title: A Report on Molecular Diagnostic Testing for Inherited Retinal Dystrophies by Targeted Genetic Analyses.
abstract: OBJECTIVE
  To test the utility of targeted sequencing as a method of clinical molecular testing in patients diagnosed with inherited retinal degeneration (IRD).
  
  
  METHODS
  After genetic counseling, peripheral blood was drawn from 188 probands and 36 carriers of IRD. Single gene testing was performed on each patient in a Clinical Laboratory Improvement Amendment (CLIA) certified laboratory. DNA was isolated, and all exons in the gene of interest were analyzed along with 20 base pairs of flanking intronic sequence. Genetic testing was most often performed on ABCA4, CTRP5, ELOV4, BEST1, CRB1, and PRPH2. Pathogenicity of novel sequence changes was predicted by PolyPhen2 and sorting intolerant from tolerant (SIFT).
  
  
  RESULTS
  Of the 225 genetic tests performed, 150 were for recessive IRD, and 75 were for dominant IRD. A positive molecular diagnosis was made in 70 (59%) of probands with recessive IRD and 19 (26%) probands with dominant IRD. Analysis confirmed 12 (34%) of individuals as carriers of familial mutations associated with IRD. Thirty-two novel variants were identified; among these, 17 sequence changes in four genes were predicted to be possibly or probably damaging including: ABCA4 (14), BEST1 (2), PRPH2 (1), and TIMP3 (1).
  
  
  CONCLUSIONS
  Targeted analysis of clinically suspected genes in 225 subjects resulted in a positive molecular diagnosis in 26% of patients with dominant IRD and 59% of patients with recessive IRD. Novel damaging mutations were identified in four genes. Single gene screening is not an ideal method for diagnostic testing given the phenotypic and genetic heterogeneity among IRD cases. High-throughput sequencing of all genes associated with retinal degeneration may be more efficient for molecular diagnosis.
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Hema L
authors.initials: HL
authors.lastname: Ramkumar
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Harini V
authors.initials: HV
authors.lastname: Gudiseva
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Kameron T
authors.initials: KT
authors.lastname: Kishaba
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: John J
authors.initials: JJ
authors.lastname: Suk
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Rohan
authors.initials: R
authors.lastname: Verma
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Keerti
authors.initials: K
authors.lastname: Tadimeti
authors.affiliation: 2 Department of Pathology, University of California , San Diego, La Jolla, California.
authors.forename: John A
authors.initials: JA
authors.lastname: Thorson
authors.affiliation: 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California.
authors.forename: Radha
authors.initials: R
authors.lastname: Ayyagari
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism; D000075002:Bestrophins; D018118:Chloride Channels / Q000235:genetics / Q000378:metabolism; D004252:DNA Mutational Analysis / Q000379:methods; D005091:Exons; D005136:Eye Proteins / Q000235:genetics / Q000378:metabolism; D005260:Female; D056726:Genetic Association Studies; D005817:Genetic Counseling; D005820:Genetic Testing / Q000379:methods; D006579:Heterozygote; D006801:Humans; D008297:Male; D025202:Molecular Diagnostic Techniques / Q000379:methods; D009154:Mutation; D064531:Peripherins / Q000235:genetics / Q000378:metabolism; D058499:Retinal Dystrophies / Q000175:diagnosis* / Q000235:genetics*; D012174:Retinitis Pigmentosa / Q000235:genetics; D019717:Tissue Inhibitor of Metalloproteinase-3 / Q000235:genetics / Q000378:metabolism
chemical_list: C056475:ABCA4 protein, human; D018528:ATP-Binding Cassette Transporters; C113133:BEST1 protein, human; D000075002:Bestrophins; D018118:Chloride Channels; D005136:Eye Proteins; C578997:PRPH2 protein, human; D064531:Peripherins; C088390:TIMP3 protein, human; D019717:Tissue Inhibitor of Metalloproteinase-3
keywords: DNA testing; inherited retinal degeneration; molecular diagnosis; retinal dystrophy; retinitis pigmentosa; targeted genetic testing