Dataset Information

Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population.

ABSTRACT:

Background

Retinitis pigmentosa and other hereditary retinal degenerations (HRD) are rare genetic diseases leading to progressive blindness. Recessive HRD are caused by mutations in more than 100 different genes. Laws of population genetics predict that, on a purely theoretical ground, such a high number of genes should translate into an extremely elevated frequency of unaffected carriers of mutations. In this study we estimate the proportion of these individuals within the general population, via the analyses of data from whole-genome sequencing.

Methodology/principal findings

We screened complete and high-quality genome sequences from 46 control individuals from various world populations for HRD mutations, using bioinformatic tools developed in-house. All mutations detected in silico were validated by Sanger sequencing. We identified clear-cut, null recessive HRD mutations in 10 out of the 46 unaffected individuals analyzed (?22%).

Conclusions/significance

Based on our data, approximately one in 4-5 individuals from the general population may be a carrier of null mutations that are responsible for HRD. This would be the highest mutation carrier frequency so far measured for a class of Mendelian disorders, especially considering that missenses and other forms of pathogenic changes were not included in our assessment. Among other things, our results indicate that the risk for a consanguineous couple of generating a child with a blinding disease is particularly high, compared to other genetic conditions.

SUBMITTER: Nishiguchi KM

PROVIDER: S-EPMC3407128 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Publications

Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population.

Nishiguchi Koji M KM Rivolta Carlo C

PloS one 20120727 7

<h4>Background</h4>Retinitis pigmentosa and other hereditary retinal degenerations (HRD) are rare genetic diseases leading to progressive blindness. Recessive HRD are caused by mutations in more than 100 different genes. Laws of population genetics predict that, on a purely theoretical ground, such a high number of genes should translate into an extremely elevated frequency of unaffected carriers of mutations. In this study we estimate the proportion of these individuals within the general popul ...[more]

PMID: 22848652

Similar Datasets

Project description:BACKGROUND:Dramatic improvements in DNA-sequencing technologies and computational analyses have led to wide use of whole exome sequencing (WES) to identify the genetic basis of Mendelian disorders. More than 180 novel rare-disease-causing genes with Mendelian inheritance patterns have been discovered through sequencing the exomes of just a few unrelated individuals or family members. As rare/novel genetic variants continue to be uncovered, there is a major challenge in distinguishing true pathogenic variants from rare benign mutations. METHODS:We used publicly available exome cohorts, together with the dbSNP database, to derive a list of genes (n?=?100) that most frequently exhibit rare (<1%) non-synonymous/splice-site variants in general populations. We termed these genes FLAGS for FrequentLy mutAted GeneS and analyzed their properties. RESULTS:Analysis of FLAGS revealed that these genes have significantly longer protein coding sequences, a greater number of paralogs and display less evolutionarily selective pressure than expected. FLAGS are more frequently reported in PubMed clinical literature and more frequently associated with diseased phenotypes compared to the set of human protein-coding genes. We demonstrated an overlap between FLAGS and the rare-disease causing genes recently discovered through WES studies (n?=?10) and the need for replication studies and rigorous statistical and biological analyses when associating FLAGS to rare disease. Finally, we showed how FLAGS are applied in disease-causing variant prioritization approach on exome data from a family affected by an unknown rare genetic disorder. CONCLUSIONS:We showed that some genes are frequently affected by rare, likely functional variants in general population, and are frequently observed in WES studies analyzing diverse rare phenotypes. We found that the rate at which genes accumulate rare mutations is beneficial information for prioritizing candidates. We provided a ranking system based on the mutation accumulation rates for prioritizing exome-captured human genes, and propose that clinical reports associating any disease/phenotype to FLAGS be evaluated with extra caution.

Dataset Information

Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population.

Background

Methodology/principal findings

Conclusions/significance

Publications

Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population.

Similar Datasets

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