Identification of New Genetic Determinants in Pediatric Patients with Familial Hypercholesterolemia Using a Custom NGS Panel

Abstract

The most common form of inherited lipid disorders is familial hypercholesterolemia (FH). It is characterized primarily by high concentrations of the clinical triad of low-density lipoprotein cholesterol, tendon xanthomas and premature CVD. The well-known genetic background are mutations in LDLR, APOB and PCSK9 gene. Causative mutations can be found in 60−80% of definite FH patients and 20−30% of those with possible FH. Their occurrence could be attributed to the activity of minor candidate genes, whose causal mechanism has not been fully discovered. The aim of the conducted study was to identify disease-causing mutations in FH-related and candidate genes in pediatric patients from Poland using next generation sequencing (NGS). An NGS custom panel was designed to cover 21 causative and candidate genes linked to primary dyslipidemia. Recruitment was performed using Simon Broome diagnostic criteria. Targeted next generation sequencing was performed on a MiniSeq sequencer (Illumina, San Diego, CA, USA) using a 2 × 150 bp paired-end read module. Sequencing data analysis revealed pathogenic and possibly pathogenic variants in 33 out of 57 studied children. The affected genes were LDLR, APOB, ABCG5 and LPL. A novel pathogenic 7bp frameshift deletion c.373_379delCAGTTCG in the exon 4 of the LDLR gene was found. Our findings are the first to identify the c.373_379delCAGTTCG mutation in the LDLR gene. Furthermore, the double heterozygous carrier of frameshift insertion c.2416dupG in the LDLR gene and missense variant c.10708C>T in the APOB gene was identified. The c.2416dupG variant was defined as pathogenic, as confirmed by its cosegregation with hypercholesterolemia in the proband’s family. Although the APOB c.10708C>T variant was previously detected in hypercholesterolemic patients, our data seem to demonstrate no clinical impact. Two missense variants in the LPL gene associated with elevated triglyceride plasma level (c.106G>A and c.953A>G) were also identified. The custom NGS panel proved to be an effective research tool for identifying new causative aberrations in a genetically heterogeneous disease as familial hypercholesterolemia (FH). Our findings expand the spectrum of variants associated with the FH loci and will be of value in genetic counseling among patients with the disease.

Keywords: LDLR gene; dyslipidemia; familial hypercholesterolemia; genetics; next generation sequencing; novel variant; pediatric patients.

Figure 1

Schematic presentation of eighteen exons and six corresponding functional domains in the LDLR gene with the positions of the variants indicated.

Figure 2

10 bp sequences bordering the deleted nucleotides (small letters). Underlining indicates the direct repeats.

Figure 3

Sanger sequencing chromatogram confirms a heterozygous c.373_379delCAGTTCG variant in the exon 4 of the LDLR gene.

Figure 4

The diagram presents the inheritance of variants c.2416dupG and c.10708C>T in the proband’s family. Phenotypically affected members are marked by black. Patients with slightly elevated total cholesterol level are flagged by a diagonal slash. Examined patients with no clinical symptoms are marked with a cross.

Figure 5

Sanger sequencing chromatograms showing heterozygous c.2416dupG variant in the exon 17 of the LDLR gene (upper chromatogram) and heterozygous c.10708C>T variant in the exon 26 of the APOB gene (lower chromatogram). The top lane picks refer to wild type sequence. The middle lane picks present described aberrations.

Figure 6

Schematic presentation of ten exons and corresponding two functional domains in the LPL gene with indicated variant positions.

Figure 7

Sanger sequencing chromatogram shows heterozygous c.106G>A variant in the exon 2 of the LPL gene.