Caucasian Cases Research Articles

HLA class III genes involvement in Kawasaki disease: a case–control study in Caucasian population

Kawasaki disease (KD) is an acute, multisystemic, febrile vasculitis of unknown aetiology, which affects young children mainly under 5years of age. The clinical variability has until now prevented to decrypt KD aetiological factors. Recently, the importance of genetics and the pivotal role of the immune system have emerged. To investigate in this direction, genomic DNA from 74 Caucasian KD cases and 440 healthy controls has been analysed to characterize functional polymorphisms of relevant HLA class III genes: AGER -429 and -374, TNF -857, -308 and -238, HSPA1A +190, HSPA1B +1267 and HSPA1L +2437. Allele, genotype and haplotype frequencies were therefore compared with the chi-squared test and Fisher's exact test. Our data showed significant deviations between patients with Kawasaki disease and controls concerning the TNF -308 polymorphism genotype (GG: P=0.0449) and allele (G,A: P=0.0433) and -238 polymorphism genotype frequencies (AA: P=0.0351). Moreover, we found differences concerning the HSPA1A +190 polymorphism (GC: P=0.0317) and the HSPA1L +2437 polymorphism (TT: P=0.0072; TC: P=0.0250; T: P=0.0037; C: P=0.0037). The calculation of TNF -238 and HSPA1L haplotype frequencies also pointed out a statistically significant decrease in patients of CG haplotype (P=0.0001), which could have a role in protecting from the inflammatory processes that characterize the disease progression. The results obtained point to a possible involvement of the entire HLA class III region in KD susceptibility.

Functional single-nucleotide variant of HSPD1 in sudden infant death syndrome

An insufficient stress response due to a genetically impaired heat shock protein (Hsp) could play a role in the pathogenesis in a subgroup of sudden infant death syndrome (SIDS) cases. Herein, we are the first to investigate whether a functionally impairing and thus pathogenic variant of the gene for Hsp60, encoded by HSPD1 (rs72466451), is correlated with the occurrence of SIDS. In a case-control study of a series of 133 cases of SIDS and 192 gender-matched German Caucasian control cases, the occurrence and distribution of the HSPD1 single-nucleotide variant (SNV) was analyzed using SNV genotyping by minisequencing. The results show significantly increased frequency of the pathogenic variant of the HSPD1 SNV in a subgroup (4.5%) of SIDS cases. The results suggest that the pathogenic variant of rs72466451 may play a role in a subgroup of SIDS cases with impaired Hsp60-mediated stress response.

Genome-Wide Association Study Identifies Possible Genetic Risk Factors for Colorectal Adenomas

Colorectal cancer is the second leading cause of cancer-related death, and most colorectal cancer usually arises from colorectal adenomas. Removal of polyps reduces mortality from colorectal cancer. Colorectal adenomas are known to aggregate in families; however, the genetic determinants for risk of polyps are largely unknown. In this study, we used data from the Tennessee Colorectal Polyp Study and the Tennessee-Indiana Adenoma Recurrence Study to conduct a GWAS of adenoma cases and controls. Our design consisted of discovery and replication phases for a total of 2,551 Caucasian adenoma cases and 3,285 Caucasian controls. We carried out logistic regression to test for association in both the discovery and replication phase and further examined the results with meta-analysis. No single nucleotide polymorphism (SNP) achieved a genome-wide significant P value; however, the most significantly associated SNPs were either previously associated with colorectal cancer in GWAS, such as rs10505477 in the gene POU5F1 [odds ratio (OR) = 0.87; 95% confidence interval (CI) 0.81-0.94; P = 4.4 × 10(-4)), or have been biologically linked to benign growths in other tissues, such as rs1919314 in the gene histone deacetylase 9 (OR = 1.32; 95% CI, 1.18-1.47; P = 1.1 × 10(-6)). This study suggests that several SNPs may be related to adenoma risk and provides clues for future studies. These results suggest that some known genetic risk factors of colorectal cancer are necessary but not sufficient for carcinogenesis.

