Haplotype analysis of the CETP gene: not TaqIB,but the closely linked -629C-->A polymorphism and a novel promoter variant are independently associated with CETP concentration

The TaqIB polymorphism in intron 1 of the cholesteryl ester transfer protein (CETP) gene is associated with plasma CETP concentration, high-density lipoprotein cholesterol (HDL-C) and coronary artery disease (CAD). These associations are generally thought to arise from linkage disequilibrium between TaqIB and (an)other functional polymorphism(s). To identify putative functional sites, we investigated phenotypic associations of TaqIB and four tightly linked polymorphisms (novel -2708G-->A and +784CCC-->A, and previously identified -971G-->A and -629C-->A) in 709 males with CAD (REGRESS). In addition to genotype analyses, a novel method to estimate haplotype effects was used to examine the individual and joint effects of these DNA variants on CETP concentration and HDL-C. All polymorphisms were associated with CETP concentration and HDL-C, except for -971 with HDL-C. Stepwise regression and haplotype analyses indicated that only -629 was independently associated with HDL-C. Similar analyses additionally indicated that -2708 and -629 were independently associated with CETP concentration, whereby the most frequent alleles acted in a cumulative manner. Nonetheless, detailed haplotype analysis revealed that a 3-polymorphism haplotype model consisting of -2708, -629 and -971 explained the variation in CETP concentration best. The involvement of -971 could be due to interaction effects that were observed between -971 and both -629 (P<0.001) and -2708 (P=0.047). In conclusion, the TaqIB polymorphism is not instrumental in determining CETP or HDL-C levels, but is a marker for the -629 promoter variant. Our analyses, furthermore, indicate that the -2708 and -971 polymorphisms are likely to play a role in determining CETP concentration.     

Haplotype analyses of cholesteryl ester transfer protein gene promoter: a clue to an unsolved mystery of<Emphasis Type="Italic"> Taq</Emphasis>IB polymorphism

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesteryl esters from HDL to triglyceride-rich lipoproteins. TaqIB polymorphism (B2 allele) identified in intron 1 is associated with lower plasma CETP concentrations and higher HDL cholesterol levels and may play an antiatherogenic role in humans. However, its molecular mechanism remains unclear. To evaluate the association between the promoter polymorphisms and CETP/HDL cholesterol levels, ten novel and three previously reported polymorphisms located within 3.3 kb of the CETP gene promoter were investigated in a sample of 357 elderly Japanese men. All the promoter polymorphisms were in linkage disequilibrium with each other and with TaqIB. The -2505A allele, the "S" allele of the [gaaa](n) repeat ("S" denotes [gaaa](n)=329 bp and longer, "L" denotes >329 bp) and TaqIB2 allele were significantly associated with both lower plasma CETP concentrations and higher HDL cholesterol levels whereas -971G/A and -629A/C were significantly associated with CETP concentrations but not with HDL-C levels. The 12-polymorphism haplotypes consisting of -2804, -2505, [gaaa](n), -1930, -1674, -1129, -1046, -971, -875, -827, -629, and TaqIB were analyzed. These 12 polymorphisms generated eight main haplotypes, accounting for 86% of the observed haplotypes. The G/A/S/T/T/C/T/A/C/C/A/B2 haplotype was significantly associated with lower CETP concentrations (2.0+/-0.6 micro g/ml) and higher HDL cholesterol levels (55.1+/-12.7 mg/dl) than the other seven main haplotypes. The 5- and 3-polymorphism haplotype analyses consisting of -2505 and the [gaaa](n) repeat indicated the -2505C/A polymorphism might explain the variation in the CETP concentrations best, and the [gaaa](n) repeat and/or the -2505C/A polymorphism may independently determine the variation in HDL cholesterol levels, whereas the -629A/C and TaqIB polymorphisms were not instrumental in determining CETP concentrations as well as HDL cholesterol levels, although the latter has been frequently examined in many association studies.     

