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Contribution of noncoding pathogenic variants to RPGRIP1-mediated inherited retinal degeneration

Abstract

Purpose

With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision-making. Yet the genetic cause of disease cannot be identified using exon-based sequencing for a significant portion of patients. We hypothesized that noncoding pathogenic variants contribute significantly to the genetic causality of IRDs and evaluated patients with single coding pathogenic variants in RPGRIP1 to test this hypothesis.

Methods

IRD families underwent targeted panel sequencing. Unsolved cases were explored by exome and genome sequencing looking for additional pathogenic variants. Candidate pathogenic variants were then validated by Sanger sequencing, quantitative polymerase chain reaction, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing.

Results

Among 1722 families, 3 had biallelic loss-of-function pathogenic variants in RPGRIP1 while 7 had a single disruptive coding pathogenic variants. Exome and genome sequencing revealed potential noncoding pathogenic variants in these 7 families. In 6, the noncoding pathogenic variants were shown to lead to loss of function in vitro.

Conclusion

Noncoding pathogenic variants were identified in 6 of 7 families with single coding pathogenic variants in RPGRIP1. The results suggest that noncoding pathogenic variants contribute significantly to the genetic causality of IRDs and RPGRIP1-mediated IRDs are more common than previously thought.

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Acknowledgements

This work was supported by grants from the National Eye Institute (RO1EY012910 [EAP], R01EY026904 [KMB/EAP], and P30EY014104 [MEEI core support]), and the Foundation Fighting Blindness (USA, EAP). Sequencing and analysis was provided by the Center for Mendelian Genomics at the Broad Institute of MIT and Harvard and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute grant UM1 HG008900 to Daniel MacArthur and Heidi Rehm. The authors would like to thank the patients and their family members for their participation in this study and the Ocular Genomics Institute Genomics Core members for their experimental assistance. The authors would like to thank the Exome Aggregation Consortium, the Genome Aggregation Database (gnomAD), and the groups that provided exome variant data for comparison. A full list of contributing groups can be found at http://exac.broadinstitute.org/about and http://gnomad.broadinstitute.org/about.

Author information

Correspondence to Eric A. Pierce M.D., Ph.D. or Kinga M. Bujakowska Ph.D..

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Disclosure

The authors declare no conflict of interest.

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Keywords

  • Inherited retinal degeneration
  • Noncoding pathogenic variants
  • RPGRIP1
  • Intronic pathogenic variants
  • genome sequencing

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Fig. 1
Fig. 2: Exon 1 and 2 duplication in OGI-237 and identification of a novel exon.
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