Susceptibility Haplotype Research Articles

Polymorphisms spanning the 0N exon and promoter of the estrogen receptor‐beta (ERβ) gene ESR2 are associated with venous ulceration

Venous ulcers are characterized by excessive inflammation and raised levels of proinflammatory cytokines. Estrogen has been shown to accelerate the rate of wound healing in elderly subjects by dampening the inflammatory response. The estrogen receptor (ER) proteins, ER-alpha (ERalpha) and ER-beta (ERbeta) mediate the actions of estrogen during wound repair through the activation or repression of target gene transcription. Recent evidence implicates the chromosomal region harboring the ERbeta gene with venous ulceration in a British Caucasian population, highlighting the need to conduct further genetic interrogation. To address this, we conducted a case-control study to investigate whether single nucleotide polymorphisms in the ERbeta gene are associated with venous ulceration in elderly (age >50 years) subjects. We recruited a case group (n = 124, 56 males and 68 females) consisting of patients with an active venous ulcer and a control group consisting of individuals from the general population with no evidence of venous disease or history of venous ulceration (n = 380, 189 males and 191 females). Polymorphisms in close proximity to upstream regulatory regions of the ERbeta gene, including the 0N exon and promoter transcribed in inflammatory cells, were significantly (p < 0.05) associated with venous ulceration. A major susceptibility haplotype carried by 23% (26/112) of cases compared with only 10% (27/276) of controls (odds ratio = 2.8, 95% confidence interval = 1.6-5.0) was significantly (p < 0.01) associated with elevated serum levels of tumor necrosis factor-alpha. In conclusion, common variation in the regulatory regions of the ERbeta gene may pre-dispose to venous ulceration in a British Caucasian population.

Association of an IRF5 gene functional polymorphism with Sjögren's syndrome

Interferon regulatory factor 5 (IRF-5) is a transcription factor involved in the regulation of the host defense. Previous studies have demonstrated a significant association of various IRF5 gene polymorphisms with systemic lupus erythematosus (SLE) in Caucasians. The purpose of this case-control study was to investigate whether IRF5 polymorphisms are involved in the genetic predisposition to primary Sjögren's syndrome (SS), an autoimmune disease closely related to SLE. We analyzed IRF5 rs2004640, rs2070197, rs10954213, and rs2280714 polymorphisms in a cohort of 212 primary SS patients and 162 healthy blood donors, all of whom were of Caucasian origin. The 4 polymorphisms examined were genotyped by competitive allele-specific polymerase chain reaction using fluorescence resonance energy transfer technology. The IRF5 rs2004640 GT or TT genotype (T allele carriers) was identified in 87% of primary SS patients compared with 77% of controls (P = 0.01, odds ratio [OR] 1.93 [95% confidence interval (95% CI) 1.15-3.42]). The IRF5 rs2004640 T allele was found on 59% of chromosomes from primary SS patients compared with 52% of chromosomes from controls (P = 0.04, OR 1.36 [95% CI 1.01-1.83]). No significant association of primary SS with rs2070197, rs10954213, or rs2280714 was seen when they were analyzed independently. Nevertheless, haplotype reconstructions based on the 4 polymorphisms examined suggest that various allele combinations of rs2004640 and rs2070197 could define susceptibility or protective haplotypes. This study is the first to demonstrate a significant association between primary SS and the IRF5 rs2004640 T allele. These results, which require further replication on larger populations, suggest that besides their association with identical major histocompatibility complex gene polymorphisms, primary SS and SLE share IRF gene polymorphisms as a common genetic susceptibility factor.

