title: Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing.
abstract: OBJECTIVE
  Next-generation sequencing-based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques with regard to test accuracy and reproducibility have not been fully defined.
  
  
  METHODS
  We developed a targeted enrichment and next-generation sequencing approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy, and glaucoma. In preparation for providing this genetic eye disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, and reproducibility, as well as the clinical sensitivity, of the test.
  
  
  RESULTS
  The GEDi test is highly reproducible and accurate, with sensitivity and specificity of 97.9 and 100%, respectively, for single-nucleotide variant detection. The sensitivity for variant detection was notably better than the 88.3% achieved by whole-exome sequencing using the same metrics, because of better coverage of targeted genes in the GEDi test as compared with a commercially available exome capture set. Prospective testing of 192 patients with inherited retinal degenerations indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%.
  
  
  CONCLUSIONS
  Based on quantified performance metrics, the data suggest that selective targeted enrichment is preferable to whole-exome sequencing for genetic diagnostic testing.
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Consugar
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Daniel
authors.initials: D
authors.lastname: Navarro-Gomez
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Place
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Kinga M
authors.initials: KM
authors.lastname: Bujakowska
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Sousa
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Zoë D
authors.initials: ZD
authors.lastname: Fonseca-Kelly
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Taub
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Maria
authors.initials: M
authors.lastname: Janessian
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Dan Yi
authors.initials: DY
authors.lastname: Wang
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Elizabeth D
authors.initials: ED
authors.lastname: Au
authors.affiliation: Neurogenetics DNA Diagnostic Lab, Neurology Department, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114.
authors.forename: Katherine B
authors.initials: KB
authors.lastname: Sims
authors.affiliation: Massachusetts General Hospital Department of Pediatrics, Divisions of Medical Genetics and Hematology/Oncology, Boston, MA 02114.
authors.forename: David A
authors.initials: DA
authors.lastname: Sweetser
authors.affiliation: Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115.
authors.forename: Anne B
authors.initials: AB
authors.lastname: Fulton
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Qin
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Janey L
authors.initials: JL
authors.lastname: Wiggs
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Gai
authors.affiliation: Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA, 02114.|Berman-Gund Laboratory, Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, MA, 02114.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Pierce
mesh_terms: D059472:Exome / Q000235:genetics; D005128:Eye Diseases / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D005820:Genetic Testing; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity