进行全面文献回顾，可以提高WES在隐性遗传ID中的诊断结果。因此，如果在1-3年内进行，它可以减少可能需要其他昂贵诊断方法（如全基因组测序）的病例数量。