Haplotypes in the Complement Factor H (CFH) Gene: Associations with Drusen and Advanced Age-Related Macular Degeneration

BackgroundAge-related macular degeneration (AMD), the leading cause of blindness in the Western world, is a complex disease that affects people over 50 years old. The complement factor H (CFH) gene has been repeatedly shown to be a major factor in determining susceptibility to the advanced form of the condition. We aimed to better understand the functional role of this gene in the AMD disease process and assess whether it is associated with earlier forms of the disease.Methodology/Principal FindingsWe genotyped SNPs at the CFH gene locus in three independent populations with AMD: (a) extended families where at least 3 family members had AMD; (b) sporadic cases of advanced AMD and (c) cases from the Age-Related Eye Disease Study (AREDS). We investigated polymorphisms and haplotypes in and around the CFH gene to assess their role in AMD. CFH is associated with early/intermediate and advanced AMD in both familial and sporadic cases. In our populations, the CFH SNP, rs2274700, is most strongly associated with AMD and when incorporated into a haplotype with the Y402H SNP and rs1061147, the strongest association is observed (p<10−9).Conclusions/SignificanceOur results, reproduced in three populations that represent the spectrum of AMD cases, provide evidence that the CFH gene is associated with drusen as well as with advanced AMD. We also identified novel susceptibility and protective haplotypes in the AMD populations.

Evidence for HLA Class II Susceptible and Protective Haplotypes for Osteomyelitis in Pediatric Patients with Sickle Cell Anemia.

Background and Objective: Osteomyelitis (OM) is a common complication and significant cause of morbidity in patients with sickle cell anemia (SCA); however, its mechanisms are poorly understood. In view of their link to inflammatory diseases and autoimmune disorders, we investigated the association of HLA class II alleles and haplotypes with the pathogenesis of OM in Bahraini SCA patients.Patients and Methods. SCA patients comprised 42 with and 150 patients without OM; HLA-DRB1* and -DQB1* genotyping was done by PCR-SSP. HLA allele frequency was determined by the gene counting method, and haplotype frequency was determined by the maximum-likelihood method.Results. At the allele level, only DRB1*100101 (0.229 vs. 0.082, Pc = 0.003) was positively associated with OM after applying the Bonferrni correction factor. At the haplotype level, DRB1*070101-DQB1*0201 (Pc = 0.001), and DRB1*100101-DQB1*050101 (Pc = 0.001) were more prevalent among patients, while DRB1*030101-DQB1*0201 (Pc = 0.020) and DRB1*040101-DQB1*0302 (Pc = 0.039) was more prevalent among controls, thereby conferring disease susceptibility or protection to these DRB1*-DQB1* haplotypes, respectively.Conclusion. These results demonstrate that specific HLA halpotypes influence osteomyelitis risk in SCA, thereby suggesting that specific HLA types may serve as a marker for identifying SCA patients at high risk for osteomyelitis.HLA-DRB1* and DQB1* Haplotype FrequenciesHaplotypeOM PatientsControlsPPcORDRB1*030101-DQB1*02010.0150.1410.0020.0200.07DRB1*030201-DQB1*04010.0420.0160.2120.9082.95DRB1*040101-DQB1*03020.0160.1260.0040.0390.08DRB1*070101-DQB1*02010.2190.060<0.0010.0014.58DRB1*110101-DQB1*0301010.0560.1080.2780.9620.53DRB1*100101-DQB1*0501010.2080.063<0.0010.0014.03DRB1*130101-DQB1*0601010.0420.0340.7731.0001.45DRB1*150101-DQB1*0601010.0850.0680.7741.0001.27DRB1*160101-DQB1*02010.0640.0200.1210.7253.10DRB1*160101-DQB1*0501010.0110.0990.0160.1490.11

SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians

This study is an extension to previously published work that has linked variation in the human leukocyte antigen (HLA) class I region with susceptibility to multiple sclerosis (MS) in Australians from the Island State of Tasmania. Single nucleotide polymorphism (SNP) mapping was performed on an 865-kb candidate region (D6S1683-D6S265) in 166 Tasmanian MS families, and seven candidate genes [ubiquitin D (UBD), olfactory receptor 2H3 (OR2H3), gamma-aminobutyric acid B receptor 1 (GABBR1), myelin oligodendrocyte glycoprotein (MOG), HLA-F, HLA complex group 4 (HCG4) and HLA-G] were resequenced. SNPs tagging the extended MS susceptibility haplotype were genotyped in an independent sample of 356 Australian MS trios and SNPs in the MOG gene were significantly over-transmitted to MS cases. We identified significant effects on MS susceptibility of HLA-A*2 (OR: 0.51; P = 0.05) and A*3 (OR: 2.85; P = 0.005), and two coding polymorphisms in the MOG gene (V145I: P = 0.01, OR: 2.2; V142L: P = 0.04, OR: 0.45) after full conditioning on HLA-DRB1. We have therefore identified plausible candidates for the causal MS susceptibility allele, and although not conclusive at this stage, our data provide suggestive evidence for multiple class I MS susceptibility genes.

Haplotypes of the interleukin 7 receptor alpha gene are correlated with altered expression in whole blood cells in multiple sclerosis

IL7 regulates T cell survival, differentiation and proliferation. The alpha chain of its receptor, CD127, is polymorphic, and its haplotypes are associated with recovery from transplantation and with the autoimmune disease multiple sclerosis (MS), especially primary progressive MS (PPMS). We demonstrate that two CD127 haplotypes are highly associated with the proportion of the mRNA encoding the soluble isoform of CD127 (P<or=0.001). The soluble isoform is over-represented (P<or=0.002) in PPMS peripheral blood, irrespective of haplotype, and the MS susceptibility haplotype produces more of the soluble isoform. CD127 mRNA is underexpressed (P<or=0.001) in PPMS. Neutrophils, which produce very low levels of CD127 mRNA, were over-represented in our PPMS cohort (P<0.02). CD127 expression is lower in more differentiated cells, such as Th1s, which can be elevated in MS. A higher proportion of these two abundant cell types in peripheral blood could be the basis for the observed reduction in CD127 mRNA. CD127 expression may be a biomarker for these potentially pathologically significant leukocyte types. These significant haplotypic effects on expression are likely to modulate regulation, differentiation and function of T cell subsets in health and disease.

Islet autoantibodies are associated with HLA‐DQ genotypes in Han Chinese patients with type 1 diabetes and their relatives

The objective of this study was to explore the relationship between islet autoantibodies of glutamic acid decarboxylase (GADA), islet antigen-2A (IA-2A), insulin autoantibody (IAA), and human leukocyte antigen (HLA)-DQ genotypes in type 1 diabetes (T1D) patients and their first-degree relatives (FDRs). Cross-sectional and case-control study. Four hundred and ninety-five T1D patients, 419 FDRs, and 376 control subjects in Han Chinese populations were recruited and tested for GADA and IA-2A, while 71 cases, all FDRs and 300 controls were tested for IAA. The 338 T1D patients (including 187 antibody-positive and 151 antibody-negative patients), 173 FDRs and 278 controls were genotyped for HLA-DQ with polymerase chain reaction sequencing-based method. Compared with the control, the frequency of DQA1*03-DQB1*0303, DQA1*05-DQB1*0201, and DQA1*03-DQB1*0401 haplotypes was higher (P < 0.05-0.01) but DQA1*0102-DQB1*0602 haplotype was lower (P < 0.01) in T1D patients. DQA1*03 allele was less in the FDRs than in their probands (P < 0.05). GADA was more prevalent in T1D patients carrying DQA1*05-DQB1*0201 or DQA1*03-DQB1*0401 haplotype (55.8% vs 41.0%, 65.5% vs 40.3%, P < 0.05-0.01), whereas IA-2A presented more in the patients carrying DQA1*03-DQB1*0303 haplotype (27.0% vs 7.9%, P < 0.05-0.01), both GADA and IA-2A showed frequently in the patients with DQA1*03-DQB1*0303/DQA1*05-DQB1*0201 haplotypes (34.5% vs 9.7%, P < 0.01). GADA positivity was lower in the patients with DQA1*0102-DQB1*0602 haplotype (16.7% vs 45.9%, P < 0.05). The frequency of IAA was not different between patients with and without susceptible DQ haplotypes (P > 0.05). GADA, IA-2A or IAA presented frequently in FDRs with DQA1*03-DQB1*0303 haplotype. The findings in the study indicate that some of specific HLA-DQA1/-DQB1 genotypes and haplotypes not only confer susceptibility to T1D but also are associated with the presence of the islet autoantibodies in the Han Chinese population.

