Computational protocol: Whole exome sequencing identifies novel mutation in eight Chinese children with isolated tetralogy of Fallot

Similar protocols

Protocol publication

[…] WES and subsequent variant annotation were performed on genomic DNA derived from the eight TOF children and their parents. Paired-end libraries were prepared according to the manufacturer’s protocols (Agilent). Exome libraries for the eight families were constructed using Agilent SureSelectXT Target Enrichment System according to Illumina Paired End Sequencing Protocol (Agilent Technologies, CA, USA). Capturing of whole exon was carried out according to the protocol of Agilent’s Sure Select Human All 1 UTRs 71 MB v4 kit. The flow cells were sequenced as paired-end 150 base pair reads on an Illumina HiSeq ×10 platform to a minimum depth of 50× targeted region coverage using TruSeq SBS sequencing kit version 3 and HiSeq data collection version software (Illumina, Inc., San Diego, CA, USA).The raw sequence reads we obtained were aligned to the human genome reference sequence (hg19) using Burrows–Wheeler Aligner (BWA) with standard parameters []. The BWA-aligned reads were statistically calculated using PICARD software to exclude polymerase chain reaction duplicates. Regional realignment and quality score recalibration were carried out using Genome Analysis Toolkit [] with recommended parameters, which included local realignment of the sequences around InDels, base quality score recalibration, variant calling and variant quality score recalibration. […]

Pipeline specifications

Software tools BWA, Picard, GATK
Application WES analysis
Organisms Homo sapiens
Diseases Heart Diseases, Tetralogy of Fallot