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Zhao JY, Qiao B, Duan WY, Gong XH, Peng QQ, Jiang SS, Lu CQ, Chen YJ, Shen HB, Huang GY, Jin L, Wang HY. Genetic variants reducing MTR gene expression increase the risk of congenital heart disease in Han Chinese populations. Eur Heart J 2013; 35:733-42. [DOI: 10.1093/eurheartj/eht221] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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152
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Grarup N, Sulem P, Sandholt CH, Thorleifsson G, Ahluwalia TS, Steinthorsdottir V, Bjarnason H, Gudbjartsson DF, Magnusson OT, Sparsø T, Albrechtsen A, Kong A, Masson G, Tian G, Cao H, Nie C, Kristiansen K, Husemoen LL, Thuesen B, Li Y, Nielsen R, Linneberg A, Olafsson I, Eyjolfsson GI, Jørgensen T, Wang J, Hansen T, Thorsteinsdottir U, Stefánsson K, Pedersen O. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. PLoS Genet 2013; 9:e1003530. [PMID: 23754956 PMCID: PMC3674994 DOI: 10.1371/journal.pgen.1003530] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/11/2013] [Indexed: 11/26/2022] Open
Abstract
Genome-wide association studies have mainly relied on common HapMap sequence variations. Recently, sequencing approaches have allowed analysis of low frequency and rare variants in conjunction with common variants, thereby improving the search for functional variants and thus the understanding of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined samples of 45,576 and 37,341 individuals with serum B12 and folate measurements, respectively. We found six novel loci associating with serum B12 (CD320, TCN2, ABCD4, MMAA, MMACHC) or folate levels (FOLR3) and confirmed seven loci for these traits (TCN1, FUT6, FUT2, CUBN, CLYBL, MUT, MTHFR). Conditional analyses established that four loci contain additional independent signals. Interestingly, 13 of the 18 identified variants were coding and 11 of the 13 target genes have known functions related to B12 and folate pathways. Contrary to epidemiological studies we did not find consistent association of the variants with cardiovascular diseases, cancers or Alzheimer's disease although some variants demonstrated pleiotropic effects. Although to some degree impeded by low statistical power for some of these conditions, these data suggest that sequence variants that contribute to the population diversity in serum B12 or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations. Genome-wide association studies have in recent years revealed a wealth of common variants associated with common diseases and phenotypes. We took advantage of the advances in sequencing technologies to study the association of low frequency and rare variants in conjunction with common variants with serum levels of vitamin B12 (B12) and folate in Icelanders and Danes. We found 18 independent signals in 13 loci associated with serum B12 or folate levels. Interestingly, 13 of the 18 identified variants are coding and 11 of the 13 target genes have known functions related to B12 and folate pathways. These data indicate that the target genes at all of the loci have been identified. Epidemiological studies have shown a relationship between serum B12 and folate levels and the risk of cardiovascular diseases, cancers, and Alzheimer's disease. We investigated association between the identified variants and these diseases but did not find consistent association.
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Affiliation(s)
- Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Camilla H. Sandholt
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tarunveer S. Ahluwalia
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Thomas Sparsø
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | - Karsten Kristiansen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lise Lotte Husemoen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | - Betina Thuesen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | | | - Rasmus Nielsen
- Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Allan Linneberg
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
| | - Isleifur Olafsson
- Landspitali, The National University Hospital of Iceland, Department of Clinical Biochemistry, Reykjavik, Iceland
| | | | - Torben Jørgensen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | - Jun Wang
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- University of Iceland Faculty of Medicine, Reykjavik, Iceland
| | - Kari Stefánsson
- deCODE Genetics, Reykjavik, Iceland
- University of Iceland Faculty of Medicine, Reykjavik, Iceland
- * E-mail: (K. Stefánsson); (O. Pedersen)
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
- Hagedorn Research Institute, Gentofte, Denmark
- Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (K. Stefánsson); (O. Pedersen)
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153
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van der Valk RJP, Kiefte-de Jong JC, Sonnenschein-van der Voort AMM, Duijts L, Hafkamp-de Groen E, Moll HA, Tiemeier H, Steegers EAP, Hofman A, Jaddoe VWV, de Jongste JC. Neonatal folate, homocysteine, vitamin B12 levels and methylenetetrahydrofolate reductase variants in childhood asthma and eczema. Allergy 2013; 68:788-95. [PMID: 23692062 DOI: 10.1111/all.12146] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To assess the associations of folate, homocysteine and vitamin B12 levels of children at birth and their methylenetetrahydrofolate reductase (MTHFR) variants with asthma and eczema in childhood. METHODS This study was embedded in a population-based prospective cohort study (n = 2,001). Neonatal cord blood folate, homocysteine and vitamin B12 levels were measured, and MTHFR C677T and A1298C genotyped. Wheezing and physician-diagnosed eczema were annually obtained by questionnaire until 4 years. At 6 years, we collected information on physician-diagnosed asthma ever and self-reported eczema ever, measured fractional exhaled nitric oxide (FeNO), and interrupter resistance (Rint). Data were analysed with generalized estimating equations or logistic regression: continuous outcomes with linear regression models. RESULTS Folate, homocysteine and vitamin B12 levels of children at birth were not associated with wheezing or eczema until 4 years, asthma and eczema ever, or FeNO or Rint at 6 years. In children carrying C677T mutations in MTHFR, higher folate levels were associated with an increased risk of eczema (repeated eczema until 4 years: OR 1.40 (95% CI 1.09-1.80) (SD change) P-interaction = 0.003, eczema ever at 6 years: OR 1.41 (0.97-2.03) P-interaction = 0.011). No interactions between MTHFR and child folate and homocysteine levels were observed for wheezing and asthma. CONCLUSIONS Folate, homocysteine and vitamin B12 levels of children at birth did not affect asthma- and eczema-related outcomes up to the age of 6 years. Further studies are warranted to establish the role of MTHFR variants in these associations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - A. Hofman
- Department of Epidemiology; Erasmus MC; Rotterdam; The Netherlands
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Chery C, Hehn A, Mrabet N, Oussalah A, Jeannesson E, Besseau C, Alberto JM, Gross I, Josse T, Gérard P, Guéant-Rodriguez RM, Freund JN, Devignes J, Bourgaud F, Peyrin-Biroulet L, Feillet F, Guéant JL. Gastric intrinsic factor deficiency with combined GIF heterozygous mutations and FUT2 secretor variant. Biochimie 2013; 95:995-1001. [PMID: 23402911 DOI: 10.1016/j.biochi.2013.01.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/30/2013] [Indexed: 11/27/2022]
Abstract
Several genome-wide association studies (GWAS) have identified a strong association between serum vitamin B12 and fucosyltransferase 2 (FUT2), a gene associated with susceptibility to Helicobacter pylori infection. Hazra et al. conducted a meta-analysis of three GWAS and found three additional loci in MUT, CUBN and TCN1. Other GWAS conducted in Italy and China confirmed the association for FUT2 gene. Alpha-2-fucosyltransferase (FUT2) catalyzes fucose addition to form H-type antigens in exocrine secretions. FUT2 non-secretor variant produces no secretion of H-type antigens and is associated with high-plasma vitamin B12 levels. This association was explained by the influence of FUT2 on H. pylori, which is a risk factor of gastritis, a main cause of vitamin B12 impaired absorption. However, we recently showed that H. pylori serology had no influence on FUT2 association with vitamin B12, in a large sample population, suggesting the involvement of an alternative mechanism. GIF is another gene associated with plasma levels of vitamin B12 and gastric intrinsic factor (GIF) is a fucosylated protein needed for B12 absorption. Inherited GIF deficiency produces B12 deficiency unrelated with gastritis. We report 2 families with heterozygous GIF mutation, 290T>C, M97T, with decreased binding affinity of GIF for vitamin B12 and one family with heterozygous GIF mutation 435_437delGAA, K145_N146delinsN and no B12 binding activity of mutated GIF. All cases with vitamin B12 deficit carried the FUT2 rs601338 secretor variant. Ulex europeus binding to GIF was influenced by FUT2 genotypes and GIF concentration was lower, in gastric juice from control subjects with the secretor genotype. GIF290C allele was reported in 5 European cases and no Africans among 1282 ambulatory subjects and was associated with low plasma vitamin B12 and anaemia in the single case bearing the FUT2 secretor variant. We concluded that FUT2 secretor variant worsens B12 status in cases with heterozygous GIF mutations by impairing GIF secretion, independently from H. pylori-related gastritis.
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Affiliation(s)
- Celine Chery
- Inserm-U954, National reference centre for inherited metabolic diseases, University Hospital Center, Nancy-Université, 54500 Vandoeuvre lès Nancy, France
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Kinoshita M, Numata S, Tajima A, Shimodera S, Imoto I, Ohmori T. Plasma total homocysteine is associated with DNA methylation in patients with schizophrenia. Epigenetics 2013; 8:584-90. [PMID: 23774737 PMCID: PMC3857338 DOI: 10.4161/epi.24621] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Schizophrenia (SCZ) is a devastating psychiatric disorder with a median lifetime prevalence rate of 0.7?0.8%. Elevated plasma total homocysteine has been suggested as a risk factor for SCZ, and various biological effects of hyperhomocysteinemia have been proposed to be relevant to the pathophysiology of SCZ. As increased attention is paid to aberrant DNA methylation in SCZ, homocysteine is attracting additional interest as a potential key substance. Homocysteine is formed in the methionine cycle, which is involved in one-carbon methyl group-transfer metabolism, and it acts as a methyl donor when it is converted to S-adenosyl-methionine. To date, no studies have examined the relationship between homocysteine and genome-wide DNA methylation in SCZ. We examined the relationship between plasma total homocysteine and DNA methylation patterns in the peripheral leukocytes of patients with SCZ (n = 42) using a quantitative high-resolution DNA methylation array (485,764 CpG sites). Significant homocysteine-related changes in DNA methylation were observed at 1,338 CpG sites that were located across whole gene regions, including promoters, gene bodies and 3?-untranslated regions. Of the 1,338 sites, 758 sites (56.6%) were located in the CpG islands (CGIs) and in the regions flanking CGIs (CGI: 15.8%; CGI shore: 28.2%; CGI shelf: 12.6%), and positive correlations between plasma total homocysteine and DNA methylation were observed predominantly at CpG sites in the CGIs. Our results suggest that homocysteine might play a role in the pathogenesis of SCZ via a molecular mechanism that involves alterations to DNA methylation.
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Affiliation(s)
- Makoto Kinoshita
- Department of Psychiatry; Course of Integrated Brain Sciences; Medical Informatics; Institute of Health Biosciences; The University of Tokushima Graduate School; Tokushima, Japan
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156
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MTHFR, MTR and MTRR polymorphisms and risk of chronic kidney disease in Japanese: cross-sectional data from the J-MICC Study. Int Urol Nephrol 2013; 45:1613-20. [PMID: 23595572 DOI: 10.1007/s11255-013-0432-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/27/2013] [Indexed: 01/21/2023]
Abstract
PURPOSE Chronic kidney disease (CKD) is well known as a strong risk factor for both of end-stage renal disease and cardiovascular disease. To clarify the associations of MTHFR, MTR, and MTRR polymorphisms with the risk of CKD in Japanese, we examined this association among Japanese subjects using cross-sectional data. METHODS The subjects for this analysis were 3,318 participants consecutively selected from the Japan Multi-institutional Collaborative Cohort (J-MICC) Study. The polymorphisms were genotyped by a multiplex polymerase chain reaction-based Invader assay. Age- and sex-adjusted odds ratio (aOR) of CKD with stage 3-5 was calculated for each genotype. RESULTS When those with MTHFR C677T C/C were defined as references, those with MTHFR C677T C/T and T/T demonstrated the aORs for CKD of 1.14 (95 % CI 0.93-1.40) and 1.39 (1.06-1.82), respectively. Marginally significantly decreased risk of CKD with increasing number of MTR A2756G G allele (p = 0.058) was observed. Stratified analyses by plasma folate low (<7.4 ng/ml) or high (≥7.4 ng/ml) suggested significantly higher OR of CKD for those with MTHFR C677T T/T and low serum folate with the aOR of 2.07 (95 % CI 1.30-3.31) compared with that for those with MTHFR C677T T/T and high serum folate. CONCLUSIONS The present study found a significant association between the subjects with the T/T genotype of MTHFR C677T polymorphism and the elevated risk of CKD, which may suggest the possibility of the risk evaluation and prevention of this potentially life-threatening disease based on genetic traits in the near future.