Beta‐globin gene cluster haplotypes in Afro‐Uruguayans from two geographical regions (South and North)

The β‐globin gene cluster haplotypes were identified in 52 and 40 chromosomes from two Afro‐Uruguayan populations located in the South and North of the country, respectively. In both regions, the 5′ haplotype 2 (+ ? ? ? ?), characteristic of non‐African populations, was the most frequent, reflecting a strong process of admixture in Afro‐Uruguayans (0.355 and 0.262, respectively). The haplotypes 3 (? ? ? ? +) and 4 (? + ? ? +), characteristics of African sub‐Saharan populations, present inverse frequencies in North and South: whereas in the South haplotype 3 is the second most frequent (0.232), and haplotype 4 presents a low frequency (0.019), in the North haplotype 4 is the third most frequent (0.140), and haplotype 3 only reaches an intermediate frequency (0.088). The pairwise F_ST and the exact test of differentiation show genetic heterogeneity between both regions. Nei's genetic distance show that South and North present affinities with Bantu groups, although the North present the smallest genetic distance with the Mandenka, a Senegalese population. With respect to 3′ haplotypes, haplotype I was the most frequent in both populations, followed by haplotype II, characteristic of sub‐Saharan Africans. The high frequencies of haplotype III‐Asian could indicate admixture with Native American populations. The differences observed between both Uruguayan regions could be explained by microevolutionary events as genetic drift, founder effects, differential admixture, and/or distinct origin of the African slaves introduced in those regions. Am. J. Hum. Biol. 2010. © 2009 Wiley‐Liss, Inc.     

Characterization of Variants in the Glucosylceramide Synthase Gene and their Association with Type 1 Gaucher Disease Severity

The extreme phenotypic variability of patients with Gaucher disease (GD) is not completely explained by glucocerebrosidase gene mutations. It has been proposed that genetic modifiers might influence GD phenotype. We examined seven polymorphisms of the glucosylceramide synthase gene (UGCG) and their correlation with severity of GD. Five UGCG variants were significantly associated with disease severity, according to the DS3 scoring system: c.‐295C>T, c.‐232_‐241ins10, c.98+50A>G, c.98+68A>T, and c.861A>G. Heterozygous [N370S]+[L444P] patients with c.[‐232_‐241ins10;98+50G] haplotype had a significantly lower DS3 score in relation to patients carrying only one of these polymorphisms. Electrophoretic mobility shift assay analysis showed an increased nuclear protein binding ability for the G allele at the cDNA position c.98+50, as well as an altered pattern for the c.‐232_‐241ins10 allele. The promoter activity of the haplotypes decreased significantly with respect to wild type activity in HepG2 and COS‐7 cells (?14% and ?16% for the c.[‐232_‐241ins10;98+50A] haplotype, ?44% and ?25% for c.[‐222nonins;98+50G] haplotypes, and ?64% and ?75% for c.[‐232_‐241ins10;98+50G] haplotype, respectively). These data indicate that the c.‐232_‐241ins10 and c.98+50A>G variants are modifying factors of GD severity, which can partly explain the variability in severity of the disease.     

Vascular endothelial growth factor gene polymorphisms are associated with the risk of developing adenomyosis

