title: Phenotype-driven gene target definition in clinical genome-wide sequencing data interpretation.
abstract: Genome-wide sequencing approaches are increasingly being used in place of disease gene panel sequencing approaches. Despite the well-recognized benefits of these approaches, they also carry with them an increased burden of analyzing overwhelmingly large gene targets and an increased possibility of detecting incidental findings.
  
  
  
  We propose a novel approach for design of individualized phenotype gene panels using the set of signs and symptoms observed and selecting relevant genes on the basis of known phenotype-gene associations.
  
  
  
  We used results of diagnostic exome sequencing in 405 cases submitted to our institution to show retrospectively that using the phenotype gene panel increases the sensitivity of masked exome analysis (increase from 25.4 to 29.7% in overall diagnostic yield). We also show that such a strategy enables the possibility of masked analysis of genome-wide sequencing data in patients with poorly defined and multifaceted clinical presentations. Ultimately, we show that this approach enables control over the incidental findings rate (0.25% in phenotype gene panels). Finally, we provide a Web tool for customized phenotype panel creation (available at http://www.kimg.eu/generator).
  
  
  
  In conclusion, we present a novel approach to a phenotype-driven diagnostic process of genome scale sequencing data that harnesses the sensitivity of these approaches while restricting the analysis to genes relevant to clinical presentation in patient.Genet Med 18 11, 1102-1110.
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Ales
authors.identifier: 0000-0002-9826-0534
authors.initials: A
authors.lastname: Maver
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Luca
authors.initials: L
authors.lastname: Lovrecic
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Marija
authors.identifier: 0000-0003-2807-6114
authors.initials: M
authors.lastname: Volk
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Gorazd
authors.initials: G
authors.lastname: Rudolf
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Karin
authors.initials: K
authors.lastname: Writzl
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Ana
authors.initials: A
authors.lastname: Blatnik
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Alenka
authors.identifier: 0000-0002-7874-6430
authors.initials: A
authors.lastname: Hodzic
authors.affiliation: Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
authors.forename: Peterlin
authors.initials: P
authors.lastname: Borut
mesh_terms: D059472:Exome / Q000235:genetics*; D005260:Female; D018390:Gene Targeting / Q000379:methods*; D056726:Genetic Association Studies; D014644:Genetic Variation / Q000235:genetics; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000639:trends; D006801:Humans; D033162:Incidental Findings; D008297:Male; D017422:Sequence Analysis, DNA