Genetic analysis of Indian subjects with clinical features of possible type IIa hypercholesterolemia

Whole-Exomes Sequencing Delineates Gene Variants Profile in a Young Saudi Male with Familial Hypercholesterolemia: Case Report

Familial hypercholesterolemia is an autosomal dominant genetic disease characterized by earlier elevated Low-Density Lipoprotein (LDL) cholesterol levels and increased risk for premature Myocardial Infarction (MI). Albeit the diagnosis of some medical Familial Hypercholesterolemia (FH) cases are due to mutations in PCSK9, APOB, or LDLR, detection of mutation rate and profiles relies heavily on different gene pools and ethnicity. We ran exome sequencing on blood genomic DNA (gDNA) from a 26-year-old Saudi patient on Ion Proton Platform (Ion Torrent, Guilford, Connecticut, USA) as part of a pilot study preluding the establishment of the Saudi Human Genome project. The sequencing results were analysed using Ion suit Bioinformatics system. The patient was matched with a lady of lean body mass and Welsh descent, who suffered from hypercholesterolemia. The first analysis of known FH genes identified five mutations in APOB, 25 mutations of known genes linked to FH, six mutations in LPR2, one mutation in LDLR, and three mutations in PCSK9. Finally, using disease filter algorithms, we filtered out more than 2000 intronic synonymous variants with likely no biological functions. No major new locus was found in FH. However, via variant reduction and TVC protocols we detected 15 new variants, among which 14 genes are linked to hypercholesterolemia, type-I, and type-II diabetes. We also detected three mutations in PCSK9 and confirmed one by Sanger. Taken together, this report suggests that the genetic determinant of FH in this Saudi patient is likely to be heterogeneous, complicating the diagnostic and novel gene discovery process.

Gender specific effect of LIPC C-514T polymorphism on obesity and relationship with plasma lipid levels in Chinese children

Hepatic lipase (LIPC) is a key rate-limiting enzyme in lipoprotein catabolism pathways involved in the development of obesity. The C-514T polymorphism in the promoter region is associated with decreased LIPC activity. We performed a case-controlled study (850 obese children and 2119 controls) and evaluated the association between LIPC C-514T polymorphism, obesity and plasma lipid profile in Chinese children and adolescents. Additionally, we conducted a meta-analysis of all results from published studies as well as our own data. A significant association between the polymorphism and obesity is observed in boys (P = 0.042), but not in girls. And we observed a significant relationship of the polymorphism with total cholesterol (TC) and high density lipoprotein cholesterol (HDL-C) independent of obesity in boys. The T allele carriers have higher levels of low density lipoprotein cholesterol (LDL-C) in obese boys, and triglyceride (TG), TC and LDL-C in non-obese girls (all P < 0.05). In the meta-analysis, under dominant model the T allele increased body mass index (BMI) level in boys, while it decreased BMI in girls, and increased the levels of TC both in the overall and subgroups, TG and HDL-C in the overall and boys, and LDL-C in the overall (all P < 0.05). Our results suggest that the T allele might carry an increased risk of obesity in Chinese boys. The meta-analysis suggests that T allele acts as a risk allele for higher BMI levels in male childhood, while it is a protective allele in female childhood. And the polymorphism is associated with the levels of plasma lipids, which may be modulated by obesity and gender.

Association of CETP and LIPC Gene Polymorphisms with HDL and LDL Sub-fraction Levels in a Group of Indian Subjects: A Cross-Sectional Study

There is an increasing interest to understand the molecular basis of high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) subfractions and their association with coronary artery disease (CAD). The formation of these subfractions is greatly influenced by hepatic lipase (HL) and cholesteryl ester transfer protein (CETP) enzymes. To identify genetic markers influencing LDL and HDL subfractions and their role in CAD we performed a case-control genetic association study on 117 healthy controls and 119 angiographically verified CAD patients. Biochemical analysis was performed using standard assays. HDL-C and LDL-C subfractions were estimated using precipitation methods. Genotyping of C-514T (rs1800588) in the LIPC gene for HL and I405V (rs5882) in the CETP gene was done using PCR-based restriction enzyme analysis and sequencing. Both the polymorphisms were not associated with CAD. The C-514T was associated with increased HDL3-C levels in controls (P = 0.049). The I405V polymorphism was found to be associated with low levels of small dense, LDL (P = 0.038). A multiple regression analysis showed that the effects were dependent on gender and triglyceride levels. We conclude that these polymorphisms are not associated with CAD but are important determinants of HDL-C and small dense LDL particles in our population.

Association of Sp1 tandem repeat polymorphism of ALOX5 with coronary artery disease in Indian subjects

Lipoxygenases have been implicated in the pathogenesis of coronary artery disease (CAD) for its potent proinflammatory role. The Sp1 addition/deletion polymorphism in promoter region of the 5-lipoxygenase gene (ALOX5) has been associated with increased risk of carotid atherosclerosis and myocardial infarction. To determine the role of this polymorphism in our population we performed a case-control-genetic association study on 117 healthy controls and 119 angiographically verified CAD patients. Biochemical analysis was performed using standard automated assays. High-density lipoprotein cholesterol (HDL-C) and LDL-C subfraction levels were estimated using precipitation methods. Genotyping of polymorphism in the ALOX5 (Sp1 variants) was done using PCR-based heteroduplex analysis and automated sequencing. The Sp1 promoter repeat variants were found to be associated with CAD (p < 0.0001, OR = 4.47, 95% confidence interval = 2.58-7.74). Furthermore, the 5/5 genotype of the ALOX5 polymorphism in the healthy subjects was found to be associated with elevated HDL-C (p= 0.004), HDL(3) -C (p= 0.04), apo A1 (p= 0.011) and sdLDL (p= 0.001). We conclude that this polymorphism influences LDL and HDL subfraction levels and is a risk factor for CAD in our population. Clin Trans Sci 2012; Volume 5: 408-411.