Background-Large gene rearrangements, not detectable by standard molecular genetic sequencing techniques, are present in a minority of patients with long QT syndrome. We aimed to screen for large rearrangements in genes responsible for long QT syndrome as part of the molecular autopsy of a 36-year-old woman who died suddenly and had a negative autopsy. A retrospective analysis of an ECG identified a long QT interval, but sequencing of known LQT genes was uninformative. Methods and Results-Array comparative genomic hybridization was used to screen for deletions and duplications in 101 genes implicated in cardiac disorders and sudden death using a postmortem blood sample. A 542 kb deletion encompassing the entire KCNJ2 gene was identified in the decedent. The mother had electrocardiographic U-wave changes consistent with Andersen-Tawil syndrome and exaggerated by exercise but none of the characteristic noncardiac features. Fluorescence in situ hybridization confirmed the deletion in the decedent and established its presence in the mother. Conclusions-A novel application of array comparative genomic hybridization and fluorescence in situ hybridization has identified that long QT syndrome and sudden cardiac death may occur as a result of a deletion of an entire gene. The case also supports recent research suggesting that noncardiac features of Andersen-Tawil syndrome occur only with missense or minor gene rearrangements in the KCNJ2 gene, resulting in a dominant negative effect on Kir2.x channels.
Methods
Deletion/Duplication Analysis-aCGHGenomic DNA was extracted from peripheral blood EDTA samples using the Gentra Puregene DNA Extraction kit (Qiagen), according to the manufacturer's instructions. The analysis of the proband and parents was undertaken as part of a coronial investigation and clinical follow-up, respectively, and proceeded according to informed consent and Health and Disability Ethics Committee approval (reference AKX 02/00/107). A Roche NimbleGen 12x135K Custom CGH Array was used for deletion/duplication analysis. This bespoke CGH array was designed to interrogate the coding regions of 101 genes associated with a range of cardiac and neuromuscular disorders, including those responsible for LQT1(KCNQ1), LQT2 (KCNH2), LQT3 and Brugada syndrome (SCN5A, SCN1B, SCN3B, GPD1L), LQT4 (ANK2), LQT5 (KCNE1), LQT6 (KCNE2), ATS/LQT7 (KCNJ2), Timothy syndrome/LQT8 (CACNA1c), LQT9 (CAV3), LQT10 (SCN4B), LQT11 (AKAP9), and LQT12 (SNTA1). See the Data Supplement for the full gene list. The probe densities in exons and introns, as well as extragenic regions of the human genome, have been described elsewhere. [8][9][10] Two hundred and fifty nanograms of genomic DNA were processed according to the manufacturer's instructions (NimbleGen Array User's Guide: CGH and CNV Arrays v6.0; http://www.nimblegen. com). In brief, extracted genomic DNA from samples and Promega controls were denatured in the presence of Cy3-(test) or Cy5-(control) labeled random primers and incubated with the Klenow fragment of DNA polymerase, toge...