Vascular endothelial growth factor (VEGF), a major mediator of angiogenesis and vascular permeability, may play a key role in the development of adenomyosis. The aim of this study was to investigate whether these four VEGF polymorphisms (?2578C/A, ?1154G/A, ?460C/T, and +936C/T) were associated with the risk of adenomyosis development. Genotypes were determined by polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay in 174 adenomyosis patients and 199 frequency‐matched control women. There were significant differences between patients and control group in allele frequencies and genotype distributions of the ?2578C/A polymorphisms (P = 0.010 and 0.044, respectively). Compared with the C/C genotype, the A/A + C/A genotype could significantly modify the risk of developing adenomyosis [odds ratio (OR) = 0.64, 95% confidence interval (CI) = 0.42–0.97]. For the ?1154G/A polymorphism, the allele frequencies and genotype distributions in patient group were significant different from those of the controls (P = 0.001 and 0.007, respectively). Compared with the G/G genotype, the A/A + G/A genotype could significantly decrease the risk of developing adenomyosis (OR = 0.51, 95% CI = 0.33–0.80). However, the genotype distributions and allele frequencies of the ?460C/T and +936C/T polymorphisms did not significantly differ between controls and patients (all P value > 0.05). The haplotype analysis suggested that the TGA (VEGF ?460/?1154/?2578) and CGA haplotypes exhibited a significant decrease in the risk of developing adenomyosis compared with the haplotype of TGC (OR = 0.64, 95% CI = 0.41–1.00; OR = 0.44, 95% CI = 0.21–0.93, respectively). The study indicated that the ?2578A or ?1154A allele of VEGF gene could significantly decrease the risk of adenomyosis and might be potentially protective factors for adenomyosis development. Environ. Mol. Mutagen., 2009. © 2009 Wiley‐Liss, Inc.     

Beta‐globin gene cluster haplotypes as evidence of African gene flow to the northeastern coast of Venezuela

In order to study the origin of mutation HBB*S in Sucre and Anzoátegui states and the genetic affinities of these Venezuelan populations with other human groups, the β‐globin gene cluster haplotypes were determined for 28 sickle cell and/or S‐beta thalassemia patients and for 37 individuals with normal hematological parameters. Bantu, Benin, Senegal, and atypical haplotypes were identified in 50%, 36%, 2%, and 12% of the HBB*S chromosomes, respectively. Similar results have been published for Venezuelan patients from the central states, but a different trend is shown in a publication based on a group of patients from different regions of the country. For HBB*A, haplotype 2 (+ ? ? ? ?), characteristic of non‐African groups, was the most common (39%), followed by haplotype 3 (? ? ? ? +) of African origin, and haplotype 6 (? + + ? +), also typical of non‐Africans. The results reveal a high level of admixture of the Sucre–Anzoátegui population. The importance of specific conditions which have acted differently in the Venezuelan populations, such as founder effect, genetic drift, isolation, and endogamy are discussed. Genetic distances between the Sucre–Anzoátegui sample and several other human populations calculated on the basis of the HBB*S and HBB*A haplotypes revealed similar results, the closest genetic relationships being observed in relation to Bantu‐speaking groups. These results confirm the utility of the β‐globin haplotypes for population studies and contribute to knowledge of the Venezuelan gene pool. Am. J. Hum. Biol. 15:29–37, 2003. © 2002 Wiley‐Liss, Inc.     

Functional interaction between -629C/A, -971G/A and -1337C/T polymorphisms in the CETP gene is a major determinant of promoter activity and plasma CETP concentration in the REGRESS Study

Cholesteryl ester transfer protein (CETP) plays a key role in the determination of high-density lipoprotein (HDL) levels via its action on intravascular HDL metabolism. The TaqIB polymorphism of the CETP gene is associated with plasma CETP and high-density lipoprotein cholesterol (HDL-C) levels and with premature coronary artery disease. Such associations appear to result from linkage disequilibrium between TaqIB and other functional polymorphisms. To date, only one functional promoter variant, which may explain the effects of TaqIB, has been identified at position -629 in the CETP gene. Here we describe a C/T polymorphism located at position -1337 in the human CETP gene (C allele frequency: 0.684), which is significantly associated with plasma HDL-C and CETP levels (P=0.0001 and P<0.0001, respectively). Transient transfection of a reporter gene construct containing the CETP promoter from -1707/+28 in liver cells (HepG2) revealed that the -1337T allele was expressed to a significantly lower degree (-34%, P<0.0001) than the -1337C allele. In addition, we clearly demonstrated that the -971G/A polymorphism is functional and that its functionality is intimately linked to the presence of the -1337 site. In vitro evaluation of potential interaction between -1337C/T and other functional variants of the CETP gene (-971G/A and -629C/A) demonstrated that these three functional CETP promoter polymorphisms can interact together to determine the overall activity of the CETP gene and thus contribute significantly to variation in plasma CETP mass concentration.     