Endothelial nitric oxide synthase Glu298Asp, 4b/a, and T‐786C polymorphisms in type 2 diabetic retinopathy

The possible association between the endothelial nitric oxide (eNOS) gene T-786C (promoter region), 27-bp repeat 4b/4a (intron 4), and Glu298Asp (exon 7) polymorphisms with diabetic retinopathy (DR) was investigated. A retrospective case-control study. A total of 872 type 2 diabetes (T2DM) patients were studied, of whom 383 presented with preproliferative/proliferative retinopathy (DR group), and 489 with absent/mild retinopathy (DWR group). Glu298Asp and T-786C genotyping was carried out by PCR-RFLP analysis, while 4b/4a was assessed by PCR. Genotype distribution was compared using the chi(2)-test, and the contributions of the polymorphisms to DR were analysed by haplotype analysis and multivariate regression analysis. Lower prevalence of mutant 4a (P = 0.011), and heterozygous 4b/4a (P = 0.042) were seen in the DR compared to the DWR groups; the allele and genotype distribution of the Glu298Asp and T-786C polymorphisms were comparable between DR and DWR groups. Three-loci haplotype analysis demonstrated significant association between eNOS variants and DR, with protective [haplotype 122 (Glu298/4a/-786C)], and susceptible haplotypes [haplotypes 112 (Glu298/4b/-786C) and 222 (Asp298/4a/-786C)] identified. Multivariate regression analysis confirmed the association between haplotypes 122 (P = 0.015); 112 (P = 0.027), and 222 (P = 0.048) and DR, after controlling for potential covariates (including age, sex, age of disease onset; HbA1c; hypertension, total cholesterol). This study identifies genetic variation at the eNOS locus as genetic risk factor for diabetic retinopathy, which may serve as a useful marker of increased susceptibility to the risk of retinopathy.

Prion protein polymorphisms in autochthonous European sheep breeds in respect to scrapie eradication in affected flocks

Resistance or susceptibility of sheep to scrapie is influenced by polymorphisms in the prion protein (PrP) gene ( PRNP). Consequently, scrapie eradication in affected sheep flocks within the European Community (EC) aims at quickly removing the highly susceptible haplotype for classical scrapie, V 136R 154Q 171 (VRQ), and increasing the number of sheep with the most resistant genotype for classical scrapie, ARR/ARR. In total, 1672 blood samples of 56 sheep breeds originating from 15 European and Middle Eastern countries were analyzed for nucleotide polymorphisms at codons 136, 154 and 171 of PRNP using improved restriction-fragment-length-polymorphism analyses. The frequency of the genotype ARR/ARR ranged from 0 to 42%. This genotype was absent in the samples from 11 breeds. Genotypes with at least one VRQ haplotype but no ARR haplotype showed frequencies from 0 to 21%. Such genotypes were not found in 34 of the 56 investigated breeds. The observed differences in the frequencies of PrP haplotypes and genotypes would have different consequences regarding culling of sheep in respect to genetically based scrapie eradication in affected flocks of these breeds. Furthermore, the rare ARK haplotype has been described for the first time in the Italian Bergamasca breed.

