Objective-There are several known monogenic causes of high and low high-density lipoprotein cholesterol (HDL-C) levels, but traditional sequencing studies have had limited success in identifying mutations in the majority of individuals with extreme HDL-C levels. The aim of this study was to assess the power of a targeted high-throughput sequencing strategy to elucidate the genetic basis of extreme HDL-C phenotypes. Approach and Results-We sequenced 195 genes with either established or implicated roles in lipid and lipoprotein metabolism plus 78 lipid-unrelated genes in patients with HDL-C <1st (n=40) or >99th (n=40) percentile values, and the results were compared with those of 498 individuals representative of the Dutch general population and 95 subjects with normal HDL-C (between 40th and 60th percentile values). The extreme HDL cohort carried more rare nonsynonymous variants in the lipid geneset than both the general population (odds ratio, 1.39; P=0.019) and normal HDL-C (odds ratio, 1.43; P=0.040) cohorts. The prevalence of such variants in the lipid-related and lipid-unrelated genesets was similar in the control groups, indicative of equal mutation rates. In the extreme HDL cohort, however, there was enrichment of rare nonsynonymous variants in the lipid versus the control geneset (odds ratio, 2.23; P<0.0001), and 70% of the lipidrelated variants altered conserved nucleotides. The lipid geneset comprised 4 nonsense, 10 splice-site, and 8 coding indel variants, whereas the control geneset contained only 1 such variant. In the lipid geneset, 87% and 28% of the patients carried ≥2 and ≥5 rare variants. Correspondence to Mohammad Mahdi Motazacker, PhD, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. E-mail m.m.motazacker@amc.uva.nl; or Jan A. Kuivenhoven, PhD, Molecular Genetics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands. E-mail j.a.kuivenhoven@umcg.nl
Conclusions-This
Evidence of a Polygenic Origin of Extreme High-DensityLipoprotein Cholesterol Levels 14,20 Since the start of large-scale GWAS in 2008 until to date, the number of candidate genes associated with plasma lipid phenotypes has steadily increased. These studies have underscored that most candidate genes affect multiple lipoprotein traits, and this is especially true for genes affecting HDL and triglyceride (TG) metabolism. 16 With this in mind, we set out to assess the burden of rare variants in 195 lipid-associated genes in individuals with HDL-C levels in the range observed in heterozygotes for Mendelian disorders of HDL metabolism.
Materials and MethodsMaterials and Methods are available in the online-only Supplement. We studied 40 individuals with very low and 40 with very high HDL-C levels (<1 st and >99 th percentile for age and gender) from general patient population in the center of the Netherlands. Written informed consent was obtained and the study protocol was approved by the IRB. Coding sequence and exon-intron boundaries of 195 lipid-re...