Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.

Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families c...

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Autores principales:	Marta de Castro-Miró, Esther Pomares, Laura Lorés-Motta, Raul Tonda, Joaquín Dopazo, Gemma Marfany, Roser Gonzàlez-Duarte
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d0a48a4c4e1d4db78d8ccac696c64cc0
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spelling	oai:doaj.org-article:d0a48a4c4e1d4db78d8ccac696c64cc02021-11-18T08:33:16ZCombined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.1932-620310.1371/journal.pone.0088410https://doaj.org/article/d0a48a4c4e1d4db78d8ccac696c64cc02014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24516651/?tool=EBIhttps://doaj.org/toc/1932-6203Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3-up to now only associated to Leber Congenital Amaurosis- was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.Marta de Castro-MiróEsther PomaresLaura Lorés-MottaRaul TondaJoaquín DopazoGemma MarfanyRoser Gonzàlez-DuartePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88410 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marta de Castro-Miró Esther Pomares Laura Lorés-Motta Raul Tonda Joaquín Dopazo Gemma Marfany Roser Gonzàlez-Duarte Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
description	Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3-up to now only associated to Leber Congenital Amaurosis- was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.
format	article
author	Marta de Castro-Miró Esther Pomares Laura Lorés-Motta Raul Tonda Joaquín Dopazo Gemma Marfany Roser Gonzàlez-Duarte
author_facet	Marta de Castro-Miró Esther Pomares Laura Lorés-Motta Raul Tonda Joaquín Dopazo Gemma Marfany Roser Gonzàlez-Duarte
author_sort	Marta de Castro-Miró
title	Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
title_short	Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
title_full	Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
title_fullStr	Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
title_full_unstemmed	Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
title_sort	combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/d0a48a4c4e1d4db78d8ccac696c64cc0
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Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.

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