AB0705 Pleuropericardial effusion, a rare presenting feature in patients with sarcoidosis – a case series

BackgroundPulmonary involvement is very common and occurs in up to 70% of patients with Sarcoidosis. However, Sarcoidosis presenting with pleural or pericardial effusion is very rare as per published series....

THU0014 Association between a polymorphism in the fractalkine receptor, CX3CR1, and rheumatoid arthritis

BackgroundRheumatoid arthritis (RA) is a chronic, autoimmune disease characterized by hyperplasia and inflammatory changes within the synovium. The recruitment and accumulation of monocytes in the synovium contribute to inflammatory response...

AB0418 The carotid artery atherosclerosis burden and its associated cardiovascular risk factors in african black and caucasian patients with established rheumatoid arthritis

BackgroundCompared to persons from developed populations, those that belong to developing populations are at an earlier epidemiological health transition stage [1-3]. Accordingly, black Africans still experience a distinctly low prevalence...

VPS35 and EIF4G1 mutations are rare in Parkinson's disease among Indians

Mutations in 2 genes, vacuolar protein sorting homolog 35 (VPS35) and eukaryotic translation initiation factor 4 gamma 1 (EIF4G1), have been recently reported as causal in autosomal dominant Parkinson's disease (PD) among Caucasians. Their contribution to PD in other ethnic groups remains limited with 1% of VPS35 mutations observed in Caucasian and Japanese populations, but none in Chinese, and 11.57% of EIF4G1 mutations in Caucasian families and 0.09% and 0.17% in Caucasian and Chinese sporadic cases, respectively. We investigated the contribution, if any, of these 2 genes to familial and sporadic PD among the ethnically distinct Indian population. Complete exonic regions of these 2 genes were resequenced in 15 well-characterized PD families; the reported p.Asp620Asn in VPS35 and p.Arg1205His in EIF4G1 mutations were screened in an additional 54 familial and 251 sporadic PD cases, and no mutations were observed. These results, together with our previous reports on the absence of mutations in SNCA and LRRK2, warrant a continuing search for novel causative genes for PD among Indians.

BRCA1 and BRCA2 Gene Mutations Screening In Sporadic Breast Cancer Patients In Kazakhstan.

BackgroundA large number of distinct mutations in the BRCA1 and BRCA2 genes have been reported worldwide, but little is known regarding the role of these inherited susceptibility genes in breast cancer risk among Kazakhstan women.AimTo evaluate the role of BRCA1/2 mutations in Kazakhstan women presenting with sporadic breast cancer.MethodsWe investigated the distribution and nature of polymorphisms in BRCA1 and BRCA2 entire coding regions in 156 Kazakhstan sporadic breast cancer cases and 112 age-matched controls using automatic direct sequencing.ResultsWe identified 22 distinct variants, including 16 missense mutations and 6 polymorphisms in BRCA1/2 genes. In BRCA1, 9 missense mutations and 3 synonymous polymorphisms were observed. In BRCA2, 7 missense mutations and 3 polymorphisms were detected. There was a higher prevalence of observed mutations in Caucasian breast cancer cases compared to Asian cases (p<0.05); higher frequencies of sequence variants were observed in Asian controls. No recurrent or founder mutations were observed in BRCA1/2 genes. There were no statistically significant differences in age at diagnosis, tumor histology, size of tumor, and lymph node involvement between women with breast cancer with or without the BRCA sequence alterations.ConclusionsConsidering the majority of breast cancer cases are sporadic, the present study will be helpful in the evaluation of the need for the genetic screening of BRCA1/2 mutations and reliable genetic counseling for Kazakhstan sporadic breast cancer patients. Evaluation of common polymorphisms and mutations and breast cancer risk in families with genetic predisposition to breast cancer is ongoing in another current investigation.

