Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing
Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing
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DOI：
10.1172/jci141500
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发表时间：
2021-01-04
影响因子：
15.9
通讯作者：
Lee, Brendan
中科院分区：
文献类型：
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作者：
Murdock, David R.;Dai, Hongzheng;Lee, Brendan
背景转录组测序（RNA-seq）在不同程度上提高了疑似孟德尔疾病个体的诊断率，主要是通过指导外显子组或基因组测序（ES/GS）上鉴定的候选DNA变体的优先顺序。在这里，我们实施了一种RNA-seq引导的方法来诊断各种年龄和临床表型的个体。2014年至2020年，115名具有不同表型的未确诊成人和儿童患者以及67名家庭成员（共182名个体）在贝勒医学院（Baylor College of Medicine）未诊断疾病网络临床站点接受了全血和皮肤成纤维细胞的RNA-seq。我们实施了一个工作流程来检测基因表达和剪接中的异常值，尽管进行了标准的基因组和转录组学分析，但这些异常值仍未被诊断出来。转录组导向的方法在整个队列中的诊断率为12%，或在排除ES/GS单独解决的病例后为17%。新诊断的疾病包括Koolen-de弗里斯综合征（KANSL 1）、Renpenning综合征（PQBP 1）、TBCK相关脑病、NSD 2和CLTC相关智力残疾等，所有这些疾病的常规基因组检测结果均为阴性，包括ES和染色体微阵列（CMA）。皮肤成纤维细胞比全血表现出更高和更一致的临床相关基因的表达。在两种组织的RNA-seq解决的病例中，一半病例的血液中漏失了致病缺陷，但成纤维细胞中没有。对于我们的未确诊的疑似孟德尔疾病个体队列，转录组指导的基因组分析促进了诊断，主要是通过鉴定ES和CMA遗漏的变异。
BACKGROUND. Transcriptome sequencing (RNA-seq) improves diagnostic rates in individuals with suspected Mendelian conditions to varying degrees, primarily by directing the prioritization of candidate DNA variants identified on exome or genome sequencing (ES/GS). Here we implemented an RNA-seq-guided method to diagnose individuals across a wide range of ages and clinical phenotypes.METHODS. One hundred fifteen undiagnosed adult and pediatric patients with diverse phenotypes and 67 family members (182 total individuals) underwent RNA-seq from whole blood and skin fibroblasts at the Baylor College of Medicine (BCM) Undiagnosed Diseases Network clinical site from 2014 to 2020. We implemented a workflow to detect outliers in gene expression and splicing for cases that remained undiagnosed despite standard genomic and transcriptomic analysis.RESULTS. The transcriptome-directed approach resulted in a diagnostic rate of 12% across the entire cohort, or 17% after excluding cases solved on ES/GS alone. Newly diagnosed conditions included Koolen-de Vries syndrome (KANSL1), Renpenning syndrome (PQBP1), TBCK-associated encephalopathy, NSD2- and CLTC-related intellectual disability, and others, all with negative conventional genomic testing, including ES and chromosomal microarray (CMA). Skin fibroblasts exhibited higher and more consistent expression of clinically relevant genes than whole blood. In solved cases with RNA-seq from both tissues, the causative defect was missed in blood in half the cases but none from fibroblasts.CONCLUSIONS. For our cohort of undiagnosed individuals with suspected Mendelian conditions, transcriptome-directed genomic analysis facilitated diagnoses, primarily through the identification of variants missed on ES and CMA.