03039nas a2200385   4500008004100000022001400041245012200055210006900177260001600246300000700262490000700269520175100276653001502027653001102042653001302053653004202066653001102108653002302119653001802142100002802160700002302188700002602211700002402237700002602261700003202287700003302319700002802352700003002380700001802410700002102428700002002449700001902469700002502488856014002513       2025                        eng d  a1479-587600aA genomic strategy for precision medicine in rare diseases: integrating customized algorithms into clinical practice.0 agenomic strategy for precision medicine in rare diseases integra  c2025 Jan 20  a860 v233 a<p><b>BACKGROUND: </b>Despite the use of Next-Generation Sequencing (NGS) as the gold standard for the diagnosis of rare diseases, its clinical implementation has been challenging, limiting the cost-effectiveness of NGS and the understanding, control and safety essential for decision-making in clinical applications. Here, we describe a personalized NGS-based strategy integrating precision medicine into a public healthcare system and its implementation in the routine diagnosis process during a five-year pilot program.</p><p><b>METHODS: </b>Our approach involved customized probe designs, the generation of virtual panels and the development of a personalized medicine module (PMM) for variant prioritization. This strategy was applied to 6500 individuals including 6267 index patients and 233 NGS-based carrier screenings.</p><p><b>RESULTS: </b>Causative variants were identified in 2061 index patients (average 32.9%, ranging from 12 to 62% by condition). Also, 131 autosomal-recessive cases could be partially genetically diagnosed. These results led to over 5000 additional studies including carrier, prenatal and preimplantational tests or pharmacological and gene therapy treatments.</p><p><b>CONCLUSION: </b>This strategy has shown promising improvements in the diagnostic rate, facilitating timely diagnosis and gradually expanding our services portfolio for rare diseases. The steps taken towards the integration of clinical and genomic data are opening new possibilities for conducting both retrospective and prospective healthcare studies. Overall, this study represents a major milestone in the ongoing efforts to improve our understanding and clinical management of rare diseases, a crucial area of medical research and care.</p>10aAlgorithms10aFemale10aGenomics10aHigh-Throughput Nucleotide Sequencing10aHumans10aPrecision Medicine10arare diseases1 aMéndez-Vidal, Cristina1 aBravo-Gil, Nereida1 aPerez-Florido, Javier1 aMarcos-Luque, Irene1 aFernández, Raquel, M1 aFernandez-Rueda, Jose, Luis1 adel Pozo, María, González-1 aMartín-Sánchez, Marta1 aFernández-Suárez, Elena1 aMena, Marcela1 aCarmona, Rosario1 aDopazo, Joaquin1 aBorrego, Salud1 aAntiňolo, Guillermo  uhttp://clinbioinfosspa.es/content/genomic-strategy-precision-medicine-rare-diseases-integrating-customized-algorithms-clinical-practice02756nas a2200397   4500008004100000022001400041245012200055210006900177260001600246300001000262490000600272520143100278653001201709653002401721653003101745653002801776653001701804653001701821653003201838653002601870653002001896653004201916653001101958653001301969653001401982653002401996100002302020700002802043700002502071700003302096700003602129700002002165700001902185700002502204856012902229       2016                        eng d  a2045-232200aImproving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel.0 aImproving the management of Inherited Retinal Dystrophies by tar  c2016 Apr 01  a239100 v63 a<p>Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management. </p>10aAlleles10aComputer Simulation10aDNA Copy Number Variations10aDNA Mutational Analysis10aEye Proteins10aGene Library10aGenetic Association Studies10aGenetic Heterogeneity10aGenetic Therapy10aHigh-Throughput Nucleotide Sequencing10aHumans10amutation10aPhenotype10aRetinal Dystrophies1 aBravo-Gil, Nereida1 aMéndez-Vidal, Cristina1 aRomero-Pérez, Laura1 adel Pozo, María, González-1 ade la Rúa, Enrique, Rodríguez1 aDopazo, Joaquin1 aBorrego, Salud1 aAntiňolo, Guillermo  uhttp://clinbioinfosspa.es/content/improving-management-inherited-retinal-dystrophies-targeted-sequencing-population-specific02531nas a2200361   4500008004100000022001400041245008000055210006900135260001300204300001300217490000800230520137100238653001801609653004901627653003401676653001701710653001101727653002801738653002301766653001301789653002501802653002701827653001001854100003301864700002301897700002801920700003301948700002201981700002002003700001902023700002502042856010202067       2015                        eng d  a1552-483300aRe-evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F.0 aReevaluation casts doubt on the pathogenicity of homozygous USH2  c2015 Jul  a1597-6000 v1673 a<p>Mutations in USH2A are a common cause of Retinitis Pigmentosa (RP). Among the most frequently reported USH2A variants, c.2276G>T (p.C759F) has been found in both affected and healthy individuals. The pathogenicity of this variant remains controversial since it was detected in homozygosity in two healthy siblings of a Spanish family (S23), eleven years ago. The fact that these individuals remain asymptomatic today, prompted us to study the presence of other pathogenic variants in this family using targeted resequencing of 26 retinal genes in one of the affected individuals. This approach allowed us to identify one novel pathogenic homozygous mutation in exon 13 of PDE6B (c.1678C>T; p.R560C). This variant cosegregated with the disease and was absent in 200 control individuals. Remarkably, the identified variant in PDE6B corresponds to the mutation responsible of the retinal degeneration in the naturally occurring rd10 mutant mice. To our knowledge, this is the first report of the identification of the rd10 mice mutation in a RP family. These findings, together with a review of the literature, support the hypothesis that homozygous p.C759F mutations are not pathogenic and led us to exclude the implication of p.C759F in the RP of family S23. Our results indicate the need of re-evaluating all families genetically diagnosed with this mutation.