RESUMO
Fast and efficient high-throughput techniques are essential for the molecular diagnosis of highly heterogeneous hereditary diseases, such as retinitis pigmentosa (RP). We had previously approached RP genetic testing by devising a chip based on co-segregation analysis for the autosomal recessive forms. In this study, we aimed to design a diagnostic tool for all the known genes (40 up to now) responsible for the autosomal dominant and recessive RP and Leber congenital amaurosis (LCA). This new chip analyzes 240 single nucleotide polymorphisms (SNPs) (6 per gene) on a high-throughput genotyping platform (SNPlex, Applied Biosystems), and genetic diagnosis is based on the co-segregation analysis of SNP haplotypes in independent families. In a single genotyping step, the number of RP candidates to be screened for mutations is considerably reduced, and in the most informative families, all the candidates are ruled out at once. In a panel of RP Spanish pedigrees, the disease chip became a crucial tool for selecting those suitable for genome-wide RP gene search, and saved the burdensome direct mutational screening of every known RP gene. In a large adRP family, the chip allowed ruling out of all but the causative gene, and identification of an unreported null mutation (E181X) in PRPF31. Finally, on the basis of the conservation of the SNP haplotype linked to this pathogenic variant, we propose that the E181X mutation spread through a cohort of geographically isolated families by a founder effect.
Assuntos
Efeito Fundador , Amaurose Congênita de Leber/diagnóstico , Amaurose Congênita de Leber/genética , Análise de Sequência com Séries de Oligonucleotídeos , Polimorfismo de Nucleotídeo Único/genética , Retinose Pigmentar/diagnóstico , Retinose Pigmentar/genética , Sequência de Bases , Análise Mutacional de DNA , Éxons/genética , Proteínas do Olho/genética , Família , Feminino , Fundo de Olho , Genes Dominantes/genética , Genes Recessivos/genética , Haplótipos/genética , Humanos , Masculino , Dados de Sequência Molecular , Mutação/genética , Linhagem , Penetrância , Reação em Cadeia da Polimerase Via Transcriptase Reversa , EspanhaRESUMO
PURPOSE: A large family with 11 males and 2 females with X-linked retinitis pigmentosa (XLRP) was analyzed in search of pathologic mutations. METHODS: Of the two major XLRP genes, RPGR was analyzed by SNP cosegregation and RP2 was directly screened for mutations. The pathogenicity of a new variant was assessed in silico, in vivo, and in vitro. RESULTS: The results of cosegregation analysis with SNPs closely located to RPGR excluded this gene as the cause of the disease in this family. Sequencing of RP2 showed a putative pathogenic variant in intron 3 at the conserved polypyrimidine tract (c.1073-9T>A). This substitution cosegregated with the disease and was not found in 220 control chromosomes. In silico analyses using online resources indicated a decreased score of intron 3 acceptor splice site for the mutated sequence. Real-time RT-PCR analysis of the RP2 splicing pattern in blood samples of patients and carrier females showed skipping of exon 4, causing a frame shift that introduced a premature stop codon. Further verification of the pathogenicity of this point mutation was obtained by expression of a minigene RP2 construct in cultured cells. CONCLUSIONS: A transversion (T>A) at position -9 in intron 3 of RP2 causes XLRP by altering the splicing pattern and highlights the pathogenicity of intronic variants. The single point RP2 mutation leads to a wide range of phenotypic traits in carrier females, from completely normal to severe retinal degeneration, thus supporting that RP2 is also a candidate for semidominance in XLRP.