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Genome sequencing and RNA sequencing of urinary cells reveal an intronic FBN1 variant causing aberrant splicing

Abstract

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.

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Fig. 1: Representative clinical features of the proband (III-8).
Fig. 2: Retention of intron 47 in FBN1 transcripts.
Fig. 3: Detection of minor aberrant transcripts.

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Acknowledgements

We would like to thank the patients for participating in this work. This work was supported by the Japan Agency for Medical Research and Development (AMED) (JP21ek0109549 to T.O.), Grants-in-Aid for Scientific Research (B) (JP20H03641), Grant-in-Aid for Challenging Research (Exploratory) (20K21570) from the Japan Society for the Promotion of Science, Japan Intractable Diseases (Nanbyo) Research Foundation (2020A02), and the Takeda Science Foundation.

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TO and HS contributed to the conception and design of the study. TH, KS, SM, KA, MN, TY, TK, TO, and HS contributed to the acquisition and analysis of data. TH, KS, MN, TO, and HS contributed to drafting the text and preparing the figure. All authors read and approved the final manuscript.

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Correspondence to Hirotomo Saitsu.

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Hiraide, T., Shimizu, K., Miyamoto, S. et al. Genome sequencing and RNA sequencing of urinary cells reveal an intronic FBN1 variant causing aberrant splicing. J Hum Genet 67, 387–392 (2022). https://doi.org/10.1038/s10038-022-01016-1

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