Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease
To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician. Retrospective series. One thousand consecutive families seen by a single clinician. The clinical records of all pati...
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| Published in | Ophthalmology (Rochester, Minn.) Vol. 124; no. 9; pp. 1314 - 1331 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.09.2017
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0161-6420 1549-4713 1549-4713 |
| DOI | 10.1016/j.ophtha.2017.04.008 |
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| Abstract | To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician.
Retrospective series.
One thousand consecutive families seen by a single clinician.
The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000.
Sensitivity and false genotype rate.
Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001).
Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost. |
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| AbstractList | Purpose To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician. Design Retrospective series. Participants One thousand consecutive families seen by a single clinician. Methods The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000. Main Outcome Measures Sensitivity and false genotype rate. Results Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001). Conclusions Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost. To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician. Retrospective series. One thousand consecutive families seen by a single clinician. The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000. Sensitivity and false genotype rate. Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001). Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost. To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician.PURPOSETo devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician.Retrospective series.DESIGNRetrospective series.One thousand consecutive families seen by a single clinician.PARTICIPANTSOne thousand consecutive families seen by a single clinician.The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000.METHODSThe clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000.Sensitivity and false genotype rate.MAIN OUTCOME MEASURESSensitivity and false genotype rate.Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001).RESULTSDisease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001).Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost.CONCLUSIONSGenetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost. |
| Author | Tucker, Budd A. Streb, Luan M. Stone, Edwin M. Giacalone, Joseph C. Braun, Terry A. Scheetz, Todd E. Sheffield, Val C. Whitmore, S. Scott DeLuca, Adam P. Andorf, Jeaneen L. Mullins, Robert F. |
| AuthorAffiliation | 1 Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 3 Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, IA 2 Pediatrics, the University of Iowa Carver College of Medicine, Iowa City, IA |
| AuthorAffiliation_xml | – name: 1 Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA – name: 2 Pediatrics, the University of Iowa Carver College of Medicine, Iowa City, IA – name: 3 Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, IA |
| Author_xml | – sequence: 1 givenname: Edwin M. surname: Stone fullname: Stone, Edwin M. email: edwin-stone@uiowa.edu organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 2 givenname: Jeaneen L. surname: Andorf fullname: Andorf, Jeaneen L. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 3 givenname: S. Scott orcidid: 0000-0003-0161-9625 surname: Whitmore fullname: Whitmore, S. Scott organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 4 givenname: Adam P. orcidid: 0000-0001-7798-1538 surname: DeLuca fullname: DeLuca, Adam P. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 5 givenname: Joseph C. surname: Giacalone fullname: Giacalone, Joseph C. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 6 givenname: Luan M. surname: Streb fullname: Streb, Luan M. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 7 givenname: Terry A. surname: Braun fullname: Braun, Terry A. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 8 givenname: Robert F. surname: Mullins fullname: Mullins, Robert F. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 9 givenname: Todd E. surname: Scheetz fullname: Scheetz, Todd E. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 10 givenname: Val C. surname: Sheffield fullname: Sheffield, Val C. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa – sequence: 11 givenname: Budd A. surname: Tucker fullname: Tucker, Budd A. organization: Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28559085$$D View this record in MEDLINE/PubMed |
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| Snippet | To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families... Purpose To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive... |
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| SubjectTerms | Adolescent Adult Aged Aged, 80 and over Child Child, Preschool DNA Mutational Analysis Exome - genetics Eye Diseases, Hereditary - genetics Eye Proteins - genetics Family Health Female Genetic Testing Genotype High-Throughput Nucleotide Sequencing Humans Infant Male Middle Aged Mutation Ophthalmology Pedigree Retinal Diseases - genetics Retrospective Studies Sensitivity and Specificity Sequence Analysis, DNA United States |
| Title | Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease |
| URI | https://www.clinicalkey.com/#!/content/1-s2.0-S0161642017304608 https://www.clinicalkey.es/playcontent/1-s2.0-S0161642017304608 https://dx.doi.org/10.1016/j.ophtha.2017.04.008 https://www.ncbi.nlm.nih.gov/pubmed/28559085 https://www.proquest.com/docview/1904230942 https://pubmed.ncbi.nlm.nih.gov/PMC5565704 |
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