A novel haplotype in ApoAI-CIII-AIV gene region is detrimental to Northwest Indians with coronary heart disease

The present study investigated the genetic variation of 3′ flanking region of ApoA-I ( PstI), 3′ untranslated region of ApoC-III ( SstI) and intron 2 of ApoA-IV ( XbaI) in 193 angiographically diagnosed CHD patients and 150 CHD negative controls of Punjab, Northwest India. Haplotype analysis reveals that P2-S2-X1 is a susceptibility haplotype that confers the risk of CHD (OR 2.33, CI 1.08–4.38, P < 0.05), which exacerbates (OR 2.61, CI 1.23–5.92, P < 0.01) after adjustment with the confounders. This exacerbating effect of P2-S2-X1 may umpire significant higher levels of TG, LDL/HDL ratio and lower levels of HDL in CHD patients.

Polymorphisms in the 3′ UTR in the neurocalcin δ gene affect mRNA stability, and confer susceptibility to diabetic nephropathy

Using a large-scale genotyping analysis of gene-based single nucleotide polymorphisms (SNPs) in Japanese type 2 diabetic patients, we have identified a gene encoding neurocalcin delta (NCALD) as a candidate for a susceptibility gene to diabetic nephropathy; the landmark SNP was found in the 3' UTR of NCALD (rs1131863: exon 4 +1340 A vs. G, P = 0.00004, odds ratio = 1.59, 95% CI 1.27-1.98). We also discovered two other SNPs in exon 4 of this gene (+999 T/A, +1307 A/G) that showed absolute linkage disequilibrium to the landmark SNP. Subsequent in vitro functional analysis revealed that synthetic mRNA corresponding to the disease susceptible haplotype (exon 4 +1340 G, +1307 G, +999 A) was degraded faster than mRNA corresponding to the major haplotype (exon 4 +1340 A, +1307 A, +999 T), and allelic mRNA expression of the disease susceptibility allele was significantly lower than that of the major allele in normal kidney tissues. In an experiment using a short interfering RNA targeting NCALD, we found that silencing of the NCALD led to a considerable enhancement of cell migration, accompanied by a significant reduction in E-cadherin expression, and by an elevation of alpha smooth muscle actin expression in cultured renal proximal tubular epithelial cells. We also identified the association of the landmark SNP with the progression of diabetic nephropathy in a 8-year prospective study (A vs. G, P = 0.03, odds ratio = 1.91, 95% CI 1.07-3.42). These results suggest that the NCALD gene is a likely candidate for conferring susceptibility to diabetic nephropathy.

Analysis of Candidate Genes on Chromosomes 5q and 19p in Celiac Disease

Celiac disease (CD) is a multifactorial disease with involvement of both environmental and genetic susceptibility factors. The HLA-DQ loci account for <40% of CD heritability, but linkage studies have delineated other loci at the 5q31-33 (CELIAC2), and 19p13 regions (CELIAC4), similarly as in inflammatory bowel diseases. However, data in association studies are contradictory. To evaluate whether single nucleotide polymorphisms (SNPs) tagging the MYO9B susceptibility haplotype and the IBD5 locus (5q31-33) are involved in CD predisposition, we performed case-control and family-based analyses. Additionally, any possible correlation with the HLA-DQ status was investigated. Finally, our data were pooled with the results of other studies by a meta-analysis. In all, 337 unrelated patients with CD, 424 parents (212 sets), and 452 healthy individuals were genotyped for the IGR2198a_1, rs12521868, rs1050152, and rs2631367 SNPs (IBD5 locus) and the rs962917, rs2305764, and rs1545620 SNPs of the MYO9B gene by the restriction enzyme method and the TaqMan system ABI PRISM 7700, respectively. In comparison with healthy control individuals, the allele, genotype, and haplotype frequencies of all investigated SNPs were not different in the CD patients, nor was any correlation observed with the HLA-DQ status or clinical presentation. The transmission disequilibrium test did not show a transmission distortion. Five other studies were available for meta-analysis on MYO9B variants; by pooling of data, no significant association was demonstrated by the random effect model. A significant heterogeneity (P < 0.002) among the studies was present, mainly explained by a single study in the Dutch population. Our results and those of the meta-analysis (>2000 CD patients and 4000 control individuals) question the role of MYO9B at the CELIAC4 locus as a disease-causing gene. Moreover, none of the investigated SNPs explain the linkage at the CELIAC2 locus.

HLA‐associated genetic resistance and susceptibility to type I diabetes in French North Africans and French natives

The distribution of human leukocyte antigen (HLA)-DRB1-DQA1-DQB1 haplotypes was analyzed separately in two distinct French ethnic groups with type I diabetes (T1D), i.e. French North African migrants (n= 64, mean age at diagnosis = 8.25 years) and ancient French natives (n= 60, mean age at diagnosis = 7.42 years). HLA associations were determined by calculating odds ratios (ORs) between patients and two ethnic-matched control populations. Results show highly similar ORs for the conservative DRB1*0301-DQA1*0501-DQB1*0201 haplotype of susceptibility (OR: 3.22 and 3.93 in migrants and natives, respectively) and the DRB1*1501-DQA1*0102-DQB1*0602 haplotype of resistance (OR: 0.05 and 0.03, respectively). In contrast, among the more variable DRB1*04-DQB1*0302 haplotypes of susceptibility, the DRB1*0402 (OR: 3.10 and 32.84) and 0405 (OR: 5.90 and 16.25, respectively) were associated with T1D in migrants and natives, whereas an increase of DRB1*0401, a rare allele in migrants, was significant in natives only. Also, among the DRB1*11-DQA1*0505-DQB1*0301 haplotypes of resistance, the OR observed for DRB1*1104-DQA1*0505-DQB1*0301, common in migrants, was lower (OR: 0.08) than for DRB1*1101-DQA1*0505-DQB1*0301 (OR: 0.32), common in natives. How DRB1*11 subtypes might affect differently the risk conferred by DQA1*0505-DQB1*0301 will be discussed.

Opposed independent effects and epistasis in the complex association of IRF5 to SLE

Genetic variation in the interferon regulatory factor 5 (IRF5) gene affects systemic lupus erythematosus (SLE) susceptibility. However, association is complex and incompletely defined. We obtained fourteen European sample collections with a total of 1383 SLE patients and 1614 controls to better define the role of the different IRF5 variants. Eleven polymorphisms were studied, including nine tag single nucleotide polymorphisms (SNPs) and two extra functional polymorphisms. Two tag SNPs showed independent and opposed associations: susceptibility (rs10488631, P<10(-17)) and protection (rs729302, P<10(-6)). Haplotype analyses showed that the susceptibility haplotype, identified by the minor allele of rs10488631, can be due to epistasis between three IRF5 functional polymorphisms. These polymorphisms determine increased mRNA expression, a splice variant with a different exon 1 and a longer proline-rich region in exon 6. This result is striking as none of the three polymorphisms had an independent effect on their own. Protection was independent of these polymorphisms and seemed to reside in the 5' side of the gene. In conclusion, our results help to understand the role of the IRF5 locus in SLE susceptibility by clearly separating protection from susceptibility as caused by independent polymorphisms. In addition, we have found evidence for epistasis between known functional polymorphisms for the susceptibility effect.

The ApoAI-CIII-AIV gene cluster and its relation to lipid levels in type 2 diabetes mellitus and coronary heart disease: determination of a novel susceptible haplotype

The present study investigated genetic variation in the 3' flanking region of ApoA-I (PstI), the 3' untranslated region of ApoC-III (SstI) and intron 2 of ApoA-IV (XbaI) in 435 type 2 diabetes mellitus patients, divided according to the presence or absence of coronary heart disease (CHD). Uncommon allele frequencies (P2, S2, X2) were 17.5%, 32.5%, 16.2% and 29.5%, 17.9%, 13.8% in patients with and without CHD, respectively. Linkage disequilibrium (D' = 0.31-0.73, p<0.01) was observed in all diallelic pairs except XbaI/PstI and XbaI/SstI in patients having CHD. Haplotype analysis revealed that P1-S2-X1 is a susceptibility haplotype that increases the risk of CHD in diabetes (OR 2.85, CI 1.51-5.61), exacerbating risk (OR 3.57, CI 1.81-7.45) even after adjustment for confounders. The findings in the present study suggest that each unit of P1-S2-X1 in diabetes increases the risk of CHD by a factor of 1.37+/-0.307 (beta + SE), which is manifest in its multiplicative mode.