Genetics of C‐reactive protein and complement factor H have an epistatic effect on carotid artery compliance: The Cardiovascular Risk in Young Finns Study

Atherosclerosis is characterized by a prominent inflammatory component and C‐reactive protein (CRP) has been implicated to modulate the complement activity in atherosclerotic arteries via complement factor H (CFH) binding. In this study, we examined whether the gene‐gene interactions between CRP haplotypes and CFH Tyr402His functional polymorphism exerted an effect on early atherosclerosis. Single nucleotide polymorphisms (SNPs) in CFH (Tyr402His) and CRP (?717A > G, ?286C > T > A, +1059G > C, +1444C > T and +1846G > A) were genotyped in the participants of the Cardiovascular Risk in Young Finns Study (n = 1698, aged 24–39 years). The CRP SNPs were further constructed into haplotypes and their interactive effects with the CFH Tyr402His polymorphism on the early atherogenic vascular changes [i.e. carotid artery compliance (CAC) and intima‐media thickness (IMT)] were examined. After risk factor adjustment, a significant gene‐gene interaction (P = 0·007) on CAC was observed between CRP haplotype ATGTG and CFH Tyr402His polymorphism in males. Furthermore, logistic regression analysis verified the risk‐modifying interactive effect on CAC between these loci (OR 3·70, 95% CI 1·37–10·02, P = 0·010). No effects on CAC were observed in females and no effects on IMT were detected in either sex. We conclude that the combined presence of CRP haplotype ATGTG and CFH 402His allele may be disadvantageous to carotid artery elasticity in males.     

Interleukin 10 gene promoter polymorphisms (rs1800896, rs1800871 and rs1800872) and haplotypes are associated with the activity of systemic lupus erythematosus and IL10 levels in an Iranian population

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with unknown aetiology. According to the role of interleukin 10 (IL10) in SLE pathogenesis, the genetic alterations in its promoter region could be associated with elevated IL10 levels and exacerbated disease. Here, we investigated the association of genotype and haplotype frequencies of three IL10 gene promoter polymorphisms with susceptibility to SLE, IL10 plasma levels and disease activity of patients in an Iranian population. A total of 116 SLE patients and 131 healthy subjects were enrolled. The PCR‐RFLP technique was used to detect IL10 promoter genotypes at the positions of ?1082 (G/A), ?819 (C/T) and ?592 (C/A) in association with IL10 plasma levels and SLEDAI scores. The GG genotype of ?1082 polymorphism was associated with the increased risk of SLE [OR = 2.65, 95% CI (1.21–5.82), p‐value = 0.046]. The CC genotype in ?819 region was associated with SLE susceptibility [OR = 3.38, 95% CI (1.26–9.07), p‐value = 0.034] and C allele was introduced as risk allele [OR = 1.86, 95% CI (1.15–3.01), p‐value = 0.009] in this region. IL10 plasma levels were overexpressed in CC genotype carriers of ?592 SNP and decreased in AA genotype carriers of ?1082. IL10 was also increased in SLE patients with CGT (?592/?1082/?819) haplotype. The SLEDAI score was higher among CC genotype carriers at the position of ?592 and TT genotype carriers at the region of ?819. SLEDAI was also elevated among patients with CGC (?592/?1082/?819) and CAC (p = 0.011) haplotypes. The present study suggests that the IL10 –819(C/T), ?1082(G/A) and ?592(C/A) polymorphisms and the haplotypes are associated with SLE susceptibility, increased disease activity and elevated IL10 levels. While this is the first time to report such an association in an Iranian population, further studies are needed to confirm these findings.     

