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Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement

Kai Wang12*, Cecilia Kim2, Jonathan Bradfield2, Yunfei Guo1, Elina Toskala2, Frederick G Otieno2, Cuiping Hou2, Kelly Thomas2, Christopher Cardinale2, Gholson J Lyon23, Ryan Golhar2 and Hakon Hakonarson24*

Author Affiliations

1 Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo St, Los Angeles, CA 90089, USA

2 Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, USA

3 Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Rd, NY 11724, USA

4 Department of Pediatrics, University of Pennsylvania School of Medicine, 3451 Walnut St, Philadelphia, PA 19104, USA

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Genome Medicine 2013, 5:67  doi:10.1186/gm471

Published: 26 July 2013

Abstract

Background

Whole-exome sequencing has identified the causes of several Mendelian diseases by analyzing multiple unrelated cases, but it is more challenging to resolve the cause of extremely rare and suspected Mendelian diseases from individual families. We identified a family quartet with two children, both affected with a previously unreported disease, characterized by progressive muscular weakness and cardiomyopathy, with normal intelligence. During the course of the study, we identified one additional unrelated patient with a comparable phenotype.

Methods

We performed whole-genome sequencing (Complete Genomics platform), whole-exome sequencing (Agilent SureSelect exon capture and Illumina Genome Analyzer II platform), SNP genotyping (Illumina HumanHap550 SNP array) and Sanger sequencing on blood samples, as well as RNA-Seq (Illumina HiSeq platform) on transformed lymphoblastoid cell lines.

Results

From whole-genome sequence data, we identified RBCK1, a gene encoding an E3 ubiquitin-protein ligase, as the most likely candidate gene, with two protein-truncating mutations in probands in the first family. However, exome data failed to nominate RBCK1 as a candidate gene, due to poor regional coverage. Sanger sequencing identified a private homozygous splice variant in RBCK1 in the proband in the second family, yet SNP genotyping revealed a 1.2Mb copy-neutral region of homozygosity covering RBCK1. RNA-Seq confirmed aberrant splicing of RBCK1 transcripts, resulting in truncated protein products.

Conclusions

While the exact mechanism by which these mutations cause disease is unknown, our study represents an example of how the combined use of whole-genome DNA and RNA sequencing can identify a disease-predisposing gene for a novel and extremely rare Mendelian disease.