Chromosome 21 Scan in Down Syndrome Reveals DSCAM as a Predisposing Locus in Hirschsprung Disease

Hirschsprung disease (HSCR) genetics is a paradigm for the study and understanding of multigenic disorders. Association between Down syndrome and HSCR suggests that genetic factors that predispose to HSCR map to chromosome 21. To identify these additional factors, we performed a dose-dependent association study on chromosome 21 in Down syndrome patients with HSCR. Assessing 10,895 SNPs in 26 Caucasian cases and their parents led to identify two associated SNPs (rs2837770 and rs8134673) at chromosome-wide level. Those SNPs, which were located in intron 3 of the DSCAM gene within a 19 kb-linkage disequilibrium block region were in complete association and are consistent with DSCAM expression during enteric nervous system development. We replicated the association of HSCR with this region in an independent sample of 220 non-syndromic HSCR Caucasian patients and their parents. At last, we provide the functional rationale to the involvement of DSCAM by network analysis and assessment of SOX10 regulation. Our results reveal the involvement of DSCAM as a HSCR susceptibility locus, both in Down syndrome and HSCR isolated cases. This study further ascertains the chromosome-scan dose-dependent methodology used herein as a mean to map the genetic bases of other sub-phenotypes both in Down syndrome and other aneuploidies.

Independent and epistatic effects of variants in VPS10-d receptors on Alzheimer disease risk and processing of the amyloid precursor protein (APP)

Genetic variants in the sortilin-related receptor (SORL1) and the sortilin-related vacuolar protein sorting 10 (VPS10) domain-containing receptor 1 (SORCS1) are associated with increased risk of Alzheimer's disease (AD), declining cognitive function and altered amyloid precursor protein (APP) processing. We explored whether other members of the (VPS10) domain-containing receptor protein family (the sortilin-related VPS10 domain-containing receptors 2 and 3 (SORCS2 and SORCS3) and sortilin (SORT1)) would have similar effects either independently or together. We conducted the analyses in a large Caucasian case control data set (n=11 840 cases, 10 931 controls) to determine the associations between single nucleotide polymorphisms (SNPs) in all the five homologous genes and AD risk. Evidence for interactions between SNPs in the five VPS10 domain receptor family genes was determined in epistatic statistical models. We also compared expression levels of SORCS2, SORCS3 and SORT1 in AD and control brains using microarray gene expression analyses and assessed the effects of these genes on γ-secretase processing of APP. Several SNPs in SORL1, SORCS1, SORCS2 and SORCS3 were associated with AD. In addition, four specific linkage disequilibrium blocks in SORCS1, SORCS2 and SORCS3 showed additive epistatic effects on the risk of AD (P⩽0.0006). SORCS3, but not SORCS2 or SORT1, showed reduced expression in AD compared with control brains, but knockdown of all the three genes using short hairpin RNAs in HEK293 cells caused a significant threefold increase in APP processing (from P<0.001 to P<0.05). These findings indicate that in addition to SORL1 and SORCS1, variants in other members of the VPS10 domain receptor family (that is, SORCS1, SORCS2, SORCS3) are associated with AD risk and alter APP processing. More importantly, the results indicate that variants within these genes have epistatic effects on AD risk.

Abstract 2554: Constitutive short telomere length and lung cancer risk: a large case- control study.

Abstract Background: Telomeres plays a key role in the maintenance of chromosomal stability and integrity. Telomere dysfunction is a common crucial event in malignant transformation and tumorigenesis. Short telomere length in surrogate tissues (peripheral blood leukocytes, or PBLs) has been associated with increased risks of several cancers. In this study, we used a large case control study to evaluate the association of overall telomere length in PBLs with the risk of lung cancer. Methods: We measured the overall telomere lengths in PBLs using real-time quantitative PCR method in a large case-control study with 769 Caucasian lung cancer cases and 769 age, gender, and ethnicity matched healthy controls Wilcoxon rank sum test was used to compare the differences between case patients and control subjects. Unconditional multivariate logistic regression analysis was used to assess the association between telomere length and lung cancer risk. In addition, the effect of age, gender and smoking status was evaluated and correlation analyses between variables were performed. Results: As expected, telomere length was inversely correlated with age in both cases and controls. Lung cancer patients had significantly shorter overall telomere lengths (mean ± standard deviation: 1.20 ±0.37 versus 1.25 ±0.35 p =0.002) than controls, which was only evident in men (1.15 ±0.36 versus 1.24 ±0.36 p &amp;lt;0.001) but not in women. Multivariate logistic regression analysis showed that short overall telomere length was associated with a dose-dependent increase in lung cancer risk. Compared to the individuals within the highest quartile of telomere length, the OR for those within the 3rd, 2nd and 1st quartiles was 0.88 (95% CI 0.65-1.18), 1.08 (95% CI 0.80-1.44) and 1.49 (95% CI 1.12-1.99), respectively (p for trend &amp;lt; 0.001). This effect was more pronounced in current and former smokers (p for trend &amp;lt; 0.001) than in nonsmokers. There was a significant interaction between smoking and overall telomere length in elevating lung cancer risk (p for interaction &amp;lt;0.001). Conclusions: This is the largest epidemiological study to evaluate constitutive telomere length and lung cancer risk. Our data strongly support the role of telomere dysfunction in lung carcinogenesis, highlighting its specific interaction with smoking. Citation Format: Beatriz Sanchez-Espiridion, Jian Gu, David W. Chang, Joe Y. Chang, Charles Lu, Jack A. Roth, Xifeng Wu. Constitutive short telomere length and lung cancer risk: a large case- control study. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2554. doi:10.1158/1538-7445.AM2013-2554

