Abstract
BackgroundWhole-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.MethodsWe 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.ResultsFrom 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.ConclusionsWhile 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.
Highlights
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
The vast majority of Mendelian sequencing studies used exome sequencing rather than whole-genome sequencing. This is due to several reasons, such as the lower cost of exome sequencing, the assumption that Mendelian diseases are more likely to be caused by mutations at exons than non-coding regions, and the concern that too much information on genomic variants will be too difficult to interpret bioinformatically
Whole-genome and whole-exome sequencing The whole-genome sequencing was performed by Complete Genomics (Mountain View, California, USA), and we provided 10 μg DNA samples to the company for the sequencing service
Summary
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. Over the past a few years, exome sequencing has been successfully used to identify candidate predisposing genes for multiple Mendelian diseases, and it is likely that this technique will impact clinical medicine in the relatively near future [3,4]. The vast majority of published studies attempted to solve previously known Mendelian diseases, rather than novel suspected Mendelian phenotypes that are sometimes referred to as ‘idiopathic’ diseases. This is most likely because multiple DNA samples are already readily available for known Mendelian diseases to enable statistical support for discovered variants/genes. Several examples demonstrated that it is feasible to identify disease-predisposing mutations for idiopathic diseases from only one or two families, if other prior information can help trim down candidate genes into specific linkage regions or chromosomes (such as the X-linked disease Ogden syndrome [5])
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