Association of cytochrome P450 1B1 haplotypes with head and neck cancer risk

Genetic polymorphisms have been reported in several cytochrome P450 (CYP) genes, including CYP1B1 which metabolically activates procarcinogens present in tobacco to carcinogenic intermediates. This study used a case–control approach in North Indian population to determine associations between genetic variants in CYP1B1 and risk of Head and Neck Squamous Cell Carcinoma (HNSCC). We examined the genotype and haplotype frequencies at various single‐nucleotide polymorphisms (SNPs), including SNPs previously reported in the promoter region and intron 1 of CYP1B1 in Caucasians. Using cycle sequencing, 9 SNPs were identified in the promoter region, intron 1, and exons 2 and 3. Haplotype analysis revealed that 5 SNPs (those in the promoter region, intron, and Arg48Gly and Ala119Ser in exon 2) were in strong linkage disequilibrium (LD). Cases with the T–A–T–G–T haplotype were significantly associated with increased risk of HNSCC. Interestingly, qRT‐PCR studies revealed a significant increase in mRNA expression of CYP1B1 in peripheral blood isolated from cases with the T–A–T–G–T haplotype compared with cases with the C–G–C–C–G haplotype, and in cases compared to controls for both main haplotypes. The data thus provide evidence that CYP1B1 haplotypes could be more effective in predicting HNSCC risk. Environ. Mol. Mutagen. 58:443–450, 2017. © 2017 Wiley Periodicals, Inc.     

Effect of TLR10 (2322A/G, 720A/C,and 992T/A) polymorphisms on the pathogenesis of Crimean Congo hemorrhagic fever disease

Crimean Congo hemorrhagic fever (CCHF) is a tick‐borne disease caused by the Crimean Congo hemorrhagic fever virus (CCHFV). Toll‐like receptors (TLRs) are type 1 transmembrane proteins of immune cells that play a critical role in innate and adaptive immunity. The present study first time aims to investigate the relation between TLR10 gene polymorphisms (720A/C, 992T/A, and 2322A/G), severity/non‐severity, fatality/non‐fatality, and CCFH disease by using PCR‐RFLP assay in a Turkish population. TLR10 720A/C polymorphism was determined to be statistically significant both genotype and allele frequency (P = 0,011, P = 0.015, respectively). TLR10 992T/A polymorphism was found statistically significant relationships between patient and control (P = 0.026) and individual with AA genotype have approximately three times greater risk than TT genotype (OR = 2.93). There was not a significant difference in 2322A/G genotype distribution (P = 0.152). There were also statistically significant associations between both TLR10 992T/A and 2322A/G polymorphism and patient mortality (P = 0.001 and P = 0.008, respectively). We have not found statistically any linkage among TLR10 haplotype, but individual AAA and GAT haplotype have higher risk than individual AAT haplotype (OR = 3.22, OR = 1.93, respectively). Consequently, this study shows that pathogenesis of CCHF disease is associated with the TLR10 720A/C and 992T/A polymorphisms. There is a statistically significant association in fatal/non‐fatal patients with TLR10 720A/C and 992T/A. The TLR10 992AA genotype might increase and TLR10 720CC genotype might decrease susceptibility to pathogenesis of CCHF disease. TLR 10 polymorphisms may be also an important biomarker for CCHF susceptibility and fatality rate.     

Haplotypes in the 5′‐untranslated region of the CYP1A2gene are inversely associated with lung cancer risk but do not correlate with caffeine metabolism

