title: Targeted next-generation sequencing identifies pathogenic variants in familial congenital heart disease.
abstract: BACKGROUND
  Many genes have been implicated in the development of congenital heart disease (CHD). Next-generation sequencing offers opportunities for genetic testing but is often complicated by logistic and interpretative hurdles.
  
  
  OBJECTIVE
  This study sought to apply next-generation sequencing technology to CHD families with multiple affected members using a purpose-designed gene panel to assess diagnostic potential for future clinical applications.
  
  
  METHODS
  We designed a targeted next-generation sequencing gene panel for 57 genes previously implicated in CHD. Probands were screened in 16 families with strong CHD histories and in 15 control subjects. Variants affecting protein-coding regions were classified in silico using prediction programs and filtered according to predicted mode of inheritance, minor allele frequencies, and presence in databases such as dbSNP (Single Nucleotide Polymorphism Database) and ESP (Exome Sequencing Project). Disease segregation studies were conducted in variants identified in CHD cases predicted to be deleterious and with minor allele frequencies <0.1%.
  
  
  RESULTS
  Thirteen potential disease-causing variants were identified in 9 families. Of these, 5 variants segregated with disease phenotype, revealing a likely molecular diagnosis in 31% of this cohort. Significant increases in the number of "indels, nonsense, and splice" variants, as well as variants classified as "probably damaging" were identified in CHD cases but not in control subjects. Also, there was a significant increase in the total number of "rare" and "low" frequency variants (minor allele frequencies <0.05) in the CHD cases.
  
  
  CONCLUSIONS
  When multiple relatives are affected by CHD, a gene panel-based approach may identify its cause in up to 31% of families. Identifying causal variants has implications for clinical care and future family planning.
authors.affiliation: Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Sydney, Australia.
authors.forename: Gillian M
authors.initials: GM
authors.lastname: Blue
authors.affiliation: Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.
authors.forename: Edwin P
authors.initials: EP
authors.lastname: Kirk
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; University of New South Wales, Sydney, Australia.
authors.forename: Eleni
authors.initials: E
authors.lastname: Giannoulatou
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
authors.forename: Sally L
authors.initials: SL
authors.lastname: Dunwoodie
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; University of New South Wales, Sydney, Australia.
authors.forename: Joshua W K
authors.initials: JW
authors.lastname: Ho
authors.affiliation: Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia.
authors.forename: Desiree C K
authors.initials: DC
authors.lastname: Hilton
authors.affiliation: Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia.
authors.forename: Susan M
authors.initials: SM
authors.lastname: White
authors.affiliation: Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Sydney, Australia.
authors.forename: Gary F
authors.initials: GF
authors.lastname: Sholler
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Harvey
authors.affiliation: Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Sydney, Australia. Electronic address: david.winlaw@health.nsw.gov.au.
authors.forename: David S
authors.initials: DS
authors.lastname: Winlaw
mesh_terms: D016022:Case-Control Studies; D059472:Exome; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D006330:Heart Defects, Congenital / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016014:Linear Models; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: congenital heart defects; gene panel; molecular diagnosis