Kapplinger Jamie D, Giudicessi John R, Ye Dan, Tester David J, Callis Thomas E, Valdivia Carmen R, Makielski Jonathan C, Wilde Arthur A, Ackerman Michael J
From the Departments of Medicine (Division of Cardiovascular Diseases), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, MN (J.D.K., J.R.G., D.Y., D.J.T., M.J.A.); Transgenomic Inc., New Haven, CT (T.E.C.); Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, Madison (C.R.V., J.C.M.); Department of Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands (A.A.W.); and Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, Jeddah, Kingdom of Saudi Arabia (A.A.W.).
Circ Cardiovasc Genet. 2015 Aug;8(4):582-95. doi: 10.1161/CIRCGENETICS.114.000831. Epub 2015 Apr 22.
A 2% to 5% background rate of rare SCN5A nonsynonymous single nucleotide variants (nsSNVs) among healthy individuals confounds clinical genetic testing. Therefore, the purpose of this study was to enhance interpretation of SCN5A nsSNVs for clinical genetic testing using estimated predictive values derived from protein-topology and 7 in silico tools.
Seven in silico tools were used to assign pathogenic/benign status to nsSNVs from 2888 long-QT syndrome cases, 2111 Brugada syndrome cases, and 8975 controls. Estimated predictive values were determined for each tool across the entire SCN5A-encoded Na(v)1.5 channel as well as for specific topographical regions. In addition, the in silico tools were assessed for their ability to correlate with cellular electrophysiology studies. In long-QT syndrome, transmembrane segments S3-S5+S6 and the DIII/DIV linker region were associated with high probability of pathogenicity. For Brugada syndrome, only the transmembrane spanning domains had a high probability of pathogenicity. Although individual tools distinguished case- and control-derived SCN5A nsSNVs, the composite use of multiple tools resulted in the greatest enhancement of interpretation. The use of the composite score allowed for enhanced interpretation for nsSNVs outside of the topological regions that intrinsically had a high probability of pathogenicity, as well as within the transmembrane spanning domains for Brugada syndrome nsSNVs.
We have used a large case/control study to identify regions of Na(v)1.5 associated with a high probability of pathogenicity. Although topology alone would leave the variants outside these identified regions in genetic purgatory, the synergistic use of multiple in silico tools may help promote or demote a variant's pathogenic status.
健康个体中罕见的SCN5A非同义单核苷酸变异（nsSNV）的背景发生率为2%至5%，这给临床基因检测带来了困扰。因此，本研究的目的是利用从蛋白质拓扑结构和7种计算机模拟工具得出的估计预测值，加强对SCN5A nsSNV的解读，以用于临床基因检测。
使用7种计算机模拟工具对来自2888例长QT综合征病例、2111例Brugada综合征病例和8975例对照的nsSNV进行致病性/良性状态分类。确定了每种工具在整个SCN5A编码的Na(v)1.5通道以及特定拓扑区域的估计预测值。此外，还评估了这些计算机模拟工具与细胞电生理学研究的相关性。在长QT综合征中，跨膜片段S3 - S5 + S6和DIII/DIV连接区与致病性的高概率相关。对于Brugada综合征，只有跨膜结构域具有高致病性概率。虽然单个工具能够区分病例和对照来源的SCN5A nsSNV，但多种工具的综合使用能最大程度地加强解读。综合评分的使用有助于对拓扑区域之外本质上具有高致病性概率的nsSNV进行增强解读，以及对Brugada综合征nsSNV的跨膜结构域内的情况进行增强解读。
我们通过一项大型病例/对照研究，确定了与高致病性概率相关的Na(v)1.5区域。尽管仅靠拓扑结构会使这些已确定区域之外的变异处于基因困境中，但多种计算机模拟工具的协同使用可能有助于提升或降低变异的致病状态。