In this study, we analyzed the influence of CYP1A2 genetic variation and enzyme activity on lung cancer risk in a high‐incidence area. A total of 95 lung cancer patients and 196 controls were genotyped for the ?3860G/A, ?3113A/G, ?2467T/delT, ?739T/G, and ?163C/A polymorphisms in the 5′‐untranslated region of the gene. In addition, a subset of 70 patients and 115 controls were phenotyped by high‐performance liquid chromatography determination of the caffeine metabolic ratio (CMR). The ?2467T/delT polymorphism and the CYP1A2*1V haplotype (‐163C>A, ?2467T>delT) were inversely associated with lung cancer risk (odds ratio [OR] = 0.47 [0.2–0.9]; P = 0.02 and OR = 0.13 [0.02‐1.0]; P = 0.04; respectively). In addition, the CYP*1A/*1V and *1F (‐163C>A)/*1D (?163C>A, ?2467T>delT) diplotypes were absent in the patients group, whereas accounting for 7.1% (P = 0.017) and 5.6% (P = 0.037) of controls, respectively. Mean CMR was significantly higher in patients than in controls (10.50 ± 17.31 vs. 6.52 ± 6.26, P = 0.01) but regression analyses did not yield significant ORs for the association with lung cancer risk. Similarly, no significant correlations were found between any genetic variant and enzyme activity. Several CYP1A2 haplotypes and diplotypes containing the ?2467delT variant were associated with lower lung cancer risk; however, they did not correlate with significant changes in CYP1A2 metabolic activity toward caffeine. Environ. Mol. Mutagen., 2013. © 2012 Wiley Periodicals, Inc.     

Analysis of MDR1 haplotypes in Parkinson's disease in a white population

The MDR1 multidrug transporter is important in regulating environmental xenobiotics and hence may play a causative role in Parkinson's disease (PD). MDR1 haplotype comprising 2677 G > T/A and 3435 C > T may be protective against PD. Using a case control methodology, we investigated the association of MDR1 haplotypes (single nucleotide polymorphisms (SNPs) 2677 G > T/A and 3435 C > T) in a Polish PD population. Seven SNPs, extending from the promoter to exon 28 of the MDR1 gene in 158 PD patients and 139 healthy controls were evaluated. Specifically we examined the association of haplotypes containing SNPs 2677 G > T/A and 3435 C > T and risk of PD. The multivariate logistic regression model was used to evaluate the effects of the covariates on the phenotypes. Haplotypes' frequencies were estimated using the Expectation-Maximization algorithm. The frequency of each individual SNPs; -41 A > G (intron -1), -145 C > G (exon 1), -129 T > C (exon 1), 1236 T > C (exon 12), 2677 G > T/A (exon 21), 3435 C > T (exon 26), and 4036 A > G (exon 28) did not differ between PD and controls. However, there was a trend towards significance in PD patients having the haplotype 2677G-3435C (p < 0.09, chi-square 2.85, odds ratio 0.25, 95% CI 0.06-1.08). Haplotype constructs of the other loci did not differ significantly between the two groups. There was a weak protective effect of the haplotype 2677G-3435C in our white population. However, the MDR1 haplotypes did not generally modulate the risk of PD.     

A family‐based association analysis and meta‐analysis of the reading disabilities candidate gene DYX1C1

Reading disabilities (RD) have a significant genetic basis and have shown linkage to multiple regions including chromosome 15q. Dyslexia susceptibility 1 candidate gene 1 (DYX1C1) on chromosome 15q21 was originally proposed as a candidate gene with two potentially functional polymorphisms at the ?3G/A and 1249G/T positions showing association with RD. However, subsequent studies have yielded mixed results. We performed a literature review and meta‐analysis of the ?3G/A and 1249G/T polymorphisms, including new unpublished data from two family‐based samples. Ten markers in DYX1C1 were genotyped in the two independently ascertained samples. Single marker and ?3G/A:1249G/T haplotype analyses were performed for RD in both samples, and quantitative trait analyses using standardized reading‐related measures was performed in one of the samples. For the meta‐analysis, we used a random‐effects model to summarize studies that tested for association between ?3G/A or 1249G/T and RD. No significant association was found between the DYX1C1 SNPs and RD or any of the reading‐related measures tested after correction for the number of tests performed. The previously reported risk haplotype (?3A:1249T) was not biased in transmission. A total of 9 and 10 study samples were included in the meta‐analysis of the ?3G/A and 1249G/T polymorphisms, respectively. Neither polymorphism reached statistical significance, but the heterogeneity for the 1249G/T polymorphism was high. The results of this study do not provide evidence for association between the putatively functional SNPs ?3G/A and 1249G/T and RD. © 2013 Wiley Periodicals, Inc.     