Abstract 4843: Genetic variants in Notch signaling pathway and ovarian cancer.

Abstract The Notch signaling pathway drives proliferation, differentiation, apoptosis, cell fate choices, and has a key role in the regulation of stem cells in a variety of cancers. In this study, we applied a pathway-based approach to evaluate the associations between single nucleotide polymorphisms in Notch signaling pathway and ovarian cancer risk, survival, and response to chemotherapy. Towards this, we systematically genotyped 139 SNPs from 10 genes in the pathway in 339 Caucasian ovarian cancer cases and 349 Caucasian healthy controls. Individually, four SNPs were significantly associated with the ovarian cancer risk. The most significant SNP was NOTCH4: rs397081, with an adjusted odds ratio (OR) of 0.38 (95% CI = 0.22-0.66, P=0.00057). A highly significant gene-dosage effect was observed for these top variants (P for trend &amp;lt; 0.00001) with those carrying ≥ 3 risk genotypes having a nearly 6-fold increase in risk (OR = 5.67, 95% CI = 2.58 - 12.44] . Classification and regression tree (CART) analysis further revealed potential higher order gene-gene interactions between these four SNPs, with the highest risk group having almost 7-fold increased risk. Ten SNPs were significantly associated with overall survival, of which the strongest association was identified for NOTCH4: rs3131290 (OR = 0.48, 95% CI = 0.27-0.84). Cumulative effect analysis showed that multiple adverse genotypes had a significant dose-dependent effect on overall survival. The median survival times for individuals carrying ≤3, 4 to 6, and ≥7 of these adverse genotypes were &amp;gt;186.3, 62.82, and 28.58 months, respectively. Similarly, a significant association was identified between a poor response to platinum-based chemotherapy and the number of unfavorable SNPs (P for trend &amp;lt; 0.0001). Our findings suggest that genetic variants in the Notch signaling pathway are associated with ovarian cancer risk and could serve as potential predictors of clinical outcomes in ovarian cancer patients. Citation Format: Enping Xu, Karen H. Lu, Michelle AT Hildebrandt, Maosheng Huang, Xifeng Wu, Dong Liang. Genetic variants in Notch signaling pathway and ovarian cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4843. doi:10.1158/1538-7445.AM2013-4843

Abstract 1345: Evidence for genetic mediation of lung cancer through hay fever.