Marqueurs de risque du diabète de type 1 chez les apparentés au premier degré des diabétiques tunisiens

To identify the profile of anti-pancreas autoantibodies and elucidate the HLA DRB1, DQB1 polymorphism in Tunisian first-degree relatives of patients with type 1 diabetes, we recruited 96 relatives from 21 families with at least one diabetic child. Islet cell antibodies (ICA) were detected by immunofluorescence on monkey pancreas; glutamate decarboxylase (GADA), IA2 (IA2-A) and insulin (IAA) antibodies were measured by RIA. HLA class II DRB1 and DQB1 alleles were typed by PCR-SSP. ICA, GADA, IA2-A and IAA were found in respectively 11.5, 4.2, 5.2 and 8.3% of relatives. Twenty-two out of 96 had at least one antibody and 20 out of these 22 had a susceptibility allele (DRB1*03, DRB1*04, DQB1*02 or DQB1*0302) with or without protective allele (DRB1*11, DRB1*13, DRB1*15 or DQB1*06). All of the 5 relatives having 2 autoantibodies or more carried the DRB1*04-DQB1*0302 susceptible haplotype. In conclusion, this observational study confirms in a Tunisian population known epidemiological data and demonstrates the usefulness of follow-up to determine the predictive value of studied markers.

Identification of prediabetes in first-degree relatives at intermediate risk of type I diabetes

Prevention trials of type I diabetes are limited by recruitment of individuals at high risk of the disease. We investigated whether demographic and biological characteristics can identify rapid progressors among first-degree relatives of known patients at intermediate (< 10%) 5-year risk. Diabetes-associated antibodies, random proinsulin : C-peptide (PI/C) ratio and HLA DQ genotype were determined (repeatedly) in 258 islet antibody-positive IA-2Antibody-negative (Abpos/IA-2Aneg) normoglycaemic first-degree relatives. During follow-up (median 81 months), 14 of 258 Abpos/IA-2Aneg relatives developed type I diabetes; 13 (93%) of them had persistent antibodies conferring a 12% [95% confidence interval (CI): 5-19%] 5-year risk of diabetes. In Abpos/IA-2Aneg relatives with persistent antibodies (n = 126), the presence of >/= 1 HLA DQ susceptibility haplotype in the absence of a protective haplotype (P = 0.033) and appearance on follow-up of a high PI/C ratio (P = 0.007) or IA-2A-positivity (P = 0.009) were identified as independent predictors of diabetes. In persistently antibody-positive relatives with HLA DQ risk a recurrently high PI/C ratio or development of IA-2A identified a subgroup (n = 32) comprising 10 of 13 (77%) prediabetic relatives and conferred a 35% (95% CI: 18-53%) 5-year risk. Under age 15 years, 5-year progression (95% CI) was 57% (30-84%) and sensitivity 62%. In the absence of IA-2A, the combination of antibody persistence, HLA DQ risk and elevated PI/C ratio or later development of IA-2A and young age defines a subgroup of relatives with a high risk of type I diabetes (>/= 35% in 5 years). Together with initially IA-2A-positive relatives these individuals qualify for standardized beta cell function tests in view of prevention trials.