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157
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Fekih Mrissa N, Mrad M, Klai S, Zaouali J, Sayeh A, Mazigh C, Nsiri B, Machgoul S, Gritli N, Mrissa R. Association of methylenetetrahydrofolate reductase A1298C polymorphism but not of C677T with multiple sclerosis in Tunisian patients. Clin Neurol Neurosurg 2013; 115:1657-60. [PMID: 23523621 DOI: 10.1016/j.clineuro.2013.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 11/14/2012] [Accepted: 02/23/2013] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Multiple sclerosis (MS) is a chronic neurological disease characterized by central nervous system (CNS) inflammation and demyelination of nerve axons. The aim of this study was to investigate a possible association between the methylenetetrahydrofolate reductase (MTHFR) gene and multiple sclerosis in Tunisian patients. PATIENTS AND METHODS The genotyping of two missense variants of the methylenetetrahydrofolate reductase (MTHFR) gene, C677T and A1298C was performed in 80 multiple sclerosis patients and 200 healthy controls. RESULTS No significant differences were found in the frequency of the MTHFR C677T polymorphism between MS patients and healthy controls. However, the genotype prevalence of the missense variant MTHFR A1298C was significantly different between patients and controls (A/C: 55% versus 7%, p<10(-3); C/C: 13.75% versus 0%, p<10(-3), respectively). CONCLUSION Although our preliminary findings suggest no association between the MTHFR C677T variants and MS, there is evidence to suggest a significant association between the MTHFR A1298C polymorphisms and MS.
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Affiliation(s)
- Najiba Fekih Mrissa
- Laboratory of Molecular Biology, Department of Hematology, Military Hospital of Tunisia, Tunis, Tunisia.
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Assessment of plasma prothrombotic factors in patients with Buerger's disease. Blood Coagul Fibrinolysis 2013; 24:133-9. [PMID: 23358197 DOI: 10.1097/mbc.0b013e32835b7272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The pathogenesis of Buerger' disease (thrombangiitis obliterans; TAO) remains unknown, although a strong association with tobacco use has been established. Blood coagulation and fibrinolytic factors as well as selected clinical chemistry parameters have been evaluated in 37 patients with Buerger's disease. Median levels of prothrombotic factors were higher in patients with TAO than in healthy control: annexin V (P < 0.0003), factor VII (P < 0.0001), factor VIII (P < 0.0000001), factor XI (P < 0.000003), homocysteine (P < 0.014) and fibrinogen (P = 0.00007). Patients with Buerger's disease also showed higher median plasma levels of urokinase type plasminogen activator (uPA) (P < 0.000004), its receptor (uPAR) (P < 0.0008) and uPA complex with plasminogen activator inhibitor 1 (uPA-PAI-1) P < 0.000006). In contrast, plasma concentrations of apolipoprotein A and folic acid were lower in patients with TAO than in control (P < 0.004 and P < 0.0006; respectively). Higher plasminogen (P < 0.05) and cholesterol (P < 0.003), as well as lower folic acid (P < .0.05) levels were noted in the smokers group than in nonsmoking patients. We found higher plasminogen (P < 0.05), factor VII (P < 0.05), total lipids (P < 0.003), cholesterol (P < 0.05) and triglycerides (P < 0.002) levels in patients requiring surgical treatment for limb-threatening ischaemia than the patients treated only conservatively. These findings suggest an important role of haemostatic risk factors in the pathogenesis of Buerger's disease, with special regard to hyperhomocysteinemia that might be aggravated by low serum folic acid level. In patients with aggressive clinical course, disturbances in serum lipids were more pronounced. Further studies are warranted to establish whether diet supplementation of folic acid as well as normalization of lipids balance might influence the clinical course of TAO.
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159
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Leenders M, Bhattacharjee S, Vineis P, Stevens V, Bueno-de-Mesquita HB, Shu XO, Amundadottir L, Gross M, Tobias GS, Wactawski-Wende J, Arslan AA, Duell EJ, Fuchs CS, Gallinger S, Hartge P, Hoover RN, Holly EA, Jacobs EJ, Klein AP, Kooperberg C, LaCroix A, Li D, Mandelson MT, Olson SH, Petersen G, Risch HA, Yu K, Wolpin BM, Zheng W, Agalliu I, Albanes D, Boutron-Ruault MC, Bracci PM, Buring JE, Canzian F, Chang K, Chanock SJ, Cotterchio M, Gaziano JM, Giovanucci EL, Goggins M, Hallmans G, Hankinson SE, Hoffman-Bolton JA, Hunter DJ, Hutchinson A, Jacobs KB, Jenab M, Khaw KT, Kraft P, Krogh V, Kurtz RC, McWilliams RR, Mendelsohn JB, Patel AV, Rabe KG, Riboli E, Tjønneland A, Trichopoulos D, Virtamo J, Visvanathan K, Elena JW, Yu H, Zeleniuch-Jacquotte A, Stolzenberg-Solomon RZ. Polymorphisms in genes related to one-carbon metabolism are not related to pancreatic cancer in PanScan and PanC4. Cancer Causes Control 2013; 24:595-602. [PMID: 23334854 DOI: 10.1007/s10552-012-0138-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022]
Abstract
PURPOSE The evidence of a relation between folate intake and one-carbon metabolism (OCM) with pancreatic cancer (PanCa) is inconsistent. In this study, the association between genes and single-nucleotide polymorphisms (SNPs) related to OCM and PanCa was assessed. METHODS Using biochemical knowledge of the OCM pathway, we identified thirty-seven genes and 834 SNPs to examine in association with PanCa. Our study included 1,408 cases and 1,463 controls nested within twelve cohorts (PanScan). The ten SNPs and five genes with lowest p values (<0.02) were followed up in 2,323 cases and 2,340 controls from eight case-control studies (PanC4) that participated in PanScan2. The correlation of SNPs with metabolite levels was assessed for 649 controls from the European Prospective Investigation into Cancer and Nutrition. RESULTS When both stages were combined, we observed suggestive associations with PanCa for rs10887710 (MAT1A) (OR 1.13, 95 %CI 1.04-1.23), rs1552462 (SYT9) (OR 1.27, 95 %CI 1.02-1.59), and rs7074891 (CUBN) (OR 1.91, 95 %CI 1.12-3.26). After correcting for multiple comparisons, no significant associations were observed in either the first or second stage. The three suggested SNPs showed no correlations with one-carbon biomarkers. CONCLUSIONS This is the largest genetic study to date to examine the relation between germline variations in OCM-related genes polymorphisms and the risk of PanCa. Suggestive evidence for an association between polymorphisms and PanCa was observed among the cohort-nested studies, but this did not replicate in the case-control studies. Our results do not strongly support the hypothesis that genes related to OCM play a role in pancreatic carcinogenesis.
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Affiliation(s)
- Max Leenders
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK.
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Vitamin B-12 status during pregnancy and child's IQ at age 8: a Mendelian randomization study in the Avon longitudinal study of parents and children. PLoS One 2012; 7:e51084. [PMID: 23227234 PMCID: PMC3515553 DOI: 10.1371/journal.pone.0051084] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 11/01/2012] [Indexed: 11/19/2022] Open
Abstract
Vitamin B-12 is essential for the development and maintenance of a healthy nervous system. Brain development occurs primarily in utero and early infancy, but the role of maternal vitamin B-12 status during pregnancy on offspring cognitive function is unclear. In this study we assessed the effect of vitamin B-12 status in well-nourished pregnant women on the cognitive ability of their offspring in a UK birth cohort (ALSPAC). We then examined the association of SNPs in maternal genes FUT2 (rs492602) and TCN2 (rs1801198, rs9606756) that are related to plasma vitamin B-12, with offspring IQ. Observationally, there was a positive association between maternal vitamin B-12 intake and child’s IQ that was markedly attenuated after adjustment for potential confounders (mean difference in offspring IQ score per doubling of maternal B-12 intake, before adjustment: 2.0 (95% CI 1.3, 2.8); after adjustment: 0.7 (95% CI −0.04, 1.4)). Maternal FUT2 was weakly associated with offspring IQ: mean difference in IQ per allele was 0.9 (95% CI 0.1, 1.6). The expected effect of maternal vitamin B-12 on offspring IQ, given the relationships between SNPs and vitamin B-12, and SNPs and IQ was consistent with the observational result. Our findings suggest that maternal vitamin B-12 may not have an important effect on offspring cognitive ability. However, further examination of this issue is warranted.
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Tanwar VS, Chand MP, Kumar J, Garg G, Seth S, Karthikeyan G, Sengupta S. Common variant in FUT2 gene is associated with levels of vitamin B(12) in Indian population. Gene 2012. [PMID: 23201895 DOI: 10.1016/j.gene.2012.11.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vitamin B(12) is an essential micronutrient synthesized by microorganisms. Mammals including humans have evolved ways for transport and absorption of this vitamin. Deficiency of vitamin B(12) (either due to low intake or polymorphism in genes involved in absorption and intracellular transport of this vitamin) has been associated with various complex diseases. Genome-wide association studies have recently identified several common single nucleotide polymorphisms (SNPs) in fucosyl transferase 2 gene (FUT2) to be associated with levels of vitamin B(12)-the strongest association was with a non-synonymous SNP rs602662 in this gene. In the present study, we attempted to replicate the association of this SNP (rs602662) in an Indian population since a significant proportion has been reported to have low levels of vitamin B(12) in this population. A total of 1146 individuals were genotyped for this SNP using a single base extension method and association with levels of vitamin B(12) was assessed in these individuals. Regression analysis was performed to analyze the association considering various confounding factors like for age, sex, diet, hypertension, diabetes mellitus and coronary artery disease status. We found that the SNP rs602662 was significantly associated with the levels of vitamin B(12) (p value<0.0001). We also found that individuals adhering to a vegetarian diet with GG (homozygous major genotype) have significantly lower levels of vitamin B(12) in these individuals. Thus, our study reveals that vegetarian diet along with polymorphism in the FUT2 gene may contribute significantly to the high prevalence of vitamin B(12) deficiency in India.
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Affiliation(s)
- Vinay Singh Tanwar
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi-110007, India.
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Chowdhury S, Hobbs CA, MacLeod SL, Cleves MA, Melnyk S, James SJ, Hu P, Erickson SW. Associations between maternal genotypes and metabolites implicated in congenital heart defects. Mol Genet Metab 2012; 107:596-604. [PMID: 23059056 PMCID: PMC3523122 DOI: 10.1016/j.ymgme.2012.09.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/21/2012] [Accepted: 09/21/2012] [Indexed: 01/19/2023]
Abstract
BACKGROUND The development of non-syndromic congenital heart defects (CHDs) involves a complex interplay of genetics, metabolism, and lifestyle. Previous studies have implicated maternal single nucleotide polymorphisms (SNPs) and altered metabolism in folate-related pathways as CHD risk factors. OBJECTIVE We sought to discover associations between maternal SNPs and metabolites involved in the homocysteine, folate, and transsulfuration pathways, and determine if these associations differ between CHD cases and controls. DESIGN Genetic, metabolic, demographic, and lifestyle information was available for 335 mothers with CHD-affected pregnancies and 263 mothers with unaffected pregnancies. Analysis was conducted on 1160 SNPs, 13 plasma metabolites, and 2 metabolite ratios. A two-stage multiple linear regression was fitted to each combination of SNP and metabolite/ratio. RESULTS We identified 4 SNPs in the methionine adenosyltransferase II alpha (MAT2A) gene that were associated with methionine levels. Three SNPs in tRNA aspartic acid methyltransferase 1 (TRDMT1) gene were associated with total plasma folate levels. Glutamylcysteine (GluCys) levels were associated with multiple SNPs within the glutathione peroxidase 6 (GPX6) and O-6-methylguanine-DNA methyltransferase (MGMT) genes. The regression model revealed interactions between genotype and case-control status in the association of total plasma folate, total glutathione (GSH), and free GSH, to SNPs within the MGMT, 5,10-methenyltetrahydrofolate synthetase (MTHFS), and catalase (CAT) genes, respectively. CONCLUSIONS Our study provides further evidence that genetic variation within folate-related pathways accounts for inter-individual variability in key metabolites. We identified specific SNP-metabolite relationships that differed in mothers with CHD-affected pregnancies, compared to controls. Our results underscore the importance of multifactorial studies to define maternal CHD risk.
