Exploration of multilocus effects in a highly polymorphic gene, the apolipoprotein (APOB) gene, in relation to plasma apoB levels

Clique-finding for heterogeneity and multidimensionality in biomarker epidemiology research: the CHAMBER algorithm

BACKGROUND

Commonly-occurring disease etiology may involve complex combinations of genes and exposures resulting in etiologic heterogeneity. We present a computational algorithm that employs clique-finding for heterogeneity and multidimensionality in biomedical and epidemiological research (the "CHAMBER" algorithm).

METHODOLOGY/PRINCIPAL FINDINGS

This algorithm uses graph-building to (1) identify genetic variants that influence disease risk and (2) predict individuals at risk for disease based on inherited genotype. We use a set-covering algorithm to identify optimal cliques and a Boolean function that identifies etiologically heterogeneous groups of individuals. We evaluated this approach using simulated case-control genotype-disease associations involving two- and four-gene patterns. The CHAMBER algorithm correctly identified these simulated etiologies. We also used two population-based case-control studies of breast and endometrial cancer in African American and Caucasian women considering data on genotypes involved in steroid hormone metabolism. We identified novel patterns in both cancer sites that involved genes that sulfate or glucuronidate estrogens or catecholestrogens. These associations were consistent with the hypothesized biological functions of these genes. We also identified cliques representing the joint effect of multiple candidate genes in all groups, suggesting the existence of biologically plausible combinations of hormone metabolism genes in both breast and endometrial cancer in both races.

CONCLUSIONS

The CHAMBER algorithm may have utility in exploring the multifactorial etiology and etiologic heterogeneity in complex disease.

Association of polymorphisms at restriction enzyme recognition sites of apolipoprotein B and E gene with dyslipidemia in children undergoing primary nephrotic syndrome

BACKGROUND

Dyslipidemia, a common complication, is very prevalent in children with primary nephrotic syndrome (PNS). Recent studies have shown that genetic basis may be involved in the onset of HLP secondary to PNS. ApoB and E have been identified as the important candidate genes for lipid abnormalities.

OBJECTIVE

To investigate the association of apolipoprotein B (apoB) and E (apoE) genetic polymorphisms (Xba I, EcoR I, Msp I, and Hha I) with parameters describing the serum lipid profiles in children undergoing PNS.

METHODS

Genomic DNA was extracted from 250 children diagnosed with PNS and 200 healthy controls with neither allergic nor renal disease. ApoB (Xba I, EcoR I, and Msp I) and apoE (Hha I) genotypes were determined by PCR-restriction fragment length polymorphism (RFLP) analysis. The fasting serum lipoprotein (a) [Lp(a)], total cholesterol (TC), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), apolipoprotein A1 (apoA1), apoB, and total protein from a 24-h urine sample were measured.

RESULTS

No significant differences in genotypes and alleles frequencies were observed for the apoB Xba I, EcoR I, Msp I and the apoE Hha I restriction sites in PNS patients as compared to controls (P > 0.05). Patients and controls with X + allele exhibited significantly higher serum levels of Lp(a), TC, nonHDL-C, LDL-C, LDL-C/HDL-C ratio, and apoB than that with X- allele (P < 0.05), whereas for apoA1/B ratio the opposite was found (P < 0.01). E-/E- carriers had significantly higher Lp(a), TC, HDL-C, and apoA1 concentrations than did E+/E- or E+/E+ carriers in control group (P < 0.05). Healthy children carrying the rare EcoR I allele had higher mean Lp(a), TC, and HDL-C levels than homozygotes for E+ (P < 0.05). Higher Lp(a) serum concentrations were observed in patients with E- allele (P < 0.05). No significant differences in lipid parameters were determined for the apoB Msp I and apoE Hha I the polymorphisms study (P > 0.05). When genetic variations were compared with urinary protein excretion, the Xba I X- allele was more frequent in patients with elevated proteinuria (P < 0.01).

CONCLUSION

Presence of Xba I X+ allele and/or EcoR I E- at the apoB gene may be risk factors for lipid abnormalities secondary to childhood PNS.

Polymorphisms in 33 inflammatory genes and risk of myocardial infarction--a system genetics approach

The hypothesis of a causal link between inflammation and atherosclerosis would be strengthened if variants of inflammatory genes were associated with disease. Polymorphisms of 33 genes encoding inflammatory molecules were tested for association with myocardial infarction (MI). Patients with MI and a parental history of MI (n = 312) and controls from the UK (n = 317) were genotyped for 162 polymorphisms. Thirteen polymorphisms were associated with MI (P values ranging from 0.003 to 0.041). For three genes, ITGB1, SELP, and TNFRSF1B haplotype frequencies differed between patients and controls (P values < 0.01). We further assessed the simultaneous contribution of all polymorphisms and relevant covariates to MI using a two-step strategy of data mining relying on Random Forest and DICE algorithms. In a replication study involving two independent samples from the UK (n = 649) and France (n = 706), one interaction between the ITGA4/R898Q polymorphism and current smoking status was replicated. This study illustrates a strategy for assessing the joint effect of a large number of polymorphisms on a phenotype that may provide information that single locus or single gene analysis may fail to uncover. Overall, there was weak evidence for an implication of inflammatory polymorphisms on susceptibility to MI.

