How to used Bioinformatics Tools to Disease Variant Detection?

Whole exome sequencing (WES) is a powerful tool to identifying mutations in rare genetic disorders. Theaim of present study was to identifying the genetic variants in a family with three affected members bornfrom consanguineous marriages. The affected members had frequent attacks of apnea for ۲۰–۶۰ s withbradycardia and hypotonic; abnormal breathing patterns; fast or slow breathing (hyperpnoea), abnormalmovement in eyes, distinctive facial features, ataxia and intellectual disability episodic hyperpnoea,polydactyly, syndactyly and Brain MRI showed the molar tooth sign, atrial septal defect (ASD) andventricular septal defect (VSD).After WES with using NextSeq ۵۰۰ Illumina platform with ۱۰۰ million reads (۱۰۰ X) the sequence readswere mapped to the hg۳۸ genome version. GATK pipeline were used for variant calling and in the next stepwe used the wANNOVAR tool for variant annotation. There were about ۱۷۸,۰۰۰ variants in raw data ofproband and after this we used bioinformatics analysis for sequencing results by using standardbioinformatics software and international databases. We used filtration against benign variants such commonsingle nucleotide polymorphisms that were previously reported in some genetic related databases as nonpathogenicor those variants with frequency more than ۱%. Also we excluded variants that did not fit withthe expected pattern of family pedigree. Finally, novel variants that had a deleterious effect on proteins andtissue expression were considered. We checked selected genes variants in VarElect, Phenolyzer. After thiswe used prediction software’s such as PolyPhen ۲, SIFT, MutationTaster, FATHMM, PROVEAN andinternational databases including, OMIM, GeneCards and MalaCard. Finally, we found a new variant inC۵ORF۴۲ gene (c.۳۰۸۰A>T: p. D۱۰۲۷V) which is a related gene with Joubert syndrome. Confirmation testswere carried out by PCR and Sanger sequencing for identified variant in C۵ORF۴۲ gene in proband and herfamily members.

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Keywords: Bioinformatics ، Whole exome sequencing ، Joubert syndrome ، C۵ORF۴۲ gene