Evaluation of HLA‐G5 Plasmatic Levels During Pregnancy and Relationship with the 14‐bp Polymorphism

Citation Gonzalez A, Alegre E, Torres MI, Díaz‐Lagares A, Lorite P, Palomeque T, Arroyo A. Evaluation of HLA‐G5 plasmatic levels during pregnancy and relationship with the 14‐bp polymorphism. Am J Reprod Immunol 2010 Problem Plasmatic HLA‐G levels increase during pregnancy, but the contribution of each different isoform has not been elucidated yet. Method of study HLA‐G5 was analyzed by ELISA in 19 controls, 79 women in the first 8 weeks of pregnancy and in nine women monthly until delivery. Genotyping for the 14‐bp polymorphism was performed by PCR amplification of exon 8. Results HLA‐G5 was detected in plasma from 80% of pregnant women. The levels did not change during pregnancy, and there were no differences compared to control non‐pregnant women. There was a high interindividual variation that was maintained throughout the pregnancy. The presence of +14‐bp allele was associated with HLA‐G5 positivity. Pregnant women who were heterozygotic to 14‐bp polymorphism had significantly higher levels of HLA‐G5 compared to ?14 bp/?14‐bp homozygotic. Conclusion Plasmatic HLA‐G5 levels do not change during pregnancy and its concentration depends on 14‐bp polymorphism.     

The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination

The catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide substitution (G1510A; Glu487Lys) in exon 12 of the ALDH2 locus. This SNP, and four non‐coding SNPs, including one in the promoter, span 40 kb of ALDH2; these and one downstream STRP have been tested in 37 worldwide populations. Only four major SNP‐defined haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the functional variant and is only found in East Asians. Though the SNPs showed virtually no historic recombination, LD values are quite variable because of varying haplotype frequencies, demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome, and is not a function solely of recombination. Among populations, different sets of tagging SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus, solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs globally applicable. The F_st values of the promoter region SNP and the functional SNP were about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers. These high F_st values may indicate selection has operated at these or very tightly linked sites.     

ApoE ϵ3‐haplotype modulates Alzheimer beta‐amyloid deposition in the brain

ApoE ?4 allele increases the risk of late‐onset Alzheimer disease (AD) as well as the amount of beta‐amyloid deposition in the brain. Because half of AD patients do not have ApoE ?4, it is important to search for other determinants of ApoE that modify AD risk. We tested whether the haplotype background of the most common ApoE allele, ?3, influences brain amyloid deposition or the risk of neuropathologically verified AD in a population‐based sample of elderly Finns. To exclude the effects of ApoE protein polymorphism we focused these analyses on subjects homozygous for ?3. Haplotypes were defined using polymorphisms at positions ? 491 and ? 219 of the ApoE promoter and at position +113 of intron‐1. We found that ?3‐haplotypes containing the promoter allele ? 219T were associated with reduced amyloid deposition and reduced risk of neuropathologically verified AD as compared to ?3‐haplotypes containing ? 219G. The functional polymorphism(s) responsible for the haplotypic difference remains to be identified. These results indicate that there is significant allelic variation in the ApoE gene region, which modulates brain amyloid deposition and AD risk, independent of the ApoE protein polymorphism. © 2002 Wiley‐Liss, Inc.     

Low numbers of CD8+ T lymphocytes in hereditary haemochromatosis are explained by a decrease of the most mature CD8+ effector memory T cells

