Genome wide association study on coronary heart disease in patients with familial hypercholesterolemia

Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), a disorder characterized by coronary heart disease (CHD) at young age. We aimed to apply an extreme sampling method to enhance the statistical power to identify novel genetic risk variants for CHD in individuals with FH. We selected cases and controls with an extreme contrast in CHD risk from 17 000 FH patients from the Netherlands, whose functional LDLR mutation was unequivocally established. The genome-wide association (GWA) study was performed on 249 very young FH cases with CHD and 217 old FH controls without CHD (above 65 years for males and 70 years of age for females) using the Illumina HumanHap 550K chip. In the next stage, two independent samples (one from the Netherlands and one from Italy, Norway, Spain, and the United Kingdom) of FH patients were used as replication samples. In the initial GWA analysis we identified 29 independent single nucleotide polymorphisms (SNPs) with suggestive associations with premature CHD (p<1×10-4). We examined the association of these SNPs with CHD risk in the replication samples. After Bonferroni correction, none of the SNPs either replicated or reached genome-wide significance after combining the discovery and replication samples. Therefore, we conclude that the genetics of CHD risk in FH is complex and even applying an ‘extreme genetics’ approach we did not identify new genetic risk variants. Most likely, this method is not as effective in leveraging effect size as anticipated, and may therefore not lead to significant gains in statistical power. (NB submitten and conditionally accepted at European Journal of Human Genetics-please use abstract only for internal review until submission complete)

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00010000578	Gencode case samples using 550K		249
EGAD00010000580	Gencode control samples using 550K		217

Publications	Citations
Identifying genetic risk variants for coronary heart disease in familial hypercholesterolemia: an extreme genetics approach. Versmissen J, Oosterveer DM, Yazdanpanah M, Dehghan A, Hólm H, Erdman J, Aulchenko YS, Thorleifsson G, Schunkert H, Huijgen R, Vongpromek R, Uitterlinden AG, Defesche JC, van Duijn CM, Mulder M, Dadd T, Karlsson HD, Ordovas J, Kindt I, Jarman A, Hofman A, van Vark-van der Zee L, Blommesteijn-Touw AC, Kwekkeboom J, Liem AH, van der Ouderaa FJ, Calandra S, Bertolini S, Averna M, Langslet G, Ose L, Ros E, Almagro F, de Leeuw PW, Civeira F, Masana L, Pintó X, Simoons ML, Schinkel AF, Green MR, Zwinderman AH, Johnson KJ, Schaefer A, Neil A, Witteman JC, Humphries SE, Kastelein JJ, Sijbrands EJ. Eur J Hum Genet 23: 2015 381-387	9

Publications

Citations

Identifying genetic risk variants for coronary heart disease in familial hypercholesterolemia: an extreme genetics approach.
Versmissen J, Oosterveer DM, Yazdanpanah M, Dehghan A, Hólm H, Erdman J, Aulchenko YS, Thorleifsson G, Schunkert H, Huijgen R, Vongpromek R, Uitterlinden AG, Defesche JC, van Duijn CM, Mulder M, Dadd T, Karlsson HD, Ordovas J, Kindt I, Jarman A, Hofman A, van Vark-van der Zee L, Blommesteijn-Touw AC, Kwekkeboom J, Liem AH, van der Ouderaa FJ, Calandra S, Bertolini S, Averna M, Langslet G, Ose L, Ros E, Almagro F, de Leeuw PW, Civeira F, Masana L, Pintó X, Simoons ML, Schinkel AF, Green MR, Zwinderman AH, Johnson KJ, Schaefer A, Neil A, Witteman JC, Humphries SE, Kastelein JJ, Sijbrands EJ. Eur J Hum Genet 23: 2015 381-387