Abstract Introduction: In the past decade, advances in genetics have led to the discovery of numerous lung cancer susceptibility variants. The majority of these variants have been found to influence lung cancer susceptibility via tobacco exposure or nicotine addiction; however, recently, researchers have observed lung cancer susceptibility variants that mediate through Chronic Obstructive Pulmonary Disease (COPD). Studies involving potential genetic factors related to other lung-related conditions, such as pneumonia and/or hay fever have been limited. The genetic variants related to underlying mechanism of hay fever on the development of lung cancer are interesting to pursue as hay fever has been showed to be protective against lung cancer. Methods: Cases included 1154 histological-confirmed Caucasian lung cases from MD Anderson Cancer Center in Houston, Texas, and controls included 1137 individuals recruited through the Kelsey-Seybold Clinics in Houston, Texas. These cases and controls were a subset of participants from a lung cancer case-control study conducted that has available Genome-wide association study (GWAS) data (317,498 SNPs). We first conducted an association analysis in PLINK to determine the association of each SNP with both lung cancer and hay fever and find SNPs that showed a joint significance for both hay fever and lung cancer in opposite directions (p-value &amp;lt; 0.05 for both). We then performed mediation analyses with the SNPs that showed significance for both hay fever and lung cancer. Finally, we inferred SNPs in regions that contained a collection of tag SNPs that mediate lung cancer risk through hay fever. Results: Two hundred and forty six SNPs were found to be statistically significant (p-value &amp;lt; 0.05) for both hay fever (protection) and lung cancer (risk), and 76 of these SNPs maintained their significance level after mediation analysis. SNP rs7159751 on chromosome 14 had the highest mediation effect of 19.83%. A collection of SNPs on the Neuregulin 3 gene (NRG3) that mediate lung cancer risk through hay fever was found on Chromosome 10 which has been shown to activate the JAK-STAT signal transduction pathway and stimulate lung epithelial cell proliferation. Conclusion: This is the first study to have investigated the mediation effects of hay fever on lung cancer risk. Our data supports the mediation role of certain SNPs in lung cancer through hay fever and points to specific transduction pathway. Future studies are needed to validate these results in external populations. Citation Format: Anthony D'Amelio, Chi H. Nguyen, Randa El-Zein, Margaret R. Spitz, Xifeng Wu, Carol J. Etzel. Evidence for genetic mediation of lung cancer through hay fever. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1345. doi:10.1158/1538-7445.AM2013-1345

Abstract 1349: Genetic variants in DNA repair pathway genes are associated with the risk of esophageal adenocarcinoma.

Abstract Esophageal Cancer (EC) is one of the leading causes of cancer death in the world. Over 90% of ECs are either esophageal squamous cell carcinomas (ESCC) or adenocarcinomas (EAC). EAC is the fastest growing malignancy in the US in the past three decades. In this large case/control study, we aim to assess genetic susceptibility to EAC by investigating single nucleotide polymorphisms (SNPs) in DNA repair related pathways, including nuclear excision repair (NER), base excision repair (BER) and double-strand-break repair (DSBR). The study population included 513 Caucasian EAC cases 1499 Caucasian controls. Genotyping was performed by candidate gene approach and obtained from genome-wide association study (GWAS). A total of 464 SNPs (254 SNPs in 26 NER genes, 173 SNPs in 22 BER genes and 37 SNPs in 26 DSBR genes) were included in the final analysis. Among the top significant SNPs, SNP rs10258834 in RPA3 from the NER pathway contributed to over 30% increased EAC risk (OR=1.30, 95% CI=1.12-1.51, P=5.26x10−4), SNP rs3827392 in SMC1B from the DSBR pathway was associated with a 25% increased EAC risk (OR=1.25, 95% CI=1.07-1.47, P=4.80x10−3); whereas rs3135998 in LIG3 from the BER pathway was associated with a decreased risk of EAC (OR=0.73, 95% CI=0.59-0.90, P=3.87x10−3). Unfavorable genotype analysis was performed among those SNPs showing significant association (P&amp;lt;0.05) in individual SNP analysis. We found a strong cumulative effect overall or stratified by DNA repair sub-pathway. For example, individuals carrying 10-13 unfavorable genotypes in BER pathway exhibited a nearly four-fold increased EAC risk compared to those in the reference group with fewer than 5 unfavorable genotypes. Our results suggest that genetic variants in DNA repair pathways significantly modify EAC risk individually and jointly. The results from this study, if validated in independent populations, could potentially categorize population into different risk groups and identify high-risk individuals for cost-effective screening and early detection of this deadly disease. Citation Format: Yan Wang, Jaffer A. Ajani, Yuanqing Ye, Maosheng Huang, Xifeng Wu. Genetic variants in DNA repair pathway genes are associated with the risk of esophageal adenocarcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1349. doi:10.1158/1538-7445.AM2013-1349