Low CD8⁺ T lymphocyte numbers have long been described in hereditary haemochromatosis (HH). Recently, two conserved haplotypes localized near the microsatellite D6S105 at the major histocompatibility complex (MHC) class I region were described predicting the clinical expression of HH and the CD8⁺ T lymphocyte numbers. The A‐A‐T haplotype was associated with a severe clinical expression of HH and low CD8⁺ T lymphocyte numbers, while the G‐G‐G haplotype was associated with a milder clinical expression of HH and high CD8⁺ T lymphocyte numbers. As CD8⁺ T lymphocytes are a very heterogeneous population, in this study we analysed the CD8⁺ subpopulations of naive, central memory (T_CM) and effector memory (T_EM), and further subsets of CD8⁺ T_EM cells in 47 HH patients and 68 controls. In addition, association studies were conducted between the conserved haplotypes and the CD8⁺ T cell subpopulations in HH. Variations of the numbers of naive and central memory cells with age were similar between HH patients and controls. For T_EM cells and the T_EM CD27^‐CD28^‐ subset no effect of age was observed in HH [R² = 0·001, not significant (n.s.) and R² = 0·01, n.s., respectively] contrasting with the increasing of these subpopulations with age in controls (R² = 0·09, P = 0·017 and R² = 0·22, P = 0·0005, respectively). Interestingly, patients homozygous for the A‐A‐T haplotype have lower numbers of CD8⁺ T_EM cells due especially to lower numbers of T_EM CD27^‐CD28^‐ (0·206 ± 0·119 and 0·066 ± 0·067 × 10⁶ cells/ml, respectively) than patients carrying the G‐G‐G haplotype (0·358 ± 0·195 and 0·246 ± 0·202 × 10⁶ cells/ml, respectively). This may suggest an inability of HH patients to differentiate the CD8⁺ T cells into the most mature phenotype.     

VEGF PROMOTER HAPLOTYPE AND AMYOTROPHIC LATERAL SCLEROSIS (ALS)

Vascular endothelial growth factor (VEGF) is a cytokine essential for angiogenesis. A recent study found that haplotypes, determined by three SNPs ( ? 2,578C/A, ? 1,154 G/A, and ? 634G/C) in the VEGF upstream promoter/leader sequence, were associated with risk of amyotrophic lateral sclerosis (ALS). We used samples and data from a case-control study to examine the relation of ALS to VEGF haplotype. Genotypes at each of the three polymorphic sites were determined using allele-specific primer extension reactions followed by MALDI-TOF. We found a 3-fold increased risk among individuals homozygous for the AAG or AGG haplotypes (95% CI = 0.7 ? 13.4), consistent with the findings of the previous study. Given the wide confidence interval, our findings should be interpreted cautiously.     

Interleukin‐10 microsatellite variants and the risk of acute coronary syndrome among Tunisians

The objective of the study was to investigate the association of interleukin (IL)‐10 promoter microsatellite polymorphisms, linked with altered IL‐10 secretion, with the susceptibility to acute coronary syndrome (ACS) in adult Tunisian patients. We genotyped 291 ACS patients and 291 age‐, gender‐ and ethnically matched control subjects for the microsatellites IL‐10R [X78437.2g.5325CA(11_15)] and IL‐10G [X78437.2g.8134CA(14_29)] by PCR‐based assays. Haplotypes were reconstructed using maximum likelihood method. Regression analysis was used in determining the risk imparted by specific IL‐10 genotypes and haplotypes. A significant decrease in IL‐10G12 (24 CA repeats) (P < 0.001; OR = 0.465) and IL‐10G15 (27 CA repeats) (P = 0.043; OR = 0.232), and a significant increase in the low IL‐10 producer allele, IL‐10R3 (14 CA repeats) (P = 0.049; OR = 1.461), microsatellites were seen in the ACS group compared with controls. Of the possible 14 haplotypes constructed, there was an enrichment of the R2G9 (13CA vs. 21CA) haplotype in controls [P = 0.019; adjusted OR (95% CI) = 0.67 (0.48–0.94)] and R2G15 (13CA vs. 27CA) haplotype in cases [P = 0.042; adjusted OR (95% CI) = 5.29 (1.06–26.30)], thus assigning a protective and susceptible nature to these haplotypes respectively. The differential association of IL‐10 microsatellite alleles and haplotypes with ACS suggests that IL‐10 contributes to ACS pathogenesis. While the functional attributes of these microsatellite markers remain to be seen, it is likely that they have distinct functional properties (altered IL‐10 secretion), which in turn affect the susceptibility to ACS development.