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Affiliation(s)
- Shimul Chowdhury
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
- Clinical Molecular Genetics Department, Providence Sacred Heart Medical Center, 101 W. Eighth Avenue, Spokane, WA 99204, USA
| | - Charlotte A. Hobbs
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stewart L. MacLeod
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Mario A. Cleves
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stepan Melnyk
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - S. Jill James
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Ping Hu
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stephen W. Erickson
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 4301 W. Markham Street, Slot 781, Little Rock, AR 72205, USA
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Rajagopalan P, Jahanshad N, Stein JL, Hua X, Madsen SK, Kohannim O, Hibar DP, Toga AW, Jack CR, Saykin AJ, Green RC, Weiner MW, Bis JC, Kuller LH, Riverol M, Becker JT, Lopez OL, Thompson PM. Common folate gene variant, MTHFR C677T, is associated with brain structure in two independent cohorts of people with mild cognitive impairment. NEUROIMAGE-CLINICAL 2012; 1:179-87. [PMID: 24179750 PMCID: PMC3757723 DOI: 10.1016/j.nicl.2012.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/30/2012] [Accepted: 09/26/2012] [Indexed: 02/05/2023]
Abstract
A commonly carried C677T polymorphism in a folate-related gene, MTHFR, is associated with higher plasma homocysteine, a well-known mediator of neuronal damage and brain atrophy. As homocysteine promotes brain atrophy, we set out to discover whether people carrying the C677T MTHFR polymorphism which increases homocysteine, might also show systematic differences in brain structure. Using tensor-based morphometry, we tested this association in 359 elderly Caucasian subjects with mild cognitive impairment (MCI) (mean age: 75 ± 7.1 years) scanned with brain MRI and genotyped as part of Alzheimer's Disease Neuroimaging Initiative. We carried out a replication study in an independent, non-overlapping sample of 51 elderly Caucasian subjects with MCI (mean age: 76 ± 5.5 years), scanned with brain MRI and genotyped for MTHFR, as part of the Cardiovascular Health Study. At each voxel in the brain, we tested to see where regional volume differences were associated with carrying one or more MTHFR ‘T’ alleles. In ADNI subjects, carriers of the MTHFR risk allele had detectable brain volume deficits, in the white matter, of up to 2–8% per risk T allele locally at baseline and showed accelerated brain atrophy of 0.5–1.5% per T allele at 1 year follow-up, after adjusting for age and sex. We replicated these brain volume deficits of up to 5–12% per MTHFR T allele in the independent cohort of CHS subjects. As expected, the associations weakened after controlling for homocysteine levels, which the risk gene affects. The MTHFR risk variant may thus promote brain atrophy by elevating homocysteine levels. This study aims to investigate the spatially detailed effects of this MTHFR polymorphism on brain structure in 3D, pointing to a causal pathway that may promote homocysteine-mediated brain atrophy in elderly people with MCI.
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Affiliation(s)
- Priya Rajagopalan
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
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164
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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165
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Theodoratou E, Montazeri Z, Hawken S, Allum GC, Gong J, Tait V, Kirac I, Tazari M, Farrington SM, Demarsh A, Zgaga L, Landry D, Benson HE, Read SH, Rudan I, Tenesa A, Dunlop MG, Campbell H, Little J. Systematic Meta-Analyses and Field Synopsis of Genetic Association Studies in Colorectal Cancer. J Natl Cancer Inst 2012; 104:1433-57. [DOI: 10.1093/jnci/djs369] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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166
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Aheman A, Luo HS, Gao F. Association of fucosyltransferase 2 gene variants with ulcerative colitis in Han and Uyghur patients in China. World J Gastroenterol 2012; 18:4758-64. [PMID: 23002346 PMCID: PMC3442215 DOI: 10.3748/wjg.v18.i34.4758] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 04/23/2012] [Accepted: 05/13/2012] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the contribution of fucosyltransferase 2 (FUT2) variants to the genetic susceptibility and clinical heterogeneity of ulcerative colitis (UC) between Han and Uyghur patients in Xinjiang, China. METHODS A total of 102 UC patients (53 Han patients including 22 men and 31 women, and 49 Uyghur patients including 25 men and 24 women; aged 48 ± 16 years) and 310 age- and sex-matched healthy controls were enrolled from January 2010 to May 2011 in Xinjiang People's Hospital of China. UC was diagnosed based on the clinical, endoscopic and histological findings following Lennard-Jones criteria. Blood samples were collected and genomic DNA was extracted by the routine laboratory methods. Polymerase chain reaction-sequence-based typing method was used to identify FUT2 variants rs281377, rs1047781, rs601338 and rs602662. Genotypic and allelic frequencies were documented and compared between the UC patients and the healthy controls. Genotypic frequencies were also compared between Han and Uyghur patients. Potential association of genetic variation and UC between Han and Uyghur patients was examined. RESULTS rs281377 was found significantly associated with UC in the Han population as compared with the controls (P = 0.011) while rs281377 was not associated with UC in the Uyghur population (P = 0.06). TT homozygous rs281377 frequencies were higher in the UC groups than in the controls (88.7% vs 68.7% and 55.1% vs 50.3%). rs1047781 was specifically associated with UC in the Uyghur population (P = 0.001), but not associated with UC in the Han population (P = 0.13). TT homozygous rs1047781 frequencies were lower in the UC groups than in the controls (9.5% vs 11.8% and 4.0% vs 6.7%). rs601338 was statistically related to UC in both populations (Han, P = 0.025; Uyghur, P = 8.33 × 10(-5)). AA homozygous rs601338 frequencies were lower in the UC groups than in the controls (0% vs 1.8% and 12.2% vs 13.4%). No association was found between rs602662 and UC in both Han and the Uyghur populations. Allelic analysis showed that rs281377 allele was significantly associated with UC in the Han population as compared with the controls [P = 0.001, odd ratio (OR) = 0.26], however, it was not associated with UC in the Uyghur population (P = 0.603, OR = 1.14), and rs1047781 allele was associated with UC in the Uyghur population (P = 0.001, OR = 0.029) while it was not associated with UC in the Han population (P = 0.074, OR = 0.62). Moreover, rs601338 was associated with UC in both Han (P = 0.005, OR = 0.1) and Uyghur populations (P = 0.002, OR = 0.43). Meta analysis showed that rs1047781 and rs601338 conferred risk of UC as compared with the controls [P = 0.005, OR = 0.47; P = 0.0003, OR = 0.35; 95% confidence interval (CI) = 0.31-0.72 and 0.21-0.58], but rs281377 and rs602662 showed no statistically significant differences between patients with UC and controls (P = 0.10, OR = 0.71; P = 0.68, OR = 0.09; 95% CI = 0.47-1.07 and 0.56-1.47). CONCLUSION Functionally relevant FUT2 gene variants are associated with UC, suggesting that they play a potential role in the pathogenesis of UC and may contribute to the clinical heterogeneity of UC between Han and Uyghur patients.
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167
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Clifford AJ, Chen K, McWade L, Rincon G, Kim SH, Holstege DM, Owens JE, Liu B, Müller HG, Medrano JF, Fadel JG, Moshfegh AJ, Baer DJ, Novotny JA. Gender and single nucleotide polymorphisms in MTHFR, BHMT, SPTLC1, CRBP2, CETP, and SCARB1 are significant predictors of plasma homocysteine normalized by RBC folate in healthy adults. J Nutr 2012; 142:1764-71. [PMID: 22833659 PMCID: PMC3417835 DOI: 10.3945/jn.112.160333] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Using linear regression models, we studied the main and 2-way interaction effects of the predictor variables gender, age, BMI, and 64 folate/vitamin B-12/homocysteine (Hcy)/lipid/cholesterol-related single nucleotide polymorphisms (SNP) on log-transformed plasma Hcy normalized by RBC folate measurements (nHcy) in 373 healthy Caucasian adults (50% women). Variable selection was conducted by stepwise Akaike information criterion or least angle regression and both methods led to the same final model. Significant predictors (where P values were adjusted for false discovery rate) included type of blood sample [whole blood (WB) vs. plasma-depleted WB; P < 0.001] used for folate analysis, gender (P < 0.001), and SNP in genes SPTLC1 (rs11790991; P = 0.040), CRBP2 (rs2118981; P < 0.001), BHMT (rs3733890; P = 0.019), and CETP (rs5882; P = 0.017). Significant 2-way interaction effects included gender × MTHFR (rs1801131; P = 0.012), gender × CRBP2 (rs2118981; P = 0.011), and gender × SCARB1 (rs83882; P = 0.003). The relation of nHcy concentrations with the significant SNP (SPTLC1, BHMT, CETP, CRBP2, MTHFR, and SCARB1) is of interest, especially because we surveyed the main and interaction effects in healthy adults, but it is an important area for future study. As discussed, understanding Hcy and genetic regulation is important, because Hcy may be related to inflammation, obesity, cardiovascular disease, and diabetes mellitus. We conclude that gender and SNP significantly affect nHcy.
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Affiliation(s)
- Andrew J. Clifford
- Department of Nutrition,To whom correspondence should be addressed. E-mail:
| | | | | | | | | | | | - Janel E. Owens
- Department of Nutrition,Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, CO
| | | | | | | | | | | | - David J. Baer
- Food Components and Health Laboratory, USDA, Beltsville, MD
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168
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Tanner SM, Sturm AC, Baack EC, Liyanarachchi S, de la Chapelle A. Inherited cobalamin malabsorption. Mutations in three genes reveal functional and ethnic patterns. Orphanet J Rare Dis 2012; 7:56. [PMID: 22929189 PMCID: PMC3462684 DOI: 10.1186/1750-1172-7-56] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/23/2012] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Inherited malabsorption of cobalamin (Cbl) causes hematological and neurological abnormalities that can be fatal. Three genes have been implicated in Cbl malabsorption; yet, only about 10% of ~400-500 reported cases have been molecularly studied to date. Recessive mutations in CUBN or AMN cause Imerslund-Gräsbeck Syndrome (IGS), while recessive mutations in GIF cause Intrinsic Factor Deficiency (IFD). IGS and IFD differ in that IGS usually presents with proteinuria, which is not observed in IFD. The genetic heterogeneity and numerous differential diagnoses make clinical assessment difficult. METHODS We present a large genetic screening study of 154 families or patients with suspected hereditary Cbl malabsorption. Patients and their families have been accrued over a period spanning >12 years. Systematic genetic testing of the three genes CUBN, AMN, and GIF was accomplished using a combination of single strand conformation polymorphism and DNA and RNA sequencing. In addition, six genes that were contenders for a role in inherited Cbl malabsorption were studied in a subset of these patients. RESULTS Our results revealed population-specific mutations, mutational hotspots, and functionally distinct regions in the three causal genes. We identified mutations in 126/154 unrelated cases (82%). Fifty-three of 126 cases (42%) were mutated in CUBN, 45/126 (36%) were mutated in AMN, and 28/126 (22%) had mutations in GIF. We found 26 undescribed mutations in CUBN, 19 in AMN, and 7 in GIF for a total of 52 novel defects described herein. We excluded six other candidate genes as culprits and concluded that additional genes might be involved. CONCLUSIONS Cbl malabsorption is found worldwide and genetically complex. However, our results indicate that population-specific founder mutations are quite common. Consequently, targeted genetic testing has become feasible if ethnic ancestry is considered. These results will facilitate clinical and molecular genetic testing of Cbl malabsorption. Early diagnosis improves the lifelong care required by these patients and prevents potential neurological long-term complications. This study provides the first comprehensive overview of the genetics that underlies the inherited Cbl malabsorption phenotype.
