Research

Genetic studies on the APOA1-C3-A5 gene cluster in Asian Indians with premature coronary artery disease

Jayashree Shanker¹ , Ganapathy Perumal¹ , Veena S Rao² , Natesha B Khadrinarasimhiah² , Shibu John³ , Sridhara Hebbagodi³ , Manjari Mukherjee^1,2 and Vijay V Kakkar^1,2,3,4

¹  Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, Bangalore, India

²  Tata Proteomics & Coagulation Unit, Thrombosis Research Institute, Bangalore, India

³  Elizabeth & Emmanuel Kaye Bioinformatics and Statistics Unit, Thrombosis Research Institute, Bangalore, India

⁴  Thrombosis Research Institute, London, UK

author email corresponding author email

Lipids in Health and Disease 2008, 7:33doi:10.1186/1476-511X-7-33

Published:	19 September 2008

Abstract

Background

The APOA1-C3-A5 gene cluster plays an important role in the regulation of lipids. Asian Indians have an increased tendency for abnormal lipid levels and high risk of Coronary Artery Disease (CAD). Therefore, the present study aimed to elucidate the relationship of four single nucleotide polymorphisms (SNPs) in the Apo11q cluster, namely the -75G>A, +83C>T SNPs in the APOA1 gene, the Sac1 SNP in the APOC3 gene and the S19W variant in the APOA5 gene to plasma lipids and CAD in 190 affected sibling pairs (ASPs) belonging to Asian Indian families with a strong CAD history.

Methods & results

Genotyping and lipid assays were carried out using standard protocols. Plasma lipids showed a strong heritability (h² 48% – 70%; P < 0.0001). A subset of 77 ASPs with positive sign of Logarithm of Odds (LOD) score showed significant linkage to CAD trait by multi-point analysis (LOD score 7.42, P < 0.001) and to Sac1 (LOD score 4.49) and -75G>A (LOD score 2.77) SNPs by single-point analysis (P < 0.001). There was significant proportion of mean allele sharing (pi) for the Sac1 (pi 0.59), -75G>A (pi 0.56) and +83C>T (pi 0.52) (P < 0.001) SNPs, respectively. QTL analysis showed suggestive evidence of linkage of the Sac1 SNP to Total Cholesterol (TC), High Density Lipoprotein-cholesterol (HDL-C) and Apolipoprotein B (ApoB) with LOD scores of 1.42, 1.72 and 1.19, respectively (P < 0.01). The Sac1 and -75G>A SNPs along with hypertension showed maximized correlations with TC, TG and Apo B by association analysis.

Conclusion

The APOC3-Sac1 SNP is an important genetic variant that is associated with CAD through its interaction with plasma lipids and other standard risk factors among Asian Indians.