Apolipoprotein B (APOB) Gene Polymorphism in Patients with Gallbladder Disease

Cholelithiasis is one of the most prevalent gastroenterological diseases, precipitated mainly by environmental factors. However, twin studies provided strong evidence for a role of genetic factors in the disease pathogenesis. An association between plasma lipoprotein levels and gallstone disease (GSD) was presented. Apolipoprotein B is an essential structural component of triglyceride-rich lipoprotein particles and plays an important role in the maintenance of cholesterol homeostasis in mammals. Various studies have shown a relationship between APOB gene polymorphisms and lipoprotein levels, but only few investigated a potential association between APOB polymorphism and GSD, giving contrary results. In the current study, an association between common polymorphisms in APOB gene (T2488T and E4154K) and cholesterol gallstone disease was examined. Two hundred and forty patients of Caucasian origin suffering from cholelithiasis, as well as 217 healthy individuals, were included in the study. Patients were genotyped for two single nucleotide polymorphisms (SNPs) in APOB gene: 2488C>T (XbaI), and 4154G>A (EcoRI) using PCR-RLFP method. The resulting analysis has shown that polymorphic loci in positions 2488 and 4154 in APOB gene are in full linkage in a Polish population and form only three haplotypes: 2488C-4154G, 2488T-4154G and 2488C-4154A. Frequency and distribution of 2488C>T alleles did not differ significantly between patients and controls. The 4154G allele has been found to be associated with GSD (p=0.001). A risk of gallstone formation was reduced in 4154AA homozygotes (OR=0.25, p=0.009) and heterozygous individuals (OR=0.63, p=0.03) as compared to 4154GG homozygotes. Additionally, 2488C-4154A haplotype was identified as a protective factor against GSD (p=0.04). Our results suggest that SNPs in APOB, potentially considered as one of lith genes as well as certain haplotypes, may be risk factors for GSD.

Correlations of chronic hepatitis C virus infection with Xba I polymorphism of apolipoprotein B gene and serum lipid metabolism

AIM: To investigate the Xba I locus polymorphisms of apolipoprotein B (Apo B) gene and their internal correlations with chronic hepatitis C virus infection and serum lipid metabolism.

METHODS: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to analyze the genotype of the Apo B gene in 77 patients and 62 controls, according to the design of case control study. Meanwhile, the blood samples were analyzed for hepatic function and serum lipid by automatic biochemistry analyzer.

RESULTS: The frequencies of X⁺X^- and X^-X^- of Xba I locus polymorphism were different between the patients and the controls and the frequency of X⁺ allele in the patients was lower than that in the controls (0.071 vs 0.121, P = 0.136), but no statistical significance was not found. The frequency of X⁺ allele in patients with HCV RNA≥80 000 copies/L was significantly lower than that with HCV RNA<80 000 copies/L (0.048 vs 0.179, P = 0.035). Furthermore, the levels of Apo B in the patients of X⁺X^- genotype were significantly higher than those in the patients of X^-X^- genotype (P = 0.019). The serum levels of low density lipoprotein (LDL) and Apo B were negatively correlated with serum HCV RNA levels in patients with chronic hepatitis C (r = -0.460, P = 0.016; r = -0.538, P = 0.005, respectively), and the correlation with serum alanine aminotransferase (ALT) levels was not found.

CONCLUSION: The Xba I locus polymorphism of Apo B gene is not correlated with susceptibility of Chinese people to HCV, but it may affect the HCV viral load in patients with chronic hepatitis C. The variation of X⁺ allele may affect serum Apo B levels in patients with chronic HCV infection. The serum levels of LDL and Apo B are closely correlated with serum HCV RNA levels in patients with chronic hepatitis C.

Meta-analysis of four new genome scans for lipid parameters and analysis of positional candidates in positive linkage regions

Lipid levels in plasma strongly influence the risk for coronary heart disease. To localise and subsequently identify genes affecting lipid levels, we performed four genome-wide linkage scans followed by combined linkage/association analysis. Genome-scans were performed in 701 dizygotic twin pairs from four samples with data on plasma levels of HDL- and LDL-cholesterol and their major protein constituents, apolipoprotein AI (ApoAI) and Apolipoprotein B (ApoB). To maximise power, the genome scans were analysed simultaneously using a well-established meta-analysis method that was newly applied to linkage analysis. Overall LOD scores were estimated using the means of the sample-specific quantitative trait locus (QTL) effects inversely weighted by the standard errors obtained using an inverse regression method. Possible heterogeneity was accounted for with a random effects model. Suggestive linkage for HDL-C was observed on 8p23.1 and 12q21.2 and for ApoAI on 1q21.3. For LDL-C and ApoB, linkage regions frequently coincided (2p24.1, 2q32.1, 19p13.2 and 19q13.31). Six of the putative QTLs replicated previous findings. After fine mapping, three maximum LOD scores mapped within 1 cM of major candidate genes, namely APOB (LOD=2.1), LDLR (LOD=1.9) and APOE (LOD=1.7). APOB haplotypes explained 27% of the QTL effect observed for LDL-C on 2p24.1 and reduced the LOD-score by 0.82. Accounting for the effect of the LDLR and APOE haplotypes did not change the LOD score close to the LDLR gene but abolished the linkage signal at the APOE gene. In conclusion, application of a new meta-analysis approach maximised the power to detect QTLs for lipid levels and improved the precision of their location estimate.