title: Genetic complexity in hypertrophic cardiomyopathy revealed by high-throughput sequencing.
abstract: BACKGROUND
  Clinical interpretation of the large number of rare variants identified by high throughput sequencing (HTS) technologies is challenging. The aim of this study was to explore the clinical implications of a HTS strategy for patients with hypertrophic cardiomyopathy (HCM) using a targeted HTS methodology and workflow developed for patients with a range of inherited cardiovascular diseases. By comparing the sequencing results with published findings and with sequence data from a large-scale exome sequencing screen of UK individuals, we sought to quantify the strength of the evidence supporting causality for detected candidate variants.
  
  
  RESULTS
  223 unrelated patients with HCM (46±15 years at diagnosis, 74% males) were studied. In order to analyse coding, intronic and regulatory regions of 41 cardiovascular genes, we used solution-based sequence capture followed by massive parallel resequencing on Illumina GAIIx. Average read-depth in the 2.1 Mb target region was 120. Rare (frequency<0.5%) non-synonymous, loss-of-function and splice-site variants were defined as candidates. Excluding titin, we identified 152 distinct candidate variants in sarcomeric or associated genes (89 novel) in 143 patients (64%). Four sarcomeric genes (MYH7, MYBPC3, TNNI3, TNNT2) showed an excess of rare single non-synonymous single-nucleotide polymorphisms (nsSNPs) in cases compared to controls. The estimated probability that a nsSNP in these genes is pathogenic varied between 57% and near certainty depending on the location. We detected an additional 94 candidate variants (73 novel) in desmosomal, and ion-channel genes in 96 patients (43%).
  
  
  CONCLUSIONS
  This study provides the first large-scale quantitative analysis of the prevalence of sarcomere protein gene variants in patients with HCM using HTS technology. Inclusion of other genes implicated in inherited cardiac disease identifies a large number of non-synonymous rare variants of unknown clinical significance.
authors: The Heart Hospital, 16-18 Westmoreland Street, London W1G 8PH, UK. perry.elliott@ucl.ac.uk
authors: Luis R
authors: LR
authors: Lopes
authors: Anna
authors: A
authors: Zekavati
authors: Petros
authors: P
authors: Syrris
authors: Mike
authors: M
authors: Hubank
authors: Claudia
authors: C
authors: Giambartolomei
authors: Chrysoula
authors: C
authors: Dalageorgou
authors: Sharon
authors: S
authors: Jenkins
authors: William
authors: W
authors: McKenna
authors: Vincent
authors: V
authors: Plagnol
authors: Perry M
authors: PM
authors: Elliott
mesh_terms: D000328:Adult; D019943:Amino Acid Substitution / Q000235:genetics; D002312:Cardiomyopathy, Hypertrophic / Q000235:genetics* / Q000473:pathology; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D012518:Sarcomeres / Q000235:genetics* / Q000378:metabolism
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