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Affiliation(s)
- Stephan M Tanner
- Human Cancer Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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169
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Pavlíková M, Sokolová J, Janosíková B, Melenovská P, Krupková L, Zvárová J, Kozich V. Rare allelic variants determine folate status in an unsupplemented European population. J Nutr 2012; 142:1403-9. [PMID: 22695967 DOI: 10.3945/jn.112.160549] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The role of folates as coenzymes in 1-carbon metabolism and the clinical consequences of disturbed folate metabolism are widely known. Folate status is a complex trait determined by both exogenous and endogenous factors. This study analyzed the association between 12 genetic variants and folate status in a Czech population with no folate fortification program. These 12 genetic variants were selected from 56 variant alleles found by resequencing the coding sequences and adjacent intronic regions of 6 candidate genes involved in folate metabolism or transport (FOLR1, FOLR2, FOLR3, MTHFR, PCFT, and RFC) from 29 individuals with low plasma and erythrocyte folate concentrations. Regression analyses of a cohort of 511 Czech controls not taking folate supplements revealed that only 2 variants in the MTHFR gene were associated with altered folate concentrations in plasma and/or erythrocytes. In our previous study, we observed that the common variant MTHFR c.665C > T (known as c.677C > T; p.A222V) was associated with decreased plasma folate concentrations. In the present study, we show in addition that the rare variant MTHFR c.1958C > T (p.T653M) is associated with significantly increased erythrocyte folate concentrations (P = 0.02). Multivariate regression analysis revealed that this uncommon variant, which is present in 2% of Czech control chromosomes, explains 0.9% of the total variability of erythrocyte folate concentrations; the magnitude of this effect size was comparable with that of the common MTHFR c.665C > T variant. This result indicates that the rare genetic variants may determine folate status to a similar extent as the common allelic variant.
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Affiliation(s)
- Markéta Pavlíková
- Department of Medical Informatics, Institute of Computer Science of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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170
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Abstract
Personalized nutrition has been traditionally based on the adjustment of food and diet according to individual needs and preferences. At present, this concept is being reinforced through the application of state-of-the-art high-throughput technologies to help understand the molecular mechanisms underlying a healthy state. This knowledge could enable the adjustment of general dietary recommendations to match the needs of specific population groups based on their molecular profiles. The optimal development of evidence-based nutritional guidance to promote health requires an adequate assessment of nutrient bioavailability, bioactivity, and bioefficacy. To achieve this, reliable information about exposure to nutrients, their intake, and functional effects is required; thus, the identification of valid biomarkers using standardized analytical procedures is necessary. Although some nutritional biomarkers are now successfully used (eg, serum retinol, zinc, ferritin, and folate), a comprehensive set to assess the nutritional status and metabolic conditions of nutritional relevance is not yet available. Also, there is very limited knowledge on how the extensive human genetic variability influences the interpretation of these biomarkers. In this context, nutrigenomics seems to be a promising approach to identify new biomarkers in nutrition, through an integrative application of transcriptomics, proteomics, metabolomics, epigenomics, and nutrigenetics in human nutritional research.
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171
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Homocysteinylated protein levels in internal mammary artery (IMA) fragments and its genotype-dependence. S-homocysteine-induced methylation modifications in IMA and aortic fragments. Mol Cell Biochem 2012; 369:235-46. [PMID: 22798153 DOI: 10.1007/s11010-012-1387-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 06/30/2012] [Indexed: 02/05/2023]
Abstract
The resistance of internal mammary artery (IMA) toward atherosclerosis is not well understood. In plasma, homocysteine (Hcy) occurs in reduced, oxidized, homocysteine thiolactone and a component of proteins as a result of N- or S-homocysteinylation. We evaluated S/N-homocysteinylated protein levels in IMA fragments of patients undergoing coronary artery bypass grafting, and whether they were affected by genetic common variants. We tested whether tHcy, Hcy-S-protein levels, genotypes or Hcy-induced methylation modifications were related to differences in iNOS, Ddah2, and eNOS gene expression between territories. A small percentage of Hcy-S-proteins were found in IMA fragments. The Mthfr C677T (rs1801133) and Pon-1 Leu55Met (rs854560) variants were associated with Hcy-S-proteins. We observed a gradual difference according to Hcy-S-protein levels in the methylation degree of the Ddah2 gene promoter in aortic, but not in IMA, fragments. No correlation between the degree of methylation and the Ddah2 gene expression levels was found in both types of analyzed fragments. Total Hcy but not Hcy-S-proteins correlated with iNOS promoter methylation. Analyzed variants seem to contribute to the in vivo Hcy binding properties to IMA. The contribution of the Hcy-derived methylation modifications to Ddah2 and eNOS gene expression seems to be tissue-specific and independent of the Ddah2/ADMA/eNOS pathway. Hcy-derived methylation modifications to the iNOS gene promoter contribute to a lesser extent to iNOS gene expression.
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172
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Zoldoš V, Novokmet M, Bečeheli I, Lauc G. Genomics and epigenomics of the human glycome. Glycoconj J 2012; 30:41-50. [PMID: 22648057 DOI: 10.1007/s10719-012-9397-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/11/2012] [Accepted: 05/14/2012] [Indexed: 12/17/2022]
Abstract
The majority of all proteins are glycosylated and glycans have numerous important structural, functional and regulatory roles in various physiological processes. While structure of the polypeptide part of a glycoprotein is defined by the sequence of nucleotides in the corresponding gene, structure of a glycan part results from dynamic interactions between hundreds of genes, their protein products and environmental factors. The composition of the glycome attached to an individual protein, or to a complex mixture of proteins, like human plasma, is stable within an individual, but very variable between individuals. This variability stems from numerous common genetic polymorphisms reflecting in changes in the complex biosynthetic pathway of glycans, but also from the interaction with the environment. Environment can affect glycan biosynthesis at the level of substrate availability, regulation of enzyme activity and/or hormonal signals, but also through gene-environment interactions. Epigenetics provides a molecular basis how the environment can modify phenotype of an individual. The epigenetic information (DNA methylation pattern and histone code) is especially vulnerable to environmental effects in the early intrauterine and neo-natal development and many common late-onset diseases take root already at that time. The evidences showing the link between epigenetics and glycosylation are accumulating. Recent progress in high-throughput glycomics, genomics and epigenomics enabled first epidemiological and genome-wide association studies of the glycome, which are presented in this mini-review.
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Affiliation(s)
- Vlatka Zoldoš
- University of Zagreb, Faculty of Science, Horvatovac 102a, Zagreb, Croatia.
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Mahfouz RA, Cortas NK, Charafeddine KM, Abdul Khalik RN, Sarieddine DS, Kadi RH, Daher RT. Correlation of methylenetetrahydrofolate reductase polymorphisms with homocysteine metabolism in healthy Lebanese adults. Gene 2012; 504:175-80. [PMID: 22652272 DOI: 10.1016/j.gene.2012.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 02/16/2012] [Accepted: 05/10/2012] [Indexed: 11/27/2022]
Abstract
Hyperhomocysteinemia is associated with several vascular and teratogenic conditions. Determinants of total homocysteine concentrations include genetic and nutritional factors. This study assesses the relation between homocysteine concentrations and MTHFR gene polymorphisms at two common alleles (C677T (rs1801133) and A1298C (rs1801131)) as well as other predictors of homocysteine (folate, vitamin B(12), body mass index (BMI), age, and gender) in a group of healthy Lebanese: 109 males and 124 females aged 17-55years. We used serum for the determination of homocysteine, folate and vitamin B(12) levels and blood drawn in EDTA tubes for molecular analysis of MTHFR polymorphisms. Hyperhomocysteinemia was present in 59/233 (25.3%) of the subjects, with male/female ratio of 1.95. Multivariable regression analysis showed that homocysteine levels were negatively related to folate and vitamin B(12) and positively related to male gender and C677T homozygosity; but not A1298C polymorphism, BMI or age. The prevalence of wild, heterozygous, and homozygous C677T genotypes was 45.0%, 43.3% and 11.6%, respectively; with a carrier frequency of 54.9% and allelic frequency of 33.3%. The A1298C genotypic prevalence was 39.5%, 30.9%, and 29.6% respectively; with a carrier frequency of 60.5% and allelic frequency of 45.1%. C677T/A1289C compound heterozygosity was present in 47/233 (20.2%) of volunteers. In this first pilot study, gender, folate, vitamin B(12) and C677T mutational status could explain around 32% of homocysteine variations. Future larger studies are recommended to investigate other predictors of homocysteine variation and combine them with markers explored in this and other studies, in order to evaluate their impact on vascular and/or congenital diseases.
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Affiliation(s)
- Rami A Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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174
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Abstract
BACKGROUND This review examines the associations between low vitamin B12 levels, neurodegenerative disease, and cognitive impairment. The potential impact of comorbidities and medications associated with vitamin B12 derangements were also investigated. In addition, we reviewed the evidence as to whether vitamin B12 therapy is efficacious for cognitive impairment and dementia. METHODS A systematic literature search identified 43 studies investigating the association of vitamin B12 and cognitive impairment or dementia. Seventeen studies reported on the efficacy of vitamin B12 therapy for these conditions. RESULTS Vitamin B12 levels in the subclinical low-normal range (<250 ρmol/L) are associated with Alzheimer's disease, vascular dementia, and Parkinson's disease. Vegetarianism and metformin use contribute to depressed vitamin B12 levels and may independently increase the risk for cognitive impairment. Vitamin B12 deficiency (<150 ρmol/L) is associated with cognitive impairment. Vitamin B12 supplements administered orally or parenterally at high dose (1 mg daily) were effective in correcting biochemical deficiency, but improved cognition only in patients with pre-existing vitamin B12 deficiency (serum vitamin B12 levels <150 ρmol/L or serum homocysteine levels >19.9 μmol/L). CONCLUSION Low serum vitamin B12 levels are associated with neurodegenerative disease and cognitive impairment. There is a small subset of dementias that are reversible with vitamin B12 therapy and this treatment is inexpensive and safe. Vitamin B12 therapy does not improve cognition in patients without pre-existing deficiency. There is a need for large, well-resourced clinical trials to close the gaps in our current understanding of the nature of the associations of vitamin B12 insufficiency and neurodegenerative disease.
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175
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Abstract
PURPOSE OF REVIEW This review focuses on recent developments and controversies in the diagnosis, consequences, and management of subclinical cobalamin deficiency (SCCD), which affects many elderly persons. RECENT FINDINGS Diagnosis of SCCD depends exclusively on biochemical tests whose individual limitations suggest that combinations of tests are needed, especially in epidemiologic research. The causes of SCCD are unknown in more than 60% of cases, which limits prognostic predictions and identification of health consequences. After years of varying, often inconclusive associations, new clinical trials suggest that homocysteine reduction by high doses of folic acid, cobalamin, and pyridoxine may reduce progression of structural brain changes and cognitive impairment, especially in predisposed individuals. The causative or contributory roles, if any, of SCCD itself in cognitive dysfunction require direct study. If the findings are confirmed, high-dose supplementation with three vitamins will probably be more effective than fortification of the diet. SUMMARY The story of SCCD, which is severalfold times more common in the elderly than clinical cobalamin deficiency but also differs from it in arising only infrequently from severe malabsorption and thus being less likely to progress, continues to evolve. Preventive benefits need to be confirmed and expanded, and will require fuller understanding of SCCD pathophysiology, natural history, and health consequences.
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Lin X, Lu D, Gao Y, Tao S, Yang X, Feng J, Tan A, Zhang H, Hu Y, Qin X, Kim ST, Peng T, Li L, Mo L, Zhang S, Trent JM, Mo Z, Zheng SL, Xu J, Sun J. Genome-wide association study identifies novel loci associated with serum level of vitamin B12 in Chinese men. Hum Mol Genet 2012; 21:2610-7. [PMID: 22367966 DOI: 10.1093/hmg/dds062] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Vitamin B12 (VitB12 or cobalamin) is an essential cofactor in several metabolic pathways. Clinically, VitB12 deficiency is associated with pernicious anemia, neurodegenerative disorder, cardiovascular disease and gastrointestinal disease. Although previous genome-wide association studies (GWAS) identified several genes, including FUT2, CUBN, TCN1 and MUT, that may influence VitB12 levels in European populations, common genetic determinants of VitB12 remain largely unknown, especially in Asian populations. Here we performed a GWAS in 1999 healthy Chinese men and replicated the top findings in an independent Chinese sample with 1496 subjects. We identified four novel genomic loci that were significantly associated with serum level of VitB12 at a genome-wide significance level of 5.00 × 10(-8). These four loci were MS4A3 (11q12.1; rs2298585; P= 2.64 × 10(-15)), CLYBL (13q32; rs41281112; P= 9.23 × 10(-10)), FUT6 (19p13.3; rs3760776; P= 3.68 × 10(-13)) and 5q32 region (rs10515552; P= 3.94 × 10(-8)). In addition, we also confirmed the association with the serum level of VitB12 for the previously reported FUT2 gene and identified one novel non-synonymous single-nucleotide polymorphism in FUT2 gene in this Chinese population (19q13.33; rs1047781; P= 3.62 × 10(-36)). The new loci identified offer new insights into the biochemical pathways involved in determining the serum level of VitB12 and provide opportunities to better delineate the role of VitB12 in health and disease.
