Abstract
Ciliopathies are a group of rare disorders characterized by a high genetic and phenotypic variability, which complicates their molecular diagnosis. Hence the need to use the latest powerful approaches to faster identify the genetic defect in these patients. We applied whole exome sequencing to six consanguineous families clinically diagnosed with ciliopathy-like disease, and for which mutations in predominant Bardet-Biedl syndrome (BBS) genes had previously been excluded. Our strategy, based on first applying several filters to ciliary variants and using many of the bioinformatics tools available, allowed us to identify causal mutations in BBS2, ALMS1 and CRB1 genes in four families, thus confirming the molecular diagnosis of ciliopathy. In the remaining two families, after first rejecting the presence of pathogenic variants in common cilia-related genes, we adopted a new filtering strategy combined with prioritisation tools to rank the final candidate genes for each case. Thus, we propose CORO2B, LMO7 and ZNF17 as novel candidate ciliary genes, but further functional studies will be needed to confirm their role. Our data show the usefulness of this strategy to diagnose patients with unclear phenotypes, and therefore the success of applying such technologies to achieve a rapid and reliable molecular diagnosis, improving genetic counselling for these patients. In addition, the described pipeline also highlights the common pitfalls associated to the large volume of data we have to face and the difficulty of assigning a functional role to these changes, hence the importance of designing the most appropriate strategy according to each case.
MeSH terms
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Biomarkers / metabolism
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Cell Cycle Proteins
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Cilia / metabolism
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Cilia / pathology
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Ciliopathies / diagnosis*
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Ciliopathies / genetics*
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Ciliopathies / pathology
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Consanguinity
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DNA-Binding Proteins / genetics*
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DNA-Binding Proteins / metabolism
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Exome*
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Eye Proteins / genetics
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Eye Proteins / metabolism
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Female
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Gene Expression
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Genome, Human
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Genotype
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High-Throughput Nucleotide Sequencing
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Humans
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LIM Domain Proteins / genetics*
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LIM Domain Proteins / metabolism
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Male
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Membrane Proteins / genetics
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Membrane Proteins / metabolism
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Microfilament Proteins / genetics*
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Microfilament Proteins / metabolism
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Nerve Tissue Proteins / genetics
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Nerve Tissue Proteins / metabolism
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Phenotype
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Proteins / genetics
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Proteins / metabolism
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Transcription Factors / genetics*
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Transcription Factors / metabolism
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Tripartite Motif Proteins
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Ubiquitin-Protein Ligases
Substances
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ALMS1 protein, human
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Bbs2 protein, human
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Biomarkers
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CORO2B protein, human
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CRB1 protein, human
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Cell Cycle Proteins
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DNA-Binding Proteins
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Eye Proteins
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LIM Domain Proteins
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LMO7 protein, human
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Membrane Proteins
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Microfilament Proteins
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Nerve Tissue Proteins
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Proteins
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Transcription Factors
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Tripartite Motif Proteins
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TRIM26 protein, human
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Ubiquitin-Protein Ligases
Grants and funding
This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness – Instituto de Salud Carlos III (
http://www.isciii.es/) grant PI12/01853, and the Centro Nacional de Análisis Genómico (CNAG) for the “2013 CNAG-call: 300 exomes to elucidate rare diseases” (code: SENDIS;
http://www.cnag.crg.eu/). SC-S and MA-S are recipients of Formación de Profesorado Universitario (FPU) fellowships (FPU13/01835 and FPU12/01442, respectively) from the Spanish Ministry of Education, Culture and Sports (
http://www.mecd.gob.es/portada-mecd/). SD was supported by the Torres Quevedo subprogram from the Spanish Ministry of Science and Innovation (MICINN,
http://www.idi.mineco.gob.es/portal/site/MICINN/) under the grant agreement PTQ-12-05391. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. There was no additional external funding received for this study.