Predominant genetic variants of familial hypercholesterolaemia (LDLR, APOB and PCSK9) in Malaysian primary care population using next- generation sequencing

Familial hypercholesterolaemia (FH) is an autosomal dominant disorder which impairs low-density lipoprotein cholesterol (LDL-C) clearance and leads to development of atherosclerosis. Pathogenic variants (PVs) in LDLR, APOB, and PCSK9 genes are predominantly associated with FH. For FH screening is usually based on the clinical rather than molecular diagnosis. In Malaysia, where first-line FH screening is usually conducted in primary care clinics, the screening of FH gene mutation is still under-reported. This study aimed to determine the PV’s frequency of FH-causing gene (LDLR, APOB, and PCSK9) variants among those clinically diagnosed as FH based on Dutch Lipid Clinic Network (DLCN), Simon Broome (SB) and Familial Hypercholesterolaemia Case Ascertainment Tool (FAMCAT) criteria. A total of 310 patients (mean ± SD age: 45.3 ± 9.4 years; men = 51.6%) were recruited, and blood samples were collected. DNA samples were extracted and subjected using targeted next-generation sequencing (iSeq 100, Illumina). PVs were determined based on the American College of Medical Genetics and Genomics Guidelines. DLCN provides a structured scoring system with internationally validated cut-offs, enabling reliable stratification of patients into definite, probable, or possible FH. Hence, DLCN was considered the most appropriate standard for evaluating genetic findings in this population. Based on DLCN, 97.4% were classified as Definite and Probable (Potential FH) and Possible FH. Fifty PVs were identified [LDLR = 64.0%, APOB = 36.0%, and no PCSK9]. Among 245 variants reported, 13.1% were LDLR PVs and 7.3% were APOB PVs. Overall, 27.7% of clinically diagnosed FH patients has ≥1 PV (Monogenic LDLR = 47.7%, compound homozygous in LDLR = 1.2%, compound homo and hetero in LDLR = 1.2%, compound heterozygous in LDLR = 4.7%, double heterozygous in LDLR = 4.7% monogenic APOB = 34.9%, and compound heterozygous in APOB = 5.8%). In total, only 27.7% of clinically diagnosed FH patients were positive for FH-causing gene PVs, with LDLR as the predominant gene. The low detection rate of PVs among clinically diagnosed FH patients can be due to polygenic hypercholesterolaemia or the presence of novel PVs in genes other than FH.