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Affiliation(s)
- Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, School of Life Sciences, Fudan University, Shanghai, China
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177
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Oussalah A, Besseau C, Chery C, Jeannesson E, Guéant-Rodriguez RM, Anello G, Bosco P, Elia M, Romano A, Bronowicki JP, Gerard P, Paoli J, Avogbe PH, Chabi N, Sanni A, Amouzou E, Peyrin-Biroulet L, Guéant JL. Helicobacter pylori serologic status has no influence on the association between fucosyltransferase 2 polymorphism (FUT2 461 G->A) and vitamin B-12 in Europe and West Africa. Am J Clin Nutr 2012; 95:514-21. [PMID: 22237057 DOI: 10.3945/ajcn.111.016410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Genomewide association studies have shown a relation between plasma vitamin B-12 concentration and the 461G→A polymorphism of fucosyltransferase 2 (FUT2), a gene associated with susceptibility to Helicobacter pylori infection. OBJECTIVE We evaluated in 2 populations the association of FUT2 461 G→A polymorphism with vitamin B-12 and related metabolic markers and investigated whether the influence of FUT2 on H. pylori serology is part of the mechanisms that underlie these associations. DESIGN The study included 1282 ambulatory subjects from Europe and West Africa. Blood concentrations of vitamin B-12, folate, homocysteine, and methylmalonic acid were measured. Genotyping was performed by real-time polymerase chain reaction. H. pylori serology testing was performed by using ELISA. RESULTS In univariate analysis, FUT2 461 A/A genotype was associated with higher plasma vitamin B-12 concentration in the total population (P = 0.0007) as well as in Europe (P = 0.0009) and in West Africa (P = 0.0015). Positivity for H. pylori serology was higher in West Africa (P < 0.0001) and was not associated with low plasma vitamin B-12. The prevalence of H. pylori-positive patients did not differ among FUT2 461 G→A genotypes (P = 0.2068). In multivariate analysis, FUT2 461 G→A genotype (P = 0.0008), but not positive H. pylori serology, was an independent predictor of plasma vitamin B-12 concentration. CONCLUSION This study confirms the influence of FUT2 461 G→A polymorphism on plasma vitamin B-12 concentration and showed no influence of H. pylori serologic status on this association in ambulatory subjects from Europe and West Africa.
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Affiliation(s)
- Abderrahim Oussalah
- INSERM U, Cellular and Molecular Pathology in Nutrition, Henri Poincaré University Nancy, Vandoeuvre-lès-Nancy, France
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178
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Abstract
The vitamin folate functions within the cell as a carrier of one-carbon units. The requirement for one-carbon transfers is ubiquitous and all mammalian cells carry out folate dependent reactions. In recent years, low folate status has been linked to risk of numerous adverse health conditions throughout life from birth defects and complications of pregnancy to cardiovascular disease, cancer and cognitive dysfunction in the elderly. In many instances inadequate intake of folate seems to be the primary contributor but there is also evidence that an underlying genetic susceptibility can play a modest role by causing subtle alterations in the availability, metabolism or distribution of intermediates in folate related pathways. Folate linked one-carbon units are essential for DNA synthesis and repair and as a source of methyl groups for biological methylation reactions. The notion of common genetic variants being linked to risk of disease was relatively novel in 1995 when the first functional folate-related polymorphism was discovered. Numerous polymorphisms have now been identified in folate related genes and have been tested for functionality either as a modifier of folate status or as being associated with risk of disease. Moreover, there is increasing research into the importance of folate-derived one-carbon units for DNA and histone methylation reactions, which exert crucial epigenetic control over cellular protein synthesis. It is thus becoming clear that genetic aspects of folate metabolism are wide-ranging and may touch on events as disparate as prenatal imprinting to cancer susceptibility. This chapter will review the current knowledge in this area.
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Affiliation(s)
- Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland,
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179
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Collin SM, Metcalfe C, Palmer TM, Refsum H, Lewis SJ, Smith GD, Cox A, Davis M, Marsden G, Johnston C, Lane JA, Donovan JL, Neal DE, Hamdy FC, Smith AD, Martin RM. The causal roles of vitamin B(12) and transcobalamin in prostate cancer: can Mendelian randomization analysis provide definitive answers? INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2011; 2:316-327. [PMID: 22199995 PMCID: PMC3243448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 08/23/2011] [Indexed: 05/31/2023]
Abstract
Circulating vitamin B(12) (cobalamin/B(12)) and total transcobalamin (tTC) have been associated with increased and reduced risk, respectively, of prostate cancer. Mendelian randomization has the potential to determine whether these are causal associations. We estimated associations of single nucleotide polymorphisms in B(12)-related genes (MTR, MTRR, FUT2, TCN2, TCN1, CUBN, and MUT) with plasma concentrations of B(12), tTC, holo-transcobalamin, holo-haptocorrin, folate, and homocysteine and with prostate cancer risk in a case-control study (913 cases, 895 controls) nested within the UK-wide population-based ProtecT study of prostate cancer in men age 45-69 years. Instrumental variable (IV) analysis was used to estimate odds ratios for effects of B(12) and tTC on prostate cancer. We observed that B(12) was lower in men with FUT2 204G>A (rs492602), CUBN 758C>T (rs1801222) and MUT 1595G>A (rs1141321) alleles (P(trend)<0.001); tTC was lower in men with the TCN2 776C>G (rs1801198) allele (P(trend)<0.001). FUT2 204G>A and CUBN 758C>T were selected as instruments for B(12); TCN2 776C>G for tTC. Conventional and IV estimates for the association of log(e)(B(12)) with prostate cancer were: OR=1.17 (95% CI 0.90-1.51), P=0.2 and OR=0.60 (0.16-2.15), P=0.4, respectively. Conventional and IV estimates for the association of loge(tTC) with prostate cancer were: OR=0.81 (0.54-1.20), P=0.3 and OR=0.41 (0.13-1.32), P=0.1, respectively. Confidence intervals around the IV estimates in our study were too wide to allow robust inference. Sample size estimates based on our data indicated that Mendelian randomization in this context requires much larger studies or multiple genetic variants that explain all of the variance in the intermediate phenotype.
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180
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Zhou B, Shi J, Whittemore AS. Optimal methods for meta-analysis of genome-wide association studies. Genet Epidemiol 2011; 35:581-91. [PMID: 21922536 PMCID: PMC3197760 DOI: 10.1002/gepi.20603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/29/2011] [Accepted: 05/20/2011] [Indexed: 11/08/2022]
Abstract
Meta-analysis of genome-wide association studies involves testing single nucleotide polymorphisms (SNPs) using summary statistics that are weighted sums of site-specific score or Wald statistics. This approach avoids having to pool individual-level data. We describe the weights that maximize the power of the summary statistics. For small effect-sizes, any choice of weights yields summary Wald and score statistics with the same power, and the optimal weights are proportional to the square roots of the sites' Fisher information for the SNP's regression coefficient. When SNP effect size is constant across sites, the optimal summary Wald statistic is the well-known inverse-variance-weighted combination of estimated regression coefficients, divided by its standard deviation. We give simple approximations to the optimal weights for various phenotypes, and show that weights proportional to the square roots of study sizes are suboptimal for data from case-control studies with varying case-control ratios, for quantitative trait data when the trait variance differs across sites, for count data when the site-specific mean counts differ, and for survival data with different proportions of failing subjects. Simulations suggest that weights that accommodate intersite variation in imputation error give little power gain compared to those obtained ignoring imputation uncertainties. We note advantages to combining site-specific score statistics, and we show how they can be used to assess effect-size heterogeneity across sites. The utility of the summary score statistic is illustrated by application to a meta-analysis of schizophrenia data in which only site-specific P-values and directions of association are available.
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Affiliation(s)
- Baiyu Zhou
- Department of Health Research and Policy, Stanford University, Stanford, California
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University, Stanford, California
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181
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Pathway-based analysis of genetic susceptibility to cervical cancer in situ: HLA-DPB1 affects risk in Swedish women. Genes Immun 2011; 12:605-14. [PMID: 21716314 DOI: 10.1038/gene.2011.40] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have conducted a pathway-based analysis of genome-wide single-nucleotide polymorphism (SNP) data in order to identify genetic susceptibility factors for cervical cancer in situ. Genotypes derived from Affymetrix 500k or 5.0 arrays for 1076 cases and 1426 controls were analyzed for association, and pathways with enriched signals were identified using the SNP ratio test. The most strongly associated KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were Asthma (empirical P=0.03), Folate biosynthesis (empirical P=0.04) and Graft-versus-host disease (empirical P=0.05). Among the 11 top-ranking pathways were 6 related to the immune response with the common denominator being genes in the major histocompatibility complex (MHC) region on chromosome 6. Further investigation of the MHC revealed a clear effect of HLA-DPB1 polymorphism on disease susceptibility. At a functional level, DPB1 alleles associated with risk and protection differ in key amino-acid residues affecting peptide-binding motifs in the extracellular domains. The results illustrate the value of pathway-based analysis to mine genome-wide data, and point to the importance of the MHC region and specifically the HLA-DPB1 locus for susceptibility to cervical cancer.
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182
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Hozyasz KK, Mostowska A, Szaflarska-Poplawska A, Lianeri M, Jagodzinski PP. Polymorphic variants of genes involved in homocysteine metabolism in celiac disease. Mol Biol Rep 2011; 39:3123-30. [PMID: 21688148 PMCID: PMC3271217 DOI: 10.1007/s11033-011-1077-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 06/10/2011] [Indexed: 12/31/2022]
Abstract
Celiac disease (CD) is a polygenic chronic enteropathy conferring an increased risk for various nutrient deficiency states. Hyperhomocysteinemia is a frequent finding in CD and may be related to the development of venous thrombosis, cardiovascular disease, and stroke in untreated CD patients. Recently, a possible excess in the frequency of the MTHFR c.677C>T (rs1801133) gene variant in CD patients was reported. The purpose of this study was to determine if there exist differences in the distribution of polymorphic variants of genes involved in homocysteine/methyl group metabolism between CD patients and the general population. A set of 10 gene polymorphisms (MTHFR rs1801133, MTR rs1805087, MTHFD1 rs2236225, MTRR rs1801394, CBS 844ins68, BHMT1 rs7356530 and rs3733890, BHMT2 rs526264 and rs625879, and TCN2 rs1801198) was tested in 134 patients with CD and 160 matched healthy controls. The frequency of the MTR rs1805087 GG genotype in CD patients was lower than in controls (0.01 and 0.06, respectively), although statistical significance was not achieved (P = 0.06). For the other analyzed polymorphisms, there was no evidence of difference in both allelic and genotypic distribution between cases and controls. The exhaustive Multifactor Dimensionality Reduction analysis revealed no combination of interactive polymorphisms predicting the incidence of CD. In contrast to the well-documented clinical observations of increased risks of vascular disease in patients with longstanding untreated CD, in our group of patients no significant association with CD was found for all tested polymorphic variants of genes involved in homocysteine metabolism. These findings should be replicated in studies with a larger sample size.
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Affiliation(s)
- Kamil K Hozyasz
- Department of Pediatrics, Institute of Mother and Child, 17a Kasprzaka Street, 01-211 Warsaw, Poland.
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183
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Ding K, Kullo IJ. Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease. BMC MEDICAL GENETICS 2011; 12:55. [PMID: 21507254 PMCID: PMC3103418 DOI: 10.1186/1471-2350-12-55] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 04/20/2011] [Indexed: 01/11/2023]
Abstract
BACKGROUND We hypothesized that the frequencies of risk alleles of SNPs mediating susceptibility to cardiovascular diseases differ among populations of varying geographic origin and that population-specific selection has operated on some of these variants. METHODS From the database of genome-wide association studies (GWAS), we selected 36 cardiovascular phenotypes including coronary heart disease, hypertension, and stroke, as well as related quantitative traits (eg, body mass index and plasma lipid levels). We identified 292 SNPs in 270 genes associated with a disease or trait at P < 5 × 10⁻⁸. As part of the Human Genome-Diversity Project (HGDP), 158 (54.1%) of these SNPs have been genotyped in 938 individuals belonging to 52 populations from seven geographic areas. A measure of population differentiation, F(ST), was calculated to quantify differences in risk allele frequencies (RAFs) among populations and geographic areas. RESULTS Large differences in RAFs were noted in populations of Africa, East Asia, America and Oceania, when compared with other geographic regions. The mean global F(ST) (0.1042) for 158 SNPs among the populations was not significantly higher than the mean global F(ST) of 158 autosomal SNPs randomly sampled from the HGDP database. Significantly higher global F(ST) (P < 0.05) was noted in eight SNPs, based on an empirical distribution of global F(ST) of 2036 putatively neutral SNPs. For four of these SNPs, additional evidence of selection was noted based on the integrated Haplotype Score. CONCLUSION Large differences in RAFs for a set of common SNPs that influence risk of cardiovascular disease were noted between the major world populations. Pairwise comparisons revealed RAF differences for at least eight SNPs that might be due to population-specific selection or demographic factors. These findings are relevant to a better understanding of geographic variation in the prevalence of cardiovascular disease.