</p>10aBase Sequence10aCyclic Nucleotide Phosphodiesterases, Type 610aExtracellular Matrix Proteins10aGene Library10aHumans10aMolecular Sequence Data10aMutation, Missense10aPedigree10aRetinitis pigmentosa10aSequence Analysis, DNA10aSpain1 aDel Pozo, María, González-1 aBravo-Gil, Nereida1 aMéndez-Vidal, Cristina1 aMontero-de-Espinosa, Ignacio1 aMillán, José, M1 aDopazo, Joaquin1 aBorrego, Salud1 aAntiňolo, Guillermo  uhttp://clinbioinfosspa.es/content/re-evaluation-casts-doubt-pathogenicity-homozygous-ush2a-pc759f02775nas a2200445   4500008004100000022001400041245012000055210006900175260000900244300001200253490000600265520144600271653001501717653001001732653002401742653001801766653001001784653002701794653002801821653001001849653001101859653001101870653001101881653002501892653000901917653001601926653002801942653001301970653001301983653002401996653001402020100003302034700002802067700002302095700002202118700002002140700001902160700002502179856012502204       2014                        eng d  a1932-620300aExome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies.0 aExome sequencing reveals novel and recurrent mutations with clin  c2014  ae1161760 v93 a<p>This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program. </p>10aAdolescent10aAdult10aAmino Acid Sequence10aBase Sequence10aChild10aChromosome Segregation10aDNA Mutational Analysis10aExome10aFamily10aFemale10aHumans10aInheritance Patterns10aMale10aMiddle Aged10aMolecular Sequence Data10amutation10aPedigree10aRetinal Dystrophies10aRhodopsin1 adel Pozo, María, González-1 aMéndez-Vidal, Cristina1 aBravo-Gil, Nereida1 aVela-Boza, Alicia1 aDopazo, Joaquin1 aBorrego, Salud1 aAntiňolo, Guillermo  uhttp://clinbioinfosspa.es/content/exome-sequencing-reveals-novel-and-recurrent-mutations-clinical-significance-inherited03760nas a2200397   4500008004100000022001400041245013500055210006900190260001600259300000800275490000700283520244800290653002602738653001802764653002502782653002802807653001702835653002102852653003202873653001102905653002702916653003602943653002302979653001303002653001403015653001103029653002503040100002803065700002303093700003303116700002203149700002003171700001903191700002503210856012703235       2014                        eng d  a1471-215600aNovel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree.0 aNovel RP1 mutations and a recurrent BBS1 variant explain the coe  c2014 Dec 14  a1430 v153 a<p><b>BACKGROUND: </b>Molecular diagnosis of Inherited Retinal Dystrophies (IRD) has long been challenging due to the extensive clinical and genetic heterogeneity present in this group of disorders. Here, we describe the clinical application of an integrated next-generation sequencing approach to determine the underlying genetic defects in a Spanish family with a provisional clinical diagnosis of autosomal recessive Retinitis Pigmentosa (arRP).</p><p><b>RESULTS: </b>Exome sequencing of the index patient resulted in the identification of the homozygous BBS1 p.M390R mutation. Sanger sequencing of additional members of the family showed lack of co-segregation of the p.M390R variant in some individuals. Clinical reanalysis indicated co-ocurrence of two different phenotypes in the same family: Bardet-Biedl syndrome in the individual harboring the BBS1 mutation and non-syndromic arRP in extended family members. To identify possible causative mutations underlying arRP, we conducted disease-targeted gene sequencing using a panel of 26 IRD genes. The in-house custom panel was validated using 18 DNA samples known to harbor mutations in relevant genes. All variants were redetected, indicating a high mutation detection rate. This approach allowed the identification of two novel heterozygous null mutations in RP1 (c.4582_4585delATCA; p.I1528Vfs*10 and c.5962dupA; p.I1988Nfs*3) which co-segregated with the disease in arRP patients. Additionally, a mutational screening in 96 patients of our cohort with genetically unresolved IRD revealed the presence of the c.5962dupA mutation in one unrelated family.</p><p><b>CONCLUSIONS: </b>The combination of molecular findings for RP1 and BBS1 genes through exome and gene panel sequencing enabled us to explain the co-existence of two different retinal phenotypes in a family. The identification of two novel variants in RP1 suggests that the use of panels containing the prevalent genes of a particular population, together with an optimized data analysis pipeline, is an efficient and cost-effective approach that can be reliably implemented into the routine diagnostic process of diverse inherited retinal disorders. Moreover, the identification of these novel variants in two unrelated families supports the relatively high prevalence of RP1 mutations in Spanish population and the role of private mutations for commonly mutated genes, while extending the mutational spectrum of RP1.</p>10aBardet-Biedl Syndrome10aBase Sequence10aCase-Control Studies10aDNA Mutational Analysis10aEye Proteins10aGenes, Recessive10aGenetic Association Studies10aHumans10aMicrosatellite Repeats10aMicrotubule-Associated Proteins10aMutation, Missense10aPedigree10aPhenotype10aRetina10aRetinitis pigmentosa1 aMéndez-Vidal, Cristina1 aBravo-Gil, Nereida1 adel Pozo, María, González-1 aVela-Boza, Alicia1 aDopazo, Joaquin1 aBorrego, Salud1 aAntiňolo, Guillermo  uhttp://clinbioinfosspa.es/content/novel-rp1-mutations-and-recurrent-bbs1-variant-explain-co-existence-two-distinct-retinal