Genome sequencing and RNA sequencing of urinary cells reveal an intronic FBN1 variant causing aberrant splicing
Genome sequencing and RNA sequencing of urinary cells reveal an intronic FBN1 variant causing aberrant splicing
复制标题
DOI：
10.1038/s10038-022-01016-1
复制
发表时间：
2022-01-24
影响因子：
3.5
通讯作者：
Saitsu, Hirotomo
中科院分区：
文献类型：
--
作者：
Hiraide, Takuya;Shimizu, Kenji;Saitsu, Hirotomo
外显子组测序和面板测试通过全面检测外显子区域中的致病性变体，提高了遗传分析中的诊断率。然而，重要的是鉴定非外显子致病性变体以进一步提高诊断率。在这里，我们提出了一个女性先证者和她的父亲被诊断为马凡氏综合征，一个系统性结缔组织疾病引起的致病性变异FBN 1。在父亲的兄弟姐妹中也有两个受影响的个体，这表明了这个家庭的遗传基础。然而，两个机构进行的面板测试报告没有因果变异。为了进一步探索该家族的遗传基础，我们对先证者进行了基因组测序，并对先证者及其父亲的尿液样本中的尿细胞进行了RNA测序，因为FBN 1在尿细胞中强烈表达，而在外周血单核细胞中表达较差。基因组测序鉴定了FBN 1（NM_000138.4）内含子47中的一种罕见内含子变体（c.5789- 15 G>A），其遗传自其父亲。RNA测序显示FBN 1的等位基因不平衡（单等位基因表达），内含子47的保留，以及较少的利用外显子48内的新受体位点的异常转录本，这些都通过RT-PCR证实。这些结果强调了如果致病基因在血液中没有充分表达，尿细胞作为临床上可获得的RNA测序组织，以及多组学分析对遗传疾病分子诊断的有用性。
Exome sequencing and panel testing have improved diagnostic yield in genetic analysis by comprehensively detecting pathogenic variants in exonic regions. However, it is important to identify non-exonic pathogenic variants to further improve diagnostic yield. Here, we present a female proband and her father who is diagnosed with Marfan syndrome, a systemic connective tissue disorder caused by pathogenic variants in FBN1. There are also two affected individuals in the siblings of the father, indicating the genetic basis in this family. However, panel testing performed by two institutions reported no causal variants. To further explore the genetic basis of the family, we performed genome sequencing of the proband and RNA sequencing of urinary cells derived from urine samples of the proband and her father because FBN1 is strongly expressed in urinary cells though it is poorly expressed in peripheral blood mononuclear cells. Genome sequencing identified a rare intronic variant (c.5789-15G>A) in intron 47 of FBN1 (NM_000138.4), which was transmitted from her father. RNA sequencing revealed allelic imbalance (monoallelic expression) of FBN1, retention of intron 47, and fewer aberrant transcripts utilizing new acceptor sites within exon 48, which were confirmed by RT-PCR. These results highlighted urinary cells as clinically accessible tissues for RNA sequencing if disease-causing genes are not sufficiently expressed in the blood, and the usefulness of multi-omics analysis for molecular diagnosis of genetic disorders.