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Affiliation(s)
- Keyue Ding
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN 55905, USA
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester MN 55905, USA
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184
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Wheeler HE, Kim SK. Genetics and genomics of human ageing. Philos Trans R Soc Lond B Biol Sci 2011; 366:43-50. [PMID: 21115529 DOI: 10.1098/rstb.2010.0259] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Ageing in humans is typified by the decline of physiological functions in various organs and tissues leading to an increased probability of death. Some individuals delay, escape or survive much of this age-related decline and live past age 100. Studies comparing centenarians to average-aged individuals have found polymorphisms in genes that are associated with long life, including APOE and FOXOA3, which have been replicated many times. However, the associations found in humans account for small percentages of the variance in lifespan and many other gene associations have not been replicated in additional populations. Therefore, ageing is probably a highly polygenic trait. In humans, it is important to also consider differences in age-related decline that occur within and among tissues. Longitudinal data of age-related traits can be used in association studies to test for polymorphisms that predict how an individual will change over time. Transcriptional and genetic association studies of different tissues have revealed common and unique pathways involved in human ageing. Genomic convergence is a method that combines multiple types of functional genomic information such as transcriptional profiling, expression quantitative trait mapping and gene association. The genomic convergence approach has been used to implicate the gene MMP20 in human kidney ageing. New human genetics technologies are continually in development and may lead to additional breakthroughs in human ageing in the near future.
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Affiliation(s)
- Heather E Wheeler
- Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA
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185
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Böger CA, Chen MH, Tin A, Olden M, Köttgen A, de Boer IH, Fuchsberger C, O'Seaghdha CM, Pattaro C, Teumer A, Liu CT, Glazer NL, Li M, O'Connell JR, Tanaka T, Peralta CA, Kutalik Z, Luan J, Zhao JH, Hwang SJ, Akylbekova E, Kramer H, van der Harst P, Smith AV, Lohman K, de Andrade M, Hayward C, Kollerits B, Tönjes A, Aspelund T, Ingelsson E, Eiriksdottir G, Launer LJ, Harris TB, Shuldiner AR, Mitchell BD, Arking DE, Franceschini N, Boerwinkle E, Egan J, Hernandez D, Reilly M, Townsend RR, Lumley T, Siscovick DS, Psaty BM, Kestenbaum B, Haritunians T, Bergmann S, Vollenweider P, Waeber G, Mooser V, Waterworth D, Johnson AD, Florez JC, Meigs JB, Lu X, Turner ST, Atkinson EJ, Leak TS, Aasarød K, Skorpen F, Syvänen AC, Illig T, Baumert J, Koenig W, Krämer BK, Devuyst O, Mychaleckyj JC, Minelli C, Bakker SJ, Kedenko L, Paulweber B, Coassin S, Endlich K, Kroemer HK, Biffar R, Stracke S, Völzke H, Stumvoll M, Mägi R, Campbell H, Vitart V, Hastie ND, Gudnason V, Kardia SL, Liu Y, Polasek O, Curhan G, Kronenberg F, Prokopenko I, Rudan I, Ärnlöv J, Hallan S, Navis G, Parsa A, Ferrucci L, Coresh J, Shlipak MG, Bull SB, Paterson AD, Wichmann HE, Wareham NJ, Loos RJ, Rotter JI, Pramstaller PP, Cupples LA, Beckmann JS, Yang Q, Heid IM, Rettig R, Dreisbach AW, Bochud M, Fox CS, Kao W. CUBN is a gene locus for albuminuria. J Am Soc Nephrol 2011; 22:555-70. [PMID: 21355061 PMCID: PMC3060449 DOI: 10.1681/asn.2010060598] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 10/19/2010] [Indexed: 11/03/2022] Open
Abstract
Identification of genetic risk factors for albuminuria may alter strategies for early prevention of CKD progression, particularly among patients with diabetes. Little is known about the influence of common genetic variants on albuminuria in both general and diabetic populations. We performed a meta-analysis of data from 63,153 individuals of European ancestry with genotype information from genome-wide association studies (CKDGen Consortium) and from a large candidate gene study (CARe Consortium) to identify susceptibility loci for the quantitative trait urinary albumin-to-creatinine ratio (UACR) and the clinical diagnosis microalbuminuria. We identified an association between a missense variant (I2984V) in the CUBN gene, which encodes cubilin, and both UACR (P = 1.1 × 10(-11)) and microalbuminuria (P = 0.001). We observed similar associations among 6981 African Americans in the CARe Consortium. The associations between this variant and both UACR and microalbuminuria were significant in individuals of European ancestry regardless of diabetes status. Finally, this variant associated with a 41% increased risk for the development of persistent microalbuminuria during 20 years of follow-up among 1304 participants with type 1 diabetes in the prospective DCCT/EDIC Study. In summary, we identified a missense CUBN variant that associates with levels of albuminuria in both the general population and in individuals with diabetes.
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Affiliation(s)
- Carsten A. Böger
- Department of Internal Medicine II, University Medical Center Regensburg, Regensburg, Germany
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Adrienne Tin
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Matthias Olden
- Department of Internal Medicine II, University Medical Center Regensburg, Regensburg, Germany
- Department of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
| | - Anna Köttgen
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Renal Division, University Hospital of Freiburg, Freiburg, Germany
| | - Ian H. de Boer
- Division of Nephrology, University of Washington, Seattle, Washington
| | - Christian Fuchsberger
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Conall M. O'Seaghdha
- Division of Nephrology, Brigham and Women's Hospital and Harvard Medical School, Boston Massachusetts
| | - Cristian Pattaro
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health and NHLBI's Framingham Heart Study, Boston Massachusetts
| | - Nicole L. Glazer
- Cardiovascular Health Research Unit and Department of Biostatistics, University of Washington, Seattle, Washington
| | - Man Li
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | | | - Toshiko Tanaka
- Medstar Research Institute, Baltimore, Maryland
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
| | - Carmen A. Peralta
- Division of Nephrology, University of California, San Francisco Medical School and San Francisco VA Medical Center, San Francisco, California
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Shih-Jen Hwang
- NHLBI's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
| | | | | | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Albert V. Smith
- University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
| | - Kurt Lohman
- Department of Biostatistical Sciences, Wake Forest University, Division of Public Health Sciences, Winston-Salem, North Carolina
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland
| | - Barbara Kollerits
- Innsbruck Medical University, Division of Genetic Epidemiology, Innsbruck, Austria
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Thor Aspelund
- University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gudny Eiriksdottir
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland
| | - Alan R. Shuldiner
- University of Maryland School of Medicine, Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland
| | | | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nora Franceschini
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, Maryland
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland
| | - Muredach Reilly
- University of Pennsylvania Division of Cardiology, Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania
| | - Raymond R. Townsend
- University of Pennsylvania Renal Electrolyte and Hypertension Division, Philadelphia, Pennsylvania
| | - Thomas Lumley
- Cardiovascular Health Research Unit and Department of Biostatistics, University of Washington, Seattle, Washington
| | - David S. Siscovick
- Departments of Epidemiology and Medicine, University of Washington, Seattle, Washington
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington
| | - Bryan Kestenbaum
- Division of Nephrology, University of Washington, Seattle, Washington
| | - Talin Haritunians
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Vincent Mooser
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Dawn Waterworth
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Andrew D. Johnson
- NHLBI's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
| | - Jose C. Florez
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - James B. Meigs
- Department of General Internal Medicine, Massachussetts General Hospital, Boston, Massachusetts
| | - Xiaoning Lu
- Department of Biostatistics, Boston University School of Public Health and NHLBI's Framingham Heart Study, Boston Massachusetts
| | - Stephen T. Turner
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Tennille S. Leak
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Knut Aasarød
- St Olav University Hospital, Trondheim, Norway
- Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Frank Skorpen
- Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ann-Christine Syvänen
- Molecular Medicine, Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Illig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jens Baumert
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Koenig
- Zentrum für Innere Medizin, Klinik für Innere Medizin II - Kardiologie, Universitätsklinikum Ulm, Ulm, Germany
| | - Bernhard K. Krämer
- University Medical Centre Mannheim, 5th Department of Medicine, Mannheim, Germany
| | - Olivier Devuyst
- NEFR Unit Université Catholique de Louvain Medical School, Brussels, Belgium
| | | | - Cosetta Minelli
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Stephan J.L. Bakker
- Department of Internal Medicine, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Lyudmyla Kedenko
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Stefan Coassin
- Innsbruck Medical University, Division of Genetic Epidemiology, Innsbruck, Austria
| | - Karlhans Endlich
- Institute of Anatomy and Cell Biology, University of Greifswald, Greifswald, Germany
| | - Heyo K. Kroemer
- Institute of Pharmacology, University of Greifswald, Greifswald, Germany
| | - Reiner Biffar
- Clinic for Prosthodontic Dentistry, Gerostomatology and Material Science, University of Greifswald, Greifswald, Germany
| | - Sylvia Stracke
- Nephrology Clinic for Internal Medicine A, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | | | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, and Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland
| | - Nicholas D. Hastie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland
| | - Vilmundur Gudnason
- University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
| | - Sharon L.R. Kardia
- University of Michigan School of Public Health, Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Yongmei Liu
- Department of Biostatistical Sciences, Wake Forest University, Division of Public Health Sciences, Winston-Salem, North Carolina
| | | | - Gary Curhan
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florian Kronenberg
- Innsbruck Medical University, Division of Genetic Epidemiology, Innsbruck, Austria
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, and Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, United Kingdom
| | - Igor Rudan
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland
| | - Johan Ärnlöv
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Stein Hallan
- St Olav University Hospital, Trondheim, Norway
- Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Gerjan Navis
- Department of Internal Medicine, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - the CKDGen Consortium
- Department of Internal Medicine II, University Medical Center Regensburg, Regensburg, Germany
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Department of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
- Renal Division, University Hospital of Freiburg, Freiburg, Germany
- Division of Nephrology, University of Washington, Seattle, Washington
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Division of Nephrology, Brigham and Women's Hospital and Harvard Medical School, Boston Massachusetts
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- Department of Biostatistics, Boston University School of Public Health and NHLBI's Framingham Heart Study, Boston Massachusetts
- Cardiovascular Health Research Unit and Department of Biostatistics, University of Washington, Seattle, Washington
- University of Maryland School of Medicine, Baltimore, Maryland
- Medstar Research Institute, Baltimore, Maryland
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
- Division of Nephrology, University of California, San Francisco Medical School and San Francisco VA Medical Center, San Francisco, California
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- NHLBI's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
- Jackson State University, Jackson, Mississippi
- Loyola University, Maywood, Illinois
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
- Department of Biostatistical Sciences, Wake Forest University, Division of Public Health Sciences, Winston-Salem, North Carolina
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland
- Innsbruck Medical University, Division of Genetic Epidemiology, Innsbruck, Austria
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland
- University of Maryland School of Medicine, Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland
- University of Maryland School of Medicine, Baltimore, Maryland
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, Maryland
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland
- University of Pennsylvania Division of Cardiology, Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania
- University of Pennsylvania Renal Electrolyte and Hypertension Division, Philadelphia, Pennsylvania
- Departments of Epidemiology and Medicine, University of Washington, Seattle, Washington
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, and Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of General Internal Medicine, Massachussetts General Hospital, Boston, Massachusetts
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
- St Olav University Hospital, Trondheim, Norway
- Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Molecular Medicine, Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Zentrum für Innere Medizin, Klinik für Innere Medizin II - Kardiologie, Universitätsklinikum Ulm, Ulm, Germany
- University Medical Centre Mannheim, 5th Department of Medicine, Mannheim, Germany
- NEFR Unit Université Catholique de Louvain Medical School, Brussels, Belgium
- Center for Public Health Genomics, Charlottesville, Virginia
- Department of Internal Medicine, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
