title: Clinical exome performance for reporting secondary genetic findings.
abstract: BACKGROUND
  Reporting clinically actionable incidental genetic findings in the course of clinical exome testing is recommended by the American College of Medical Genetics and Genomics (ACMG). However, the performance of clinical exome methods for reporting small subsets of genes has not been previously reported.
  
  
  METHODS
  In this study, 57 exome data sets performed as clinical (n = 12) or research (n = 45) tests were retrospectively analyzed. Exome sequencing data was examined for adequacy in the detection of potentially pathogenic variant locations in the 56 genes described in the ACMG incidental findings recommendation. All exons of the 56 genes were examined for adequacy of sequencing coverage. In addition, nucleotide positions annotated in HGMD (Human Gene Mutation Database) were examined.
  
  
  RESULTS
  The 56 ACMG genes have 18 336 nucleotide variants annotated in HGMD. None of the 57 exome data sets possessed a HGMD variant. The clinical exome test had inadequate coverage for >50% of HGMD variant locations in 7 genes. Six exons from 6 different genes had consistent failure across all 3 test methods; these exons had high GC content (76%-84%).
  
  
  CONCLUSIONS
  The use of clinical exome sequencing for the interpretation and reporting of subsets of genes requires recognition of the substantial possibility of inadequate depth and breadth of sequencing coverage at clinically relevant locations. Inadequate depth of coverage may contribute to false-negative clinical exome results.
authors.affiliation: Department of Pathology and Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX; jaspar@childrens.com.
authors.forename: Jason Y
authors.initials: JY
authors.lastname: Park
authors.affiliation: Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA;
authors.forename: Peter
authors.initials: P
authors.lastname: Clark
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA;
authors.forename: Eric
authors.initials: E
authors.lastname: Londin
authors.affiliation: Department of Internal Medicine and Medical Specialties, University of Rome "Sapienza," Rome, Italy;
authors.forename: Marialuisa
authors.initials: M
authors.lastname: Sponziello
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA;
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Kricka
authors.affiliation: Cancer Genomics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Molecular Medicine, University of Rome "Sapienza," Rome, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Fortina
mesh_terms: D004247:DNA / Q000235:genetics*; D030541:Databases, Genetic; D059472:Exome / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D033162:Incidental Findings; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA