Computational protocol: Identification of Novel Clinically Relevant Variants in 70 Southern Chinese patients with Thoracic Aortic Aneurysm and Dissection by Next-generation Sequencing

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Protocol publication

[…] Genetic testing was performed using NGS coupled with a DNA target-capture array on an IlluminaHiSeq. 2500 platform by BGI (Shenzhen, China) as previously reported. Briefly, eleven genes (ACTA2, Col3A1, Col5A2, FBN1, MSTN, MYH11, MYLK, SLC2A10, SMAD3, TGFBR1, and TGFBR2) (Table ) relevant to TAAD were selected for one capture array (NimbleGen, Roche, Madison, WI, USA), which was designed mainly to capture the CDS of 2,181 known pathogenic genes associated with 561 Mendelian diseases based on the GeneReviews (NCBI) and Genetics Home Reference. Genomic DNA from peripheral blood or abortion tissues were fragmented into lengths ranging from 200 bp to 250 bp. The primers, adapters and indexes were then ligated to the DNA fragments to construct libraries. The DNA fragments were pooled and hybridized to the capture array. After hybridization and enrichment, the DNA sample was sequenced on IlluminaHiSeq. 2500 Analyzers to generate paired-end reads (90 bps). Short reads mapping, alignment were performed using BWA software (Burrows Wheeler Aligner). SNPs and indels were detected using the SOAPsnp software and GATK IndelGenotyper (http://www.broadinstitute.org/gsa/wiki/index.php/, The Genome Analysis Toolkit) respectively. All reference sequences were based on the NCBI37/hg19 assembly of the human genome (a novel mutation of IDS gene in a Chinese patient with mucopolysaccharidosis II by NGS).Interpretation of all variants referred to the latest version of ACMG standards and guidelines for the interpretation of sequence variants (PMID:25741868). Normal population frequencies information was from dbSNP, HapMap databases, one thousand genome project database, 100 Chinese healthy adults, EXAC database, NHLBI GO Exome Sequencing Project (ESP). Other information was from HGMD database, published literatures, OMIM database, NCBI-books. In silico deleterious effect was evaluated using PolyPhen and SIFT programs. […]

Pipeline specifications

Software tools BWA, SOAPsnp, GATK, PolyPhen, SIFT
Databases dbSNP GeneReviews OMIM HGMD GHR
Application WES analysis
Organisms Homo sapiens
Diseases Aortic Aneurysm, Thoracic