- Institute of Anatomy and Cell Biology, University of Greifswald, Greifswald, Germany
- Institute of Pharmacology, University of Greifswald, Greifswald, Germany
- Clinic for Prosthodontic Dentistry, Gerostomatology and Material Science, University of Greifswald, Greifswald, Germany
- Nephrology Clinic for Internal Medicine A, University of Greifswald, Greifswald, Germany
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
- Wellcome Trust Centre for Human Genetics, and Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
- University of Michigan School of Public Health, Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
- Gen-Info Ltd., Zagreb, Croatia
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
- University of Maryland School of Medicine, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology & Clinical Research, Johns Hopkins University, Baltimore, Maryland
- General Internal Medicine, University of California, San Francisco, San Francisco, California
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Prosserman Centre for Health Research, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Institute of Physiology, University of Greifswald, Greifswald, Germany
- University of Mississippi Division of Nephrology, University of Mississippi, Jackson, Mississippi
- University Institute of Social and Preventive Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, IUMSP, Lausanne, Switzerland; and
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Afshin Parsa
- University of Maryland School of Medicine, Baltimore, Maryland
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
| | - Josef Coresh
- Welch Center for Prevention, Epidemiology & Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Michael G. Shlipak
- General Internal Medicine, University of California, San Francisco, San Francisco, California
| | - Shelley B. Bull
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Prosserman Centre for Health Research, Toronto, Ontario, Canada
| | | | - on behalf of DCCT/EDIC
- Department of Internal Medicine II, University Medical Center Regensburg, Regensburg, Germany
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Department of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
- Renal Division, University Hospital of Freiburg, Freiburg, Germany
- Division of Nephrology, University of Washington, Seattle, Washington
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Division of Nephrology, Brigham and Women's Hospital and Harvard Medical School, Boston Massachusetts
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- Department of Biostatistics, Boston University School of Public Health and NHLBI's Framingham Heart Study, Boston Massachusetts
- Cardiovascular Health Research Unit and Department of Biostatistics, University of Washington, Seattle, Washington
- University of Maryland School of Medicine, Baltimore, Maryland
- Medstar Research Institute, Baltimore, Maryland
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland
- Division of Nephrology, University of California, San Francisco Medical School and San Francisco VA Medical Center, San Francisco, California
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- NHLBI's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
- Jackson State University, Jackson, Mississippi
- Loyola University, Maywood, Illinois
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Hjartavernd, Holtasmara, Kopavogur, Iceland
- Department of Biostatistical Sciences, Wake Forest University, Division of Public Health Sciences, Winston-Salem, North Carolina
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland
- Innsbruck Medical University, Division of Genetic Epidemiology, Innsbruck, Austria
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland
- University of Maryland School of Medicine, Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland
- University of Maryland School of Medicine, Baltimore, Maryland
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, Maryland
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland
- University of Pennsylvania Division of Cardiology, Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania
- University of Pennsylvania Renal Electrolyte and Hypertension Division, Philadelphia, Pennsylvania
- Departments of Epidemiology and Medicine, University of Washington, Seattle, Washington
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, and Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of General Internal Medicine, Massachussetts General Hospital, Boston, Massachusetts
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
- St Olav University Hospital, Trondheim, Norway
- Faculty of Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Molecular Medicine, Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Zentrum für Innere Medizin, Klinik für Innere Medizin II - Kardiologie, Universitätsklinikum Ulm, Ulm, Germany
- University Medical Centre Mannheim, 5th Department of Medicine, Mannheim, Germany
- NEFR Unit Université Catholique de Louvain Medical School, Brussels, Belgium
- Center for Public Health Genomics, Charlottesville, Virginia
- Department of Internal Medicine, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
- Institute of Anatomy and Cell Biology, University of Greifswald, Greifswald, Germany
- Institute of Pharmacology, University of Greifswald, Greifswald, Germany
- Clinic for Prosthodontic Dentistry, Gerostomatology and Material Science, University of Greifswald, Greifswald, Germany
- Nephrology Clinic for Internal Medicine A, University of Greifswald, Greifswald, Germany
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
- Wellcome Trust Centre for Human Genetics, and Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, United Kingdom
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland
- University of Michigan School of Public Health, Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
- Gen-Info Ltd., Zagreb, Croatia
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
- University of Maryland School of Medicine, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology & Clinical Research, Johns Hopkins University, Baltimore, Maryland
- General Internal Medicine, University of California, San Francisco, San Francisco, California
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Prosserman Centre for Health Research, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Institute of Physiology, University of Greifswald, Greifswald, Germany
- University of Mississippi Division of Nephrology, University of Mississippi, Jackson, Mississippi
- University Institute of Social and Preventive Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, IUMSP, Lausanne, Switzerland; and
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Ruth J.F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Peter P. Pramstaller
- Institute of Genetic Medicine, European Academy of Bolzano/Bozen (EURAC), Italy and Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health and NHLBI's Framingham Heart Study, Boston Massachusetts
| | - Jacques S. Beckmann
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Iris M. Heid
- Department of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rainer Rettig
- Institute of Physiology, University of Greifswald, Greifswald, Germany
| | - Albert W. Dreisbach
- University of Mississippi Division of Nephrology, University of Mississippi, Jackson, Mississippi
| | - Murielle Bochud
- University Institute of Social and Preventive Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, IUMSP, Lausanne, Switzerland; and
| | - Caroline S. Fox
- NHLBI's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - W.H.L. Kao
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, Maryland
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Piskac-Collier AL, Monroy C, Lopez MS, Cortes A, Etzel CJ, Greisinger AJ, Spitz MR, El-Zein RA. Variants in folate pathway genes as modulators of genetic instability and lung cancer risk. Genes Chromosomes Cancer 2011; 50:1-12. [PMID: 20842733 DOI: 10.1002/gcc.20826] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic instability plays a crucial role in cancer development. The genetic stability of the cell as well as DNA methylation status could be modulated by folate levels. Several studies suggested associations between polymorphisms in folate genes and alterations in protein expression and variations in serum levels of the folate. The objective of this study was to investigate the effect of folate pathway polymorphisms on modulating genetic instability and lung cancer risk. Genotyping of 5 SNPs in folate pathway genes and cytokinesis-blocked micronucleus cytome assay analysis (to determine the genetic instability at baseline and following NNK treatment) was conducted on 180 lung cancer cases and 180 age-, gender-, and smoking-matched controls. Our results showed that individually, folate pathway SNPs were not associated with cytogenetic damage or lung cancer risk. However, in a polygenic disease such as lung cancer, gene-gene interactions are expected to play an important role in determining the phenotypic variability of the diseases. We observed that interactions between MTHFR677, MTHFR1298, and SHMT polymorphisms may have a significant impact on genetic instability in lung cancer patients. With regard to cytogenetic alterations, our results showed that lymphocytes from lung cancer patients exposed to the tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone [NNK] had considerably increased frequency of cytogenetic damage in presence of MTHFR 677, MTHFR 1298, and SHMT allelic variants. These findings support the notion that significant interactions may potentially modulate the lung cancer susceptibility and alter the overall the repair abilities of lung cancer patients when exposed to tobacco carcinogens such as NNK.
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Affiliation(s)
- Amanda L Piskac-Collier
- Division of Cancer Prevention, Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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187
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Pernicious anemia - genetic insights. Autoimmun Rev 2011; 10:455-9. [PMID: 21296191 DOI: 10.1016/j.autrev.2011.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 01/28/2011] [Indexed: 01/09/2023]
Abstract
Pernicious anemia (PA) is a complex, autoimmune, multi-factorial disease. Rapid progress has been made in the understanding of susceptibility to a spectrum of other autoimmune diseases through genome wide association studies (GWAS). However, PA has been conspicuous by its absence from this work. Here, we examine the evidence that PA has a significant heritable component through epidemiological evidence and its co-occurrence with other autoimmune diseases. Further, we consider how knowledge of the genetic susceptibility to other autoimmune diseases may provide insight into the etiology of PA.
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McCrae RR, Scally M, Terracciano A, Abecasis GR, Costa PT. An alternative to the search for single polymorphisms: toward molecular personality scales for the five-factor model. J Pers Soc Psychol 2010; 99:1014-24. [PMID: 21114353 PMCID: PMC3200527 DOI: 10.1037/a0020964] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing evidence that personality traits are affected by many genes, all of which have very small effects. As an alternative to the largely unsuccessful search for individual polymorphisms associated with personality traits, the authors identified large sets of potentially related single nucleotide polymorphisms (SNPs) and summed them to form molecular personality scales (MPSs) with from 4 to 2,497 SNPs. Scales were derived from two thirds of a large (N = 3,972) sample of individuals from Sardinia who completed the Revised NEO Personality Inventory (P. T. Costa, Jr., & R. R. McCrae, 1992) and were assessed in a genomewide association scan. When MPSs were correlated with the phenotype in the remaining one third of the sample, very small but significant associations were found for 4 of the 5e personality factors when the longest scales were examined. These data suggest that MPSs for Neuroticism, Openness to Experience, Agreeableness, and Conscientiousness (but not Extraversion) contain genetic information that can be refined in future studies, and the procedures described here should be applicable to other quantitative traits.
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Affiliation(s)
- Robert R McCrae
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health (NIH), U.S. Department of Health and Human Services, Baltimore, Maryland, USA
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Wolpin BM, Kraft P, Xu M, Steplowski E, Olsson ML, Arslan AA, Bueno-de-Mesquita HB, Gross M, Helzlsouer K, Jacobs EJ, LaCroix A, Petersen G, Stolzenberg-Solomon RZ, Zheng W, Albanes D, Allen NE, Amundadottir L, Austin MA, Boutron-Ruault MC, Buring JE, Canzian F, Chanock SJ, Gaziano JM, Giovannucci EL, Hallmans G, Hankinson SE, Hoover RN, Hunter DJ, Hutchinson A, Jacobs KB, Kooperberg C, Mendelsohn JB, Michaud DS, Overvad K, Patel AV, Sanchéz MJ, Sansbury L, Shu XO, Slimani N, Tobias GS, Trichopoulos D, Vineis P, Visvanathan K, Virtamo J, Wactawski-Wende J, Watters J, Yu K, Zeleniuch-Jacquotte A, Hartge P, Fuchs CS. Variant ABO blood group alleles, secretor status, and risk of pancreatic cancer: results from the pancreatic cancer cohort consortium. Cancer Epidemiol Biomarkers Prev 2010; 19:3140-9. [PMID: 20971884 PMCID: PMC3005538 DOI: 10.1158/1055-9965.epi-10-0751] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Subjects with non-O ABO blood group alleles have increased risk of pancreatic cancer. Glycosyltransferase activity is greater for the A(1) versus A(2) variant, whereas O01 and O02 variants are nonfunctioning. We hypothesized: 1) A(1) allele would confer greater risk than A(2) allele, 2) protective effect of the O allele would be equivalent for O01 and O02 variants, 3) secretor phenotype would modify the association with risk. METHODS We determined ABO variants and secretor phenotype from single nucleotide polymorphisms in ABO and FUT2 genes in 1,533 cases and 1,582 controls from 12 prospective cohort studies. Adjusted odds ratios (OR) for pancreatic cancer were calculated using logistic regression. RESULTS An increased risk was observed in participants with A(1) but not A(2) alleles. Compared with subjects with genotype O/O, genotypes A(2)/O, A(2)/A(1), A(1)/O, and A(1)/A(1) had ORs of 0.96 (95% CI, 0.72-1.26), 1.46 (95% CI, 0.98-2.17), 1.48 (95% CI, 1.23-1.78), and 1.71 (95% CI, 1.18-2.47). Risk was similar for O01 and O02 variant O alleles. Compared with O01/O01, the ORs for each additional allele of O02, A(1), and A(2) were 1.00 (95% CI, 0.87-1.14), 1.38 (95% CI, 1.20-1.58), and 0.96 (95% CI, 0.77-1.20); P, O01 versus O02 = 0.94, A(1) versus A(2) = 0.004. Secretor phenotype was not an effect modifier (P-interaction = 0.63). CONCLUSIONS Among participants in a large prospective cohort consortium, ABO allele subtypes corresponding to increased glycosyltransferase activity were associated with increased pancreatic cancer risk. IMPACT These data support the hypothesis that ABO glycosyltransferase activity influences pancreatic cancer risk rather than actions of other nearby genes on chromosome 9q34.
