title: The efficacy of microarray screening for autosomal recessive retinitis pigmentosa in routine clinical practice.
abstract: OBJECTIVE
  To determine the efficacy of multiple versions of a commercially available arrayed primer extension (APEX) microarray chip for autosomal recessive retinitis pigmentosa (arRP).
  
  
  METHODS
  We included 250 probands suspected of arRP who were genetically analyzed with the APEX microarray between January 2008 and November 2013. The mode of inheritance had to be autosomal recessive according to the pedigree (including isolated cases). If the microarray identified a heterozygous mutation, we performed Sanger sequencing of exons and exon-intron boundaries of that specific gene. The efficacy of this microarray chip with the additional Sanger sequencing approach was determined by the percentage of patients that received a molecular diagnosis. We also collected data from genetic tests other than the APEX analysis for arRP to provide a detailed description of the molecular diagnoses in our study cohort.
  
  
  RESULTS
  The APEX microarray chip for arRP identified the molecular diagnosis in 21 (8.5%) of the patients in our cohort. Additional Sanger sequencing yielded a second mutation in 17 patients (6.8%), thereby establishing the molecular diagnosis. In total, 38 patients (15.2%) received a molecular diagnosis after analysis using the microarray and additional Sanger sequencing approach. Further genetic analyses after a negative result of the arRP microarray (n = 107) resulted in a molecular diagnosis of arRP (n = 23), autosomal dominant RP (n = 5), X-linked RP (n = 2), and choroideremia (n = 1).
  
  
  CONCLUSIONS
  The efficacy of the commercially available APEX microarray chips for arRP appears to be low, most likely caused by the limitations of this technique and the genetic and allelic heterogeneity of RP. Diagnostic yields up to 40% have been reported for next-generation sequencing (NGS) techniques that, as expected, thereby outperform targeted APEX analysis.
authors.affiliation: Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Ramon A C
authors.initials: RA
authors.lastname: van Huet
authors.affiliation: The Rotterdam Eye Hospital, Rotterdam, The Netherlands ; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Laurence H M
authors.initials: LH
authors.lastname: Pierrache
authors.affiliation: The Rotterdam Eye Hospital, Rotterdam, The Netherlands ; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Magda A
authors.initials: MA
authors.lastname: Meester-Smoor
authors.affiliation: Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands ; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Caroline C W
authors.initials: CC
authors.lastname: Klaver
authors.affiliation: The Rotterdam Eye Hospital, Rotterdam, The Netherlands.
authors.forename: L Ingeborgh
authors.initials: LI
authors.lastname: van den Born
authors.affiliation: Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Carel B
authors.initials: CB
authors.lastname: Hoyng
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Ilse J
authors.initials: IJ
authors.lastname: de Wijs
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands ; Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
authors.forename: Rob W J
authors.initials: RW
authors.lastname: Collin
authors.affiliation: Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Lies H
authors.initials: LH
authors.lastname: Hoefsloot
authors.affiliation: Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: B Jeroen
authors.initials: BJ
authors.lastname: Klevering
mesh_terms: D015331:Cohort Studies; D004252:DNA Mutational Analysis / Q000379:methods; D005260:Female; D005808:Genes, Recessive; D005820:Genetic Testing / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012174:Retinitis Pigmentosa / Q000175:diagnosis / Q000235:genetics*; D012189:Retrospective Studies