The effect of copy number variation in the phase II detoxification genes UGT2B17 and UGT2B28 on colorectal cancer risk

Genetic polymorphisms in combination with the Western-style diet, physical inactivity, smoking, excessive alcohol consumption, and obesity have been hypothesized to affect colorectal cancer (CRC) risk. Metabolizers of environmental carcinogenic and endogenous compounds affecting CRC risk include the phase II detoxification UDP-glucuronosyltransferase (UGT) enzymes UGT2B17 and UGT2B28, which are 2 of the most commonly deleted genes in the genome. To study the effect of UGT2B17 and UGT2B28 copy number variation (CNV) on CRC risk, 665 Caucasian CRC cases and 621 Caucasian controls were genotyped who had completed extensive demographics and lifestyle questionnaires. A significant association between the UGT2B17 deletion genotype (0/0) and decreased CRC risk was found when the entire population was analyzed (P = .044). Stratification by sex yielded a decreased risk (P = .020) in men with the UGT2B17 deletion (0/0), but no association was observed in women (P = .724). A significant association between UGT2B17 (0/0) and decreased risk for rectal (P = .0065) but not colon cancer was found. No significant association was found between UGT2B28 CNV and CRC risk. The UGT2B17 deletion genotype (0/0) was associated with a decreased CRC risk in a Caucasian population. After sex stratification, the association was observed in men but not in women, which is consistent with previous findings that men have higher UGT2B17 expression and activity than women. Because UGT2B17 metabolizes certain nonsteroidal anti-inflammatory drugs and flavonoids with antioxidative properties, individuals with a gene deletion may have higher levels of these protective dietary components.

Exome sequencing overrides formal genetics: ASPM mutations in a case study of apparent X‐linked microcephalic intellectual deficit

Exome sequencing overrides formal genetics: <i><scp>ASPM</scp></i> mutations in a case study of apparent X‐linked microcephalic intellectual deficit

Association Between Celiac Disease and Iron Deficiency in Caucasians, but Not Non-Caucasians

Celiac disease is an increasingly recognized disorder in Caucasian populations of European origin. Little is known about its prevalence in non-Caucasians. Although it is thought to be a cause of iron-deficiency anemia, little is known about the extent to which celiac disease contributes to iron deficiency in Caucasians, and especially non-Caucasians. We analyzed samples collected from participants in the Hemochromatosis and Iron Overload Screening study to identify individuals with iron deficiency and to assess the frequency of celiac disease. We analyzed serum samples from white men (≥25 y) and women (≥50 y) who participated in the Hemochromatosis and Iron Overload Screening study; cases were defined as individuals with iron deficiency (serum ferritin level, ≤12 μg/L) and controls were those without (serum ferritin level, >100 μg/L in men and >50 μg/L in women). All samples also were analyzed for human recombinant tissue transglutaminase immunoglobulin A; positive results were confirmed by an assay for endomysial antibodies. Patients with positive results from both celiac disease tests were presumed to have untreated celiac disease, and those with a positive result from only 1 test were excluded from analysis. We analyzed HLA genotypes and frequencies of celiac disease between Caucasians and non-Caucasians with iron deficiency. Celiac disease occurred in 14 of 567 cases (2.5%) and in only 1 of 1136 controls (0.1%; Fisher exact test, P = 1.92 × 10(-6)). Celiac disease was more common in Caucasian cases (14 of 363; 4%) than non-Caucasian cases (0 of 204; P = .003). Only 1 Caucasian control and no non-Caucasian controls had celiac disease. The odds of celiac disease in individuals with iron deficiency was 28-fold (95% confidence interval, 3.7-212.8) that of controls; 13 of 14 cases with celiac disease carried the DQ2.5 variant of the HLA genotype. Celiac disease is associated with iron deficiency in Caucasians. Celiac disease is rare among non-Caucasians-even among individuals with features of celiac disease, such as iron deficiency. Celiac disease also is rare among individuals without iron deficiency. Men and postmenopausal women with iron deficiency should be tested for celiac disease.

