Aleksandra Divac Rankov1*, Dušan Ušjak1, Martina Mia Mitić1, and Jelena Kusic Tisma1
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, Belgrade, Serbia
aleksandradivac [at] imgge.bg.ac.rs
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disease caused by mutations in transmembrane conductance regulator (CFTR) gene. The golden standard for the diagnosis of CF is sweat chloride testing (>60 mmol/L) together with the identification of two CF-causing variants of CFTR gene. Nevertheless, about 0.01% of patients with elevated sweat chloride and high clinical suspicion of CF do not carry any CF-causing variants.
Here we present analysis of whole exome sequencing (WES) results for two patients with elevated sweat chloride levels and clinical presentation of CF in whom no CF-causing mutations were detected after CFTR gene whole coding region sequencing, and large insertion/deletion testing.
Genomic DNA was extracted from whole blood, subjected to library preparation using DNA nanoball technology from BGI and sequenced on DNBSEQ-G400 (MGI). Produced fastq files were mapped to hg38 reference genome using BWA/SAM tools. VCF files were generated using GATK (BaseRecalibrator, HaplotypeCaller) and annotated with InterVar and AnnoVar tools. Filtering of detected variants for disease relevance was done using the following criteria: QC Filter, GnomAD Allele Frequency, Functional consequences and phenotype-genotype relationship.
In both patients, similar number of variants predicted to impair protein function were detected (27 and 25). In two genes (CACNA1H and MUC5B) missense type variants were found in both patients and loss of function variants were found in 7 and 11 genes, respectively. Functional assessment of selected variants is underway.
Bioinformatics analyses are a valuable tool enabling identification of underlining genetic bases of disease phenotype, important in the context of optimal patient management and targeted therapies.
Keywords: whole exome sequencing (WES), cystic fibrosis, variant assessment
Acknowledgement: This work was supported by IMGGE work program for 2023, Ministry of Education, Science and Technological Development of the Republic of Serbia, 451-03-47/2023-01/200042.
