title: The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease.
abstract: BACKGROUND
  Exome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD.
  
  
  RESULTS
  Exome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern. Variants were filtered using two bioinformatics pipelines and prioritised according to in silico prediction programs. Segregation studies and functional analyses were used to assess co-segregation with disease and effects on protein function, respectively. Following the data and in silico analyses, ten candidate variants were prioritised. Of these, SRPK2 (c.2044C>T[p.Arg682Trp]) and NOTCH1 (c.3835C>T[p.Arg1279Cys]), co-segregated with disease in the family; however, previous functional analyses on SRPK2 make this an unlikely candidate. Functional analyses in the variant (c.3835C>T[p.Arg1279Cys]) of the known CHD gene NOTCH1 demonstrated a non-significant decrease in signalling activity.
  
  
  CONCLUSIONS
  This study demonstrates both the potential, as well as the challenges, of applying exome sequencing to complex diseases such as CHD. While in silico evidence and segregation analyses in the NOTCH1 p.Arg1279Cys variant are highly suggestive of pathogenicity, the minimal change in signalling capacity suggests that other variants may be required for CHD development. This study highlights the difficulties of applying exome sequencing in familial, non-syndromic CHD in the clinical environment and a cautionary note in the interpretation of apparently causal abnormalities in silico without supportive functional data.
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, Australia.
authors.forename: Gillian M
authors.initials: GM
authors.lastname: Blue
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.
authors.forename: David
authors.initials: D
authors.lastname: Humphreys
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia.
authors.forename: Justin
authors.initials: J
authors.lastname: Szot
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia.
authors.forename: Joelene
authors.initials: J
authors.lastname: Major
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.
authors.forename: Gavin
authors.initials: G
authors.lastname: Chapman
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia.
authors.forename: Alexis
authors.initials: A
authors.lastname: Bosman
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: The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of 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, Faculty of Science, University of New South Wales, Sydney, Australia.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Harvey
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, Faculty of Science, University of New South Wales, Sydney, Australia.
authors.forename: Sally L
authors.initials: SL
authors.lastname: Dunwoodie
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, Australia. Electronic address: david.winlaw@health.nsw.gov.au.
authors.forename: David S
authors.initials: DS
authors.lastname: Winlaw
mesh_terms: D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis; D059472:Exome / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D006330:Heart Defects, Congenital / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D009154:Mutation; D010375:Pedigree; D017346:Protein Serine-Threonine Kinases / Q000235:genetics* / Q000378:metabolism; D051881:Receptor, Notch1 / Q000235:genetics* / Q000378:metabolism; D013599:Systole
chemical_list: C497761:NOTCH1 protein, human; D051881:Receptor, Notch1; D004247:DNA; D017346:Protein Serine-Threonine Kinases; C110522:SRPK2 protein, human
keywords: Atrial septal defect; Congenital heart disease; Exome sequencing; Functional genomics