Macrophage migration inhibitory factor gene polymorphisms in inflammatory bowel disease: An association study in New Zealand Caucasians and meta-analysis

To investigate the association of macrophage migration inhibitory factor (MIF) promoter polymorphisms with inflammatory bowel disease (IBD) risk. One thousand and six New Zealand Caucasian cases and 540 Caucasian controls were genotyped for the MIF SNP -173G > C (rs755622) and the repeat polymorphism CATT₅₋₈ (rs5844572) using a pre-designed TaqMan SNP assay and capillary electrophoresis, respectively. Data were analysed for single site and haplotype association with IBD risk and phenotype. Meta-analysis was employed, to assess cumulative evidence of association of MIF -173G > C with IBD. All published genotype data for MIF -173G > C in IBD were identified using PubMed and subsequently searching the references of all PubMed-identified studies. Imputed genotypes for MIF -173G > C were generated from the Wellcome Trust Case Control Consortium (and National Institute of Diabetes and Digestive and Kidney Diseases). Separate meta-analyses were performed on Caucasian Crohn's disease (CD) (3863 patients, 6031 controls), Caucasian ulcerative colitis (UC) (1260 patients, 1987 controls), and East Asian UC (416 patients and 789 controls) datasets using the Mantel-Haenszel method. The New Zealand dataset had 93% power, and the meta-analyses had 100% power to detect an effect size of OR = 1.40 at α = 0.05, respectively. In our New Zealand dataset, single-site analysis found no evidence of association of MIF polymorphisms with overall risk of CD, UC, and IBD or disease phenotype (all P values > 0.05). Haplotype analysis found the CATT₅/-173C haplotype occurred at a higher frequency in New Zealand controls compared to IBD patients (0.6 vs 0.01; P = 0.03, OR = 0.22; 95%CI: 0.05-0.99), but this association did not survive bonferroni correction. Meta-analysis of our New Zealand MIF -173G > C data with data from seven additional Caucasian datasets using a random effects model found no association of MIF polymorphisms with CD, UC, or overall IBD. Similarly, meta-analysis of all published MIF -173G > C data from East Asian datasets (416 UC patients, 789 controls) found no association of this promoter polymorphism with UC. We found no evidence of association of MIF promoter polymorphisms with IBD.

Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate-gene studies was associated in the full case-control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.

Genetic variants in the Fat and Obesity Associated (FTO) gene and risk of Alzheimer's disease.

BackgroundRecent studies showed that polymorphisms in the Fat and Obesity-Associated (FTO) gene have robust effects on obesity, obesity-related traits and endophenotypes associated with Alzheimer's disease (AD).MethodsWe used 1,877 Caucasian cases and controls from the NIA-LOAD study and 1,093 Caribbean Hispanics to further explore the association of FTO with AD. Using logistic regression, we assessed 42 SNPs in introns 1 and 2, the region previously reported to be associated with AD endophenotypes, which had been derived by genome-wide screenings. In addition, we performed gene expression analyses of neuropathologically confirmed AD cases and controls of two independent datasets (19 AD cases, 10 controls; 176 AD cases, 188 controls) using within- and between-group factors ANOVA of log10 transformed rank invariant normalized expression data.ResultsIn the NIALOAD study, one SNP was significantly associated with AD and three additional markers were close to significance (rs6499640, rs10852521, rs16945088, rs8044769, FDR p-value: 0.05<p<0.09). Two of the SNPs are in strong LD (D′>0.9) with the previously reported SNPs. In the Caribbean Hispanic dataset, we identified three SNPs (rs17219084, rs11075996, rs11075997, FDR p-value: 0.009<p<0.01) that were associated with AD. These results were confirmed by haplotype analyses and in a metaanalysis in which we included the ADNI dataset. FTO had a significantly lower expresssion in AD cases compared to controls in two independent datasets derived from human cortex and amygdala tissue, respectively (p = 2.18×10−5 and p<0.0001).ConclusionsOur data support the notion that genetic variation in Introns 1 and 2 of the FTO gene may contribute to AD risk.