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Pipeline publication

[…] or to be of low penetrance (see Table )., A previously described custom next generation sequencing (NGS) panel containing probes for human DNA was used in the DNA from Lody’s whole blood and heart and from Kitty’s blood to sequence the coding and splicing regions of 246 genes associated with cardiovascular disorders including arrhythmias, cardiomyopathies, congenital heart defects, aortopathy, connective tissue disorders, Noonan spectrum disorders, pulmonary arterial hypertension, metabolic disorders that afflict the heart and lipid disorders. Briefly, paired-end sequencing was performed using an Illumina MiSeq sequencer (Illumina, Inc., San Diego, CA), followed by read alignment using the BWA software, local realignment, base quality recalibration, and variant identification using the GATK software, and variant annotation using ANNOVAR. A 300× average depth of coverage was obtained among variants for the three samples., Variants found in Lody’s whole blood were divided into those found in the HGMD and those not found in the HGMD (non-HGMD). The HGMD variants were classified as being pathogenic/likely pathogenic, pathogenic/likely pathogenic in autosomal recessive disorders, modifier, VUS, or benign/likely benign based on our interpretation from the literature. In order to filter the non-HGMD variants (variants that did not have a previous association with human diseases) and find those with higher likelihood of having disease association, we selected variants that were in coding regions, excluded synonymous and non […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR
Organisms Pan paniscus, Homo sapiens
Diseases Cardiovascular Diseases, Death, Cardiovascular Abnormalities, Heart Defects, Congenital, Cardiomyopathies