Contribution of the novel inflammatory bowel disease gene IL23R to disease susceptibility and phenotype

A North American genome-wide single nucleotide polymorphism (SNP) association study identified IL23R as a novel inflammatory bowel disease (IBD) susceptibility gene. Association was reported with multiple risk variants in the centromeric portion of IL23R in 3 large independent cohorts. The aims of this study were to replicate the association of IL23R with Crohn's disease (CD), examine subphenotype relationships, and look for evidence of epistasis with the known CD susceptibility gene CARD15 and susceptibility haplotype IBD5 in a large collection of CD patients. We further investigated the relationship between IL23R and ulcerative colitis (UC). In all, 604 CD and 647 UC patients who had been rigorously phenotyped and who had been recruited from a single UK center were used in this study. Controls were either spouses of patients (141) or were recruited from well-person clinics (993). Eight SNPs were genotyped using MassArray (Sequenom). All 8 SNPs genotyped were significantly associated with CD. The association with the nonsynonymous SNP rs11209026 was confirmed (P=6.65x10(-6), odds ratio [OR], 0.43, 95% confidence interval [CI]: 0.29-0.64). The most significant SNP in our study was rs7517847 (P=4.9x10(-9), OR 0.65, 0.56-0.75), which is statistically independent of rs11209026. Preliminary evidence suggests an epistatic interaction with the IBD5 risk haplotype. The effects of mutations in this IL23R appear weaker in UC (P=0.008, OR 0.63, 0.45-0.89 and 0.005 OR, 0.81, 0.71-0.94, respectively). No subphenotype associations were identified. We confirmed the findings that IL23R is a susceptibility gene for IBD with suggestive epistasis with the IBD5 locus in the CD population.

Single‐nucleotide polymorphisms in the COL1A1 regulatory regions are associated with otosclerosis

Otosclerosis (MIM 166800) has a prevalence of 0.2-1% among white adults, making it the single most common cause of hearing impairment in this ethnic group. Although measles virus, hormones, human leukocyte antigen alleles and genetic factors have been implicated in the development of otosclerosis, its etiology remains unknown. In a focused effort to identify genetic factors in otosclerosis, we have mapped four disease loci (MIM 166800/605727/608244/608787); however, cloning the disease-causing genes in these intervals has not been successful. Here, we used a case-control study design to investigate the association between collagen type I genes and otosclerosis. We identified susceptibility and protective haplotypes in COL1A1 that are significantly associated with otosclerosis in the Caucasian population. These haplotypes alter reporter gene activity in an osteoblast cell line by affecting binding of transcription factors to cis-acting elements. Our data suggest that increased amounts of collagen alpha1(I) homotrimers are causally related to the development of otosclerosis. Consistent with this hypothesis, mouse mutants homozygous for a Col1a2 frameshift mutation on a C57BL/6J background that deposit only homotrimeric type I collagen have hearing loss.

Influence of VEGF‐A gene variation and protein levels in breast cancer susceptibility and severity

Vascular endothelial growth factor-A (VEGF-A) plays an important role in tumour angiogenesis and cancer progression. VEGF gene variation may influence VEGF levels and therefore cancer susceptibility and progression. We studied the role of VEGF single nucleotide polymorphisms and haplotypes in breast cancer susceptibility and severity. We also studied the relationships of VEGF SNPs with circulating VEGF levels in healthy volunteers and protein expression in breast cancers. Single nucleotide polymorphisms (SNPs) in the regulatory regions of the VEGF gene were genotyped by high throughput methods in approximately 500 breast cancer cases and 500 appropriate controls. Haplotype frequencies were inferred using methods based on the Expectation Maximisation algorithm. The effect of VEGF genotypes on serum and plasma VEGF levels were studied in another cohort of healthy individuals. A semi-quantitative assessment of VEGF protein expression on tissue micro arrays (TMA) constructed from approximately 300 breast cancer samples was performed and compared with VEGF genotypes and with histopathological parameters and survival in breast cancer. The -460T/+405C/-7C/936C haplotype in the VEGF gene was found to be associated with decreased breast cancer risk (p = 0.029). The -7C>T polymorphism may influence overall breast cancer survival (p = 0.027). Individual polymorphisms however did not affect breast cancer susceptibility. There was no association between the individual polymorphisms and circulating VEGF levels in healthy volunteers and VEGF expression on the breast cancer micro array. VEGF expression in breast cancers was however associated with high grade (p = 0.002) and ER negative tumours (p = 0.03).