title: Clinical exome sequencing for genetic identification of rare Mendelian disorders.
abstract: OBJECTIVE
  Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders.
  
  
  OBJECTIVE
  To report on initial clinical indications for CES referrals and molecular diagnostic rates for different indications and for different test types.
  
  
  METHODS
  Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available.
  
  
  METHODS
  Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES.
  
  
  RESULTS
  Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 [95% CI, 1.6-33.1]) of trio-CES was due to the identification of de novo and compound heterozygous variants.
  
  
  CONCLUSIONS
  In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Hane
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Deignan
authors.affiliation: Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Naghmeh
authors.initials: N
authors.lastname: Dorrani
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Strom
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Sibel
authors.initials: S
authors.lastname: Kantarci
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Fabiola
authors.initials: F
authors.lastname: Quintero-Rivera
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Kingshuk
authors.initials: K
authors.lastname: Das
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Traci
authors.initials: T
authors.lastname: Toy
authors.affiliation: Institute for Digital Research and Education, University of California, Los Angeles.
authors.forename: Bret
authors.initials: B
authors.lastname: Harry
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Michael
authors.initials: M
authors.lastname: Yourshaw
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Michelle
authors.initials: M
authors.lastname: Fox
authors.affiliation: Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Brent L
authors.initials: BL
authors.lastname: Fogel
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Julian A
authors.initials: JA
authors.lastname: Martinez-Agosto
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Derek A
authors.initials: DA
authors.lastname: Wong
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Vivian Y
authors.initials: VY
authors.lastname: Chang
authors.affiliation: Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Shieh
authors.affiliation: Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles7Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Christina G S
authors.initials: CG
authors.lastname: Palmer
authors.affiliation: Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles.
authors.forename: Katrina M
authors.initials: KM
authors.lastname: Dipple
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen.
authors.forename: Wayne W
authors.initials: WW
authors.lastname: Grody
authors.affiliation: Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine.
authors.forename: Eric
authors.initials: E
authors.lastname: Vilain
authors.affiliation: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Ge.
authors.forename: Stanley F
authors.initials: SF
authors.lastname: Nelson
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D002658:Developmental Disabilities / Q000235:genetics; D059472:Exome; D005260:Female; D030342:Genetic Diseases, Inborn / Q000175:diagnosis*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D025202:Molecular Diagnostic Techniques; D009154:Mutation; D035583:Rare Diseases / Q000175:diagnosis* / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods