Computational protocol: The clinical features, outcomes and genetic characteristics of hypertrophic cardiomyopathy patients with severe right ventricular hypertrophy

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Protocol publication

[…] WGS was performed in the 11 HCM patients with SRVH whose blood samples were available. Genomic DNA was isolated from those blood samples. The concentrations and size distributions of the DNA libraries were determined using an Agilent Bioanalyzer DNA 1000 chip, and the DNA libraries were sequenced using Illumina HiSeq X (Illumina, San Diego, CA), according to the manufacturer’s instructions for paired-end 150-bp reads. Following a quality control evaluation of the raw data, we mapped valid sequencing data to the reference genome (UCSC hg19) to obtain the original mapping results. SAMtools was used for variant calling and the identification of single nucleotide polymorphisms and indels. Control-FREEC was utilized for copy number variation detection, and Crest was utilized for the detection of structure variant information in variant calling.ANNOVAR was utilized to annotate the variant call format obtained. The DbSNP, the 1000 Genome Project, the National Heart, Lung and Blood Institute (NHLBI) Exome Sequencing Project Database (ESP 6500), the International HapMap Project and the Pan Cardiomyopathy databases were utilized. In addition to the known pathogenic mutations that are present in these publicly available gene databases, possible pathogenic gene mutations should have been present within the cardiomyopathy/channelopathy-associated gene subset. Moreover, these possible pathogenic mutations must have been absent in a large panel of ethnically matched controls in these publicly available gene databases. Prediction of in silico pathogenicity for novel missense variants was performed using SIFT, Polyphen2, Mutation Taster, LRT and MetaLR prediction software. A variant was predicted to be pathogenic if classified as "damaging" by SIFT or either "possibly damaging" or "most likely damaging" by Polyphen2 [].Variants that were identified by WGS were validated using Sanger sequencing on an ABI3130XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) to avoid false-positive high-throughput sequencing results. […]

Pipeline specifications

Software tools SAMtools, Control-FREEC, ANNOVAR, PolyPhen
Databases dbSNP International HapMap Project
Application WGS analysis
Organisms Homo sapiens
Diseases Cardiomyopathy, Hypertrophic, Cardiovascular Diseases, Cardiomyopathies