Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing
Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, ca...
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| Published in | PloS one Vol. 9; no. 8; p. e104281 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Public Library of Science
18.08.2014
Public Library of Science (PLoS) |
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| Abstract | Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies.
Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing.
Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D).
Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. |
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| AbstractList | Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. PURPOSERetinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. METHODSPatient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. RESULTSMolecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). CONCLUSIONSTagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics. |
| Audience | Academic |
| Author | Logan, Clare V Sheridan, Eamonn Ali, Manir Toomes, Carmel El-Asrag, Mohammed Charlton, Ruth Taylor, Graham Morgan, Joanne E Watson, Christopher M Inglehearn, Chris F Johnson, Colin A McKibbin, Martin Carr, Ian M Parry, David A |
| AuthorAffiliation | 3 Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom 2 Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom Radboud University Nijmegen Medical Centre, Netherlands 1 Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom 4 Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom |
| AuthorAffiliation_xml | – name: Radboud University Nijmegen Medical Centre, Netherlands – name: 1 Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom – name: 3 Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – name: 4 Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom – name: 2 Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom |
| Author_xml | – sequence: 1 givenname: Christopher M surname: Watson fullname: Watson, Christopher M organization: Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom – sequence: 2 givenname: Mohammed surname: El-Asrag fullname: El-Asrag, Mohammed organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 3 givenname: David A surname: Parry fullname: Parry, David A organization: Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 4 givenname: Joanne E surname: Morgan fullname: Morgan, Joanne E organization: Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 5 givenname: Clare V surname: Logan fullname: Logan, Clare V organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 6 givenname: Ian M surname: Carr fullname: Carr, Ian M organization: Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 7 givenname: Eamonn surname: Sheridan fullname: Sheridan, Eamonn organization: Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 8 givenname: Ruth surname: Charlton fullname: Charlton, Ruth organization: Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom – sequence: 9 givenname: Colin A surname: Johnson fullname: Johnson, Colin A organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 10 givenname: Graham surname: Taylor fullname: Taylor, Graham organization: Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom – sequence: 11 givenname: Carmel surname: Toomes fullname: Toomes, Carmel organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 12 givenname: Martin surname: McKibbin fullname: McKibbin, Martin organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom; Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom – sequence: 13 givenname: Chris F surname: Inglehearn fullname: Inglehearn, Chris F organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom – sequence: 14 givenname: Manir surname: Ali fullname: Ali, Manir organization: Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom |
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| CitedBy_id | crossref_primary_10_1038_s41598_020_75841_9 crossref_primary_10_1055_a_2009_0498 crossref_primary_10_1016_j_exer_2017_10_015 crossref_primary_10_1016_j_preteyeres_2015_06_005 crossref_primary_10_3389_fcell_2021_746781 crossref_primary_10_1002_ccr3_1947 crossref_primary_10_1167_iovs_62_6_19 crossref_primary_10_1016_j_preteyeres_2017_10_003 crossref_primary_10_1080_13816810_2020_1807026 crossref_primary_10_1080_13816810_2020_1807025 crossref_primary_10_1016_j_csbj_2020_05_025 crossref_primary_10_3390_genes14010191 crossref_primary_10_1038_s41433_022_02355_1 crossref_primary_10_1167_iovs_64_13_6 crossref_primary_10_1002_mgg3_2164 |
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| Copyright | COPYRIGHT 2014 Public Library of Science 2014 Watson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2014 Watson et al 2014 Watson et al |
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| DOI | 10.1371/journal.pone.0104281 |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: CMW DAP ES RC CAJ GT CT CFI MA. Performed the experiments: CMW ME-A DAP JEM CVL. Analyzed the data: CMW ME-A DAP IMC. Contributed reagents/materials/analysis tools: MM. Wrote the paper: CMW CFI MA. Competing Interests: The authors have declared that no competing interests exist. |
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| References | SJ Bowne (ref8) 2011; 52 MI Khan (ref20) 2010; 16 M Michaelides (ref23) 2010; 51 DA Lamba (ref5) 2009; 4 DS Mackay (ref28) 2011; 52 TA Willis (ref32) 2013; 97 AI den Hollander (ref17) 2006; 79 A Fedick (ref27) 2014; 85 ME Shanks (ref14) 2013; 21 SE Wilkie (ref25) 2000; 9 HP Singh (ref19) 2006; 141 L Abu-Safieh (ref26) 2013; 23 K Neveling (ref12) 2012; 33 MH Tan (ref6) 2009; 18 AJ Lotery (ref18) 2001; 119 J O'Sullivan (ref13) 2012; 49 F Coppieters (ref11) 2012; 14 TR Burke (ref31) 2012; 53 Z Yang (ref22) 2008; 118 W Cella (ref30) 2009; 89 DA Simpson (ref9) 2011; 48 MA DePristo (ref16) 2011; 43 M Harakalova (ref15) 2011; 6 I Audo (ref10) 2012; 7 DS Mackay (ref29) 2011; 17 W Sun (ref21) 2007; 47 JW Bainbridge (ref3) 2008; 358 Z Han (ref7) 2012; 122 C Bunce (ref1) 2010; 24 M Van Ghelue (ref24) 2000; 21 AM Maguire (ref4) 2008; 358 A Darr (ref2) 1988; 25 |
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| Snippet | Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing,... Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel... PURPOSERetinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel... Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel... |
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| SubjectTerms | Analysis Biology and Life Sciences Clinical trials Congenital diseases Deoxyribonucleic acid Disease DNA DNA Mutational Analysis - methods DNA sequencing Dystrophy Enrichment Female Gene mutation Gene sequencing Genes Genetic aspects Genetic Association Studies Genetic counseling Genetic counselling Genetic Predisposition to Disease Genetic screening Genetic testing Genetics Genomes Genomics Guanylate cyclase 1 High-Throughput Nucleotide Sequencing Hospitals Humans Implantation Male Medical genetics Medical research Medicine and Health Sciences Multiprocessing Mutation Neurosciences Nucleotide sequence Patients Pedigree Prognosis Retina Retinal degeneration Retinal Dystrophies - genetics Screening Tagging USH2A protein |
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| Title | Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing |
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