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Background Familial Hypercholesterolemia (FH) is an autosomal-dominant disorder caused by mutations in one of three 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-C-raising alleles using a 12-SNP score. The aims of the study were to improve the selection of SNPs, and to replicate the results in additional samples. Methods Receiver-operating characteristic curves were used to determine the optimum number of LDL-C SNPs. For replication analysis, we genotyped patients with a clinical diagnosis of FH from six countries for six 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 an 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, while sequential removal of SNPs with smaller effects/lower frequency showed a weighted score of six SNPs performed as well as the 12-SNP score. Meta-analysis of the weighted 6-SNP score, based on polymorphisms in CELSR2, APOB, ABCG5/8, LDLR and APOE 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 quarters of the score distribution, indicated a >95% likelihood of a polygenic explanation of their increased LDL-C. Conclusion A 6-SNP LDL-C score consistently distinguishes FH/M- patients from healthy subjects. The hypercholesterolemia in 88% of mutation-negative patients is likely to have a polygenic basis.

Cascade testing using DNA-mutation information is now recommended in the UK for patients with familial hypercholesterolaemia (FH). We compared the detection rate and mutation spectrum in FH patients with a clinical diagnosis of definite (DFH) and possible (PFH) FH. Six hundred and thirty-five probands from six UK centres were tested for 18 low-density lipoprotein receptor gene (LDLR) mutations, APOB p.Arg3527Gln and PCSK9 p.Asp374Tyr using a commercial amplification refractory mutation system (ARMS) kit. Samples with no mutation detected were screened in all exons by single strand conformation polymorphism analysis (SSCP)/denaturing high performance liquid chromatography electrophoresis (dHPLC)/direct-sequencing, followed by multiplex ligation-dependent probe amplification (MLPA) to detect deletions and duplications in LDLR.The detection rate was significantly higher in the 190 DFH patients compared to the 394 PFH patients (56.3% and 28.4%, p > 0.00001). Fifty-one patients had inadequate information to determine PFH/DFH status, and in this group the detection rate was similar to the PFH group (25.5%, p = 0.63 vs PFH). Overall, 232 patients had detected mutations (107 different; 6.9% not previously reported). The ARMS kit detected 100 (44%) and the MLPA kit 11 (4.7%). Twenty-eight (12%) of the patients had the APOB p.Arg3527Gln and four (1.7%) had the PCSK9 p.Asp374Tyr mutation. Of the 296 relatives tested from 100 families, a mutation was identified in 56.1%. In 31 patients of Indian/Asian origin 10 mutations (two previously unreported) were identified. The utility of the ARMS kit was confirmed, but sequencing is still required in a comprehensive diagnostic service for FH. Even in subjects with a low clinical suspicion of FH, and in those of Indian origin, mutation testing has an acceptable detection rate.