Taniguchi Kosuke, Hasegawa Fuyuki, Okazaki Yuka, Hori Asuka, Ogata-Kawata Hiroko, Aoto Saki, Migita Ohsuke, Kawai Tomoko, Nakabayashi Kazuhiko, Okamura Kohji, Fukui Kana, Wada Seiji, Ozawa Katsusuke, Ito Yushi, Sago Haruhiko, Hata Kenichiro
Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.
Mol Genet Genomic Med. 2025 Mar;13(3):e70092. doi: 10.1002/mgg3.70092.
Whole exome sequencing (WES) aids in diagnosing monogenic diseases, yet > 50% of all cases remain undiagnosed. We aimed to improve diagnostic precision by developing an effective WES-based strategy for detecting congenital anomalies.
Initially, 128 probands with congenital anomalies were assessed using trio-WES and copy number variation analysis-variant interpretation was for exons and splice sites. Thereafter, we reanalyzed the sequence data for undiagnosed cases using the following methods. First, we performed trio-WES analysis, adding genetic intolerance scores annotation. Second, we analyzed all exons, splicing sites, and intron variants for cases with phenotypes suggestive of specific causative genes using SpliceAI. Lastly, using SpliceAI, we analyzed all exons, splicing sites, and intron variants in genetically constrained genes filtered with genetic intolerance scores.
Initial analysis diagnosed 51 of 128 cases (39.8%). In the reanalysis, first, we identified novel likely pathogenic variants in MED12 and CCDC22 associated with X-linked diseases. Second, a novel TMEM67 intron variant associated with Meckel syndrome was detected. Finally, a de novo hemizygous pathogenic intronic variant in CASK was identified in a case of intrauterine fetal death.
WES analysis, including intronic regions and utilizing genetic intolerance scores, has the potential to efficiently improve diagnostic yield.
全外显子组测序（WES）有助于诊断单基因疾病，但仍有超过50%的病例无法确诊。我们旨在通过开发一种基于WES的有效策略来检测先天性异常，以提高诊断准确性。
最初，对128例先天性异常的先证者进行三联体WES和拷贝数变异分析——变异解读针对外显子和剪接位点。此后，我们使用以下方法对未确诊病例的序列数据进行重新分析。首先，我们进行三联体WES分析，添加遗传不耐受评分注释。其次，对于具有提示特定致病基因表型的病例，我们使用SpliceAI分析所有外显子、剪接位点和内含子变异。最后，使用SpliceAI，我们分析了用遗传不耐受评分筛选出的遗传受限基因中的所有外显子、剪接位点和内含子变异。
初始分析确诊了128例中的51例（39.8%）。在重新分析中，首先，我们在与X连锁疾病相关的MED12和CCDC22中鉴定出可能的新致病变异。其次，检测到一个与梅克尔综合征相关的新的TMEM67内含子变异。最后，在一例宫内胎儿死亡病例中鉴定出CASK基因的一个新生半合子致病内含子变异。
包括内含子区域并利用遗传不耐受评分的WES分析有潜力有效提高诊断率。
