Identification of pathogenic variants in the Brazilian cohort with Familial hypercholesterolemia using exon-targeted gene sequencing

Familial hypercholesterolemia (FH) is a monogenic disease characterized by high plasma low-density lipoprotein cholesterol (LDL-c) levels and increased risk of premature atherosclerotic cardiovascular disease. Mutations in FH-related genes account for 40% of FH cases worldwide. In this study, we aimed to assess the pathogenic variants in FH-related genes in the Brazilian FH cohort FHBGEP using exon-targeted gene sequencing (ETGS) strategy. FH patients (n = 210) were enrolled at five clinical sites and peripheral blood samples were obtained for laboratory testing and genomic DNA extraction. ETGS was performed using MiSeq platform (Illumina). To identify deleterious variants in LDLR, APOB, PCSK9, and LDLRAP1, the long-reads were subjected to Burrows -Wheeler Aligner (BWA) for alignment and mapping, followed by variant calling using Genome Analysis Tool -kit (GATK) and ANNOVAR for variant annotation. The variants were further filtered using in-house custom scripts and classified according to the American College Medical Genetics and Genomics (ACMG) guidelines. A total of 174 variants were identified including 85 missense, 3 stop-gain, 9 splice-site, 6 InDel, and 71 in regu-latory regions (3 & PRIME;UTR and 5 & PRIME;UTR). Fifty-two patients (24.7%) had 30 known pathogenic or likely pathogenic variants in FH-related genes according to the American College Medical and Genetics and Genomics guidelines. Fifty-three known variants were classified as benign, or likely benign and 87 known variants have shown un-certain significance. Four novel variants were discovered and classified as such due to their absence in existing databases. In conclusion, ETGS and in silico prediction studies are useful tools for screening deleterious variants and identification of novel variants in FH-related genes, they also contribute to the molecular diagnosis in the FHBGEP cohort.

Automated summary

Familial hypercholesterolemia (FH) is a genetic disease characterized by high LDL-c levels and increased cardiovascular disease risk. This study aimed to identify pathogenic variants in FH-related genes in the Brazilian FH cohort using exon-targeted gene sequencing (ETGS). ETGS was performed on 210 FH patients and a total of 174 variants were identified. Fifty-two patients had known pathogenic or likely pathogenic variants according to ACMG guidelines, and four novel variants were discovered. ETGS and in silico prediction studies are valuable for variant screening and molecular diagnosis in FH-related genes.