Refinement of variant selection for the LDL cholesterol genetic risk score in the diagnosis of the polygenic form of clinical familial hypercholesterolemia and replication in samples from 6 countries

Abstract

Background: Familial hypercholesterolemia (FH) is an autosomal-dominant disorder caused by mutations in 1 of 3 genes. In the 60% of patients who are mutation negative, we have recently shown that the clinical phenotype can be associated with an accumulation of common small-effect LDL cholesterol (LDL-C)-raising alleles by use of a 12-single nucleotide polymorphism (12-SNP) score. The aims of the study were to improve the selection of SNPs and replicate the results in additional samples.

Methods: We used ROC curves to determine the optimum number of LDL-C SNPs. For replication analysis, we genotyped patients with a clinical diagnosis of FH from 6 countries for 6 LDL-C-associated alleles. We compared the weighted SNP score among patients with no confirmed mutation (FH/M-), those with a mutation (FH/M+), and controls from a UK population sample (WHII).

Results: Increasing the number of SNPs to 33 did not improve the ability of the score to discriminate between FH/M- and controls, whereas sequential removal of SNPs with smaller effects/lower frequency showed that a weighted score of 6 SNPs performed as well as the 12-SNP score. Metaanalysis of the weighted 6-SNP score, on the basis of polymorphisms in CELSR2 (cadherin, EGF LAG 7-pass G-type receptor 2), APOB (apolipoprotein B), ABCG5/8 [ATP-binding cassette, sub-family G (WHITE), member 5/8], LDLR (low density lipoprotein receptor), and APOE (apolipoprotein E) loci, in the independent FH/M- cohorts showed a consistently higher score in comparison to the WHII population (P < 2.2 × 10(-16)). Modeling in individuals with a 6-SNP score in the top three-fourths of the score distribution indicated a >95% likelihood of a polygenic explanation of their increased LDL-C.

Conclusions: A 6-SNP LDL-C score consistently distinguishes FH/M- patients from healthy individuals. The hypercholesterolemia in 88% of mutation-negative patients is likely to have a polygenic basis.

Figure 1

A_ROC analysis of the discrimination between healthy individuals and FH M/- patients using 12-SNP vs. 6-SNP LDL-C score. There was no significant specificity/sensitivity difference between the scores.

Figure 2

Boxplot of the LDL-C weighted SNP score in WHII control cohort and patients groups. The patients who carried the APOB p.R3527Q mutation (n=13) had significantly lower SNP score than patients with LDLR and PCSK9 mutations (0.521 vs. 0.661, P = 0.05).

Figure 3

Meta-analysis of the LDL-C SNP score in nine independent FH mutation negative cohorts in comparison to the WHII population. Highlighted in red box are two cohorts studied in the original report (25). The overall SMD was 0.381.

Figure 4

Probability of having a polygenic cause of hypercholesterolemia based on predicted LDL-C (assuming population mean =135 mg/dL or 3.5mmol/L) assuming that the frequency of unknown mutation in the population is 0.0005.