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Affiliation(s)
- Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.
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Cheng PJ, Huang SY, Shaw SW, Chueh HY, Hsieh TT. Maternal Homocysteine Level and Markers Used in First-Trimester Screening for Fetal Down Syndrome. Reprod Sci 2010; 17:1130-1134. [DOI: 10.1177/1933719110378345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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191
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Fong CS, Shyu HY, Shieh JC, Fu YP, Chin TY, Wang HW, Cheng CW. Association of MTHFR, MTR, and MTRR polymorphisms with Parkinson's disease among ethnic Chinese in Taiwan. Clin Chim Acta 2010; 412:332-8. [PMID: 21070756 DOI: 10.1016/j.cca.2010.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 10/13/2010] [Accepted: 11/01/2010] [Indexed: 11/16/2022]
Abstract
BACKGROUND Influence of folate/homocysteine conversion is considered to be important in the pathogenesis of Parkinson's disease (PD). However, association of the folate metabolic pathway gene polymorphisms with PD susceptibility remains unclear. METHODS To test this possibility in PD, we conducted a hospital-based case-control study constituting 211 patients and 218 age- and sex-matched controls of ethnic Chinese in Taiwan. Genotyping assay was performed to screen for polymorphisms of the methylenetetrahydrofolate reductase (MTHFR C677T), methyltetrahydrofolate-homocysteine methyltransferase (MTR A2756G), and 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR A1049G and C1783T) genes and assess the association between these genotype polymorphisms and PD risk using logistic regression analysis. RESULTS Of these four non-synonymous polymorphisms, the MTRR 1049GG variant was significantly associated with PD susceptibility (OR=3.17, 95%CI=1.08-9.35). Furthermore, we stratified our patients based on the MTHFR 677TT genotype in different strata, a significant association between the joint effect of polymorphisms and PD risk was observed in those patients whose genotypes were MTRR A1049G/MTR A2756G or MTRR C1783T/MTR A2756G (P<0.05). CONCLUSION Our findings provide support for the synergistic effects of polymorphisms in the folate metabolic pathway genes in PD susceptibility; the increased PD risk would be more significant in carriers with the polymorphisms of MTHFR, MTR, and MTRR genes.
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Affiliation(s)
- Chin-Shih Fong
- Department of Neurology, Buddhist Dalin Tzu Chi General Hospital, Chiayi, Taiwan
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192
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Oh SH, Kim NK, Kim HS, Kim WC, Kim OJ. Plasma total homocysteine and the methylenetetrahydrofolate reductase 677C>T polymorphism do not contribute to the distribution of cervico-cerebral atherosclerosis in ischaemic stroke patients. Eur J Neurol 2010; 18:491-6. [DOI: 10.1111/j.1468-1331.2010.03188.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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193
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Pierce BL, Ahsan H, Vanderweele TJ. Power and instrument strength requirements for Mendelian randomization studies using multiple genetic variants. Int J Epidemiol 2010; 40:740-52. [PMID: 20813862 DOI: 10.1093/ije/dyq151] [Citation(s) in RCA: 792] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mendelian Randomization (MR) studies assess the causality of an exposure-disease association using genetic determinants [i.e. instrumental variables (IVs)] of the exposure. Power and IV strength requirements for MR studies using multiple genetic variants have not been explored. METHODS We simulated cohort data sets consisting of a normally distributed disease trait, a normally distributed exposure, which affects this trait and a biallelic genetic variant that affects the exposure. We estimated power to detect an effect of exposure on disease for varying allele frequencies, effect sizes and samples sizes (using two-stage least squares regression on 10,000 data sets-Stage 1 is a regression of exposure on the variant. Stage 2 is a regression of disease on the fitted exposure). Similar analyses were conducted using multiple genetic variants (5, 10, 20) as independent or combined IVs. We assessed IV strength using the first-stage F statistic. RESULTS Simulations of realistic scenarios indicate that MR studies will require large (n > 1000), often very large (n > 10,000), sample sizes. In many cases, so-called 'weak IV' problems arise when using multiple variants as independent IVs (even with as few as five), resulting in biased effect estimates. Combining genetic factors into fewer IVs results in modest power decreases, but alleviates weak IV problems. Ideal methods for combining genetic factors depend upon knowledge of the genetic architecture underlying the exposure. CONCLUSIONS The feasibility of well-powered, unbiased MR studies will depend upon the amount of variance in the exposure that can be explained by known genetic factors and the 'strength' of the IV set derived from these genetic factors.
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Affiliation(s)
- Brandon L Pierce
- Department of Health Studies, University of Chicago, Chicago, IL, USA.
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194
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Miyaki K. Genetic polymorphisms in homocysteine metabolism and response to folate intake: a comprehensive strategy to elucidate useful genetic information. J Epidemiol 2010; 20:266-70. [PMID: 20571252 PMCID: PMC3900785 DOI: 10.2188/jea.je20100042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homocysteine is a risk factor for atherosclerosis, and the level of homocysteine in plasma is known to be strongly influenced by genetic factors-not only rare variants, but also common polymorphisms. This report describes a comprehensive postgenomic strategy for elucidating useful genetic information about homocysteine metabolism. The standard method for gathering such information is the candidate gene approach, which is an effective method based on known biological information. After collecting evidence from independent research projects, a critical epidemiological review permits a determination as to whether a putative association is true or not. A genome-wide association study (GWAS), which requires no biological information, can identify new candidates and confirm associations suggested by the candidate gene approach. The importance of methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, which was shown in a randomized controlled trial conducted by the present author, and in other studies, was independently confirmed by a large-scale GWAS. GWASs have also identified new candidate genes, but these must be confirmed by independent studies. In homocysteine metabolism, the classical candidate gene approach was sufficiently robust to detect the true association. However, candidate markers newly discovered by GWAS need to be confirmed by well-designed epidemiological studies to determine their significance. International statements, such as CONSORT and STREGA, provide useful principles for conducting such research.
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Affiliation(s)
- Koichi Miyaki
- Division of Clinical Epidemiology, Department of Clinical Research and Informatics, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
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195
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Johansson I, Van Guelpen B, Hultdin J, Johansson M, Hallmans G, Stattin P. Validity of food frequency questionnaire estimated intakes of folate and other B vitamins in a region without folic acid fortification. Eur J Clin Nutr 2010; 64:905-13. [PMID: 20502473 DOI: 10.1038/ejcn.2010.80] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND/OBJECTIVES B vitamins have been implicated in major chronic diseases but results have been inconsistent. This study evaluated the accuracy of dietary intakes of folate, vitamin B12, riboflavin and vitamin B6 as measured by the Northern Sweden Food Frequency Questionnaire (FFQ) against repeated 24-h recalls (24HR) and plasma levels, taking into consideration the MTHFR 677C>T polymorphism. SUBJECTS/METHODS B vitamin intakes assessed by a semi-quantitative FFQ designed to measure the intake over the previous year were compared with those from 10 24HR, as well as to plasma levels of folate and vitamin B12, in randomly selected men (n=96) and women (n=99) aged 30-60 years. FFQ-based B-vitamin intakes were also compared with plasma levels of B-vitamins and with MTHFR 677C4T genotype in 878 men, aged 40-61 years. RESULTS Intakes of vitamins B12 and riboflavin were similar, whereas folate and B6 intakes were 16-27% higher, as estimated by FFQ versus 24HR. Spearman correlation coefficients between the two methods ranged from 0.31 to 0.63 (all P<or=0.002), and were lowest for vitamin B12. Intakes estimated by FFQ were correlated with plasma levels, but coefficients were lower (range: 0.13-0.33), particularly for vitamin B12 in men (0.15-0.18). Folate intake was not correlated with plasma levels in subjects with the MTHFR 677 T/T genotype. CONCLUSIONS The validity of the Northern Sweden FFQ for assessing B vitamin intake is similar to that of many other FFQs used in large-scale studies. The FFQ is suitable for ranking individuals by intake of folate, riboflavin, vitamin B6 and to a lesser extent vitamin B12.
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Affiliation(s)
- I Johansson
- Department of Odontology, Umeå University, Umeå, Sweden.
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196
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Cantor RM, Lange K, Sinsheimer JS. Prioritizing GWAS results: A review of statistical methods and recommendations for their application. Am J Hum Genet 2010; 86:6-22. [PMID: 20074509 DOI: 10.1016/j.ajhg.2009.11.017] [Citation(s) in RCA: 422] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/10/2009] [Accepted: 11/20/2009] [Indexed: 12/27/2022] Open
Abstract
Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. A substantial number of recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. This review is written from the viewpoint that findings from the GWAS provide preliminary genetic information that is available for additional analysis by statistical procedures that accumulate evidence, and that these secondary analyses are very likely to provide valuable information that will help prioritize the strongest constellations of results. We review and discuss three analytic methods to combine preliminary GWAS statistics to identify genes, alleles, and pathways for deeper investigations. Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable. Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact. Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases. Reviews of published methods with recommendations for their application are provided within the framework for each approach.
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197
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Abstract
To investigate genetic variants that affect iron concentrations in persons not affected by overt genetic disorders of iron metabolism, a genome-wide association study was conducted in the InCHIANTI Study (N = 1206) and the Baltimore Longitudinal Study of Aging (N = 713). The top 2 single-nucleotide polymorphisms were examined for replication in the Women's Health and Aging Study (WHAS) I and II (N = 569). The single-nucleotide polymorphism most strongly associated with lower serum iron concentration was rs4820268 (P = 5.12 x 10(-9)), located in exon 13 of the transmembrane protease serine 6 (TMPRSS6) gene, an enzyme that promotes iron absorption and recycling by inhibiting hepcidin antimicrobial peptide transcription. The allele associated with lower iron concentrations was also associated with lower hemoglobin levels, smaller red cells, and more variability in red cell size (high red blood cell distribution width). Our results confirm the association of TMPRSS6 variants with iron level and provide further evidence of association with other anemia-related phenotypes.
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198
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Hazra A, Kraft P, Lazarus R, Chen C, Chanock SJ, Jacques P, Selhub J, Hunter DJ. Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. Hum Mol Genet 2009; 18:4677-87. [PMID: 19744961 DOI: 10.1093/hmg/ddp428] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Low plasma B-vitamin levels and elevated homocysteine have been associated with cancer, cardiovascular disease and neurodegenerative disorders. Common variants in FUT2 on chromosome 19q13 were associated with plasma vitamin B12 levels among women in a genome-wide association study in the Nurses' Health Study (NHS) NCI-Cancer Genetic Markers of Susceptibility (CGEMS) project. To identify additional loci associated with plasma vitamin B12, homocysteine, folate and vitamin B6 (active form pyridoxal 5'-phosphate, PLP), we conducted a meta-analysis of three GWA scans (total n = 4763, consisting of 1658 women in NHS-CGEMS, 1647 women in Framingham-SNP-Health Association Resource (SHARe) and 1458 men in SHARe). On chromosome 19q13, we confirm the association of plasma vitamin B12 with rs602662 and rs492602 (P-value = 1.83 x 10(-15) and 1.30 x 10(-14), respectively) in strong linkage disequilibrium (LD) with rs601338 (P = 6.92 x 10(-15)), the FUT2 W143X nonsense mutation. We identified additional genome-wide significant loci for plasma vitamin B12 on chromosomes 6p21 (P = 4.05 x 10(-08)), 10p12 (P-value=2.87 x 10(-9)) and 11q11 (P-value=2.25 x 10(-10)) in genes with biological relevance. We confirm the association of the well-studied functional candidate SNP 5,10-methylene tetrahydrofolate reductase (MTHFR) Ala222Val (dbSNP ID: rs1801133; P-value=1.27 x 10(-8)), on chromosome 1p36 with plasma homocysteine and identify an additional genome-wide significant locus on chromosome 9q22 (P-value=2.06 x 10(-8)) associated with plasma homocysteine. We also identified genome-wide associations with variants on chromosome 1p36 with plasma PLP (P-value=1.40 x 10(-15)). Genome-wide significant loci were not identified for plasma folate. These data reveal new biological candidates and confirm prior candidate genes for plasma homocysteine, plasma vitamin B12 and plasma PLP.
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Affiliation(s)
- Aditi Hazra
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.
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199
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Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study. Blood 2009; 114:1417-22. [PMID: 19525478 DOI: 10.1182/blood-2009-04-215269] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Total plasma homocysteine concentration (tHcy) is a biomarker for atherothrombotic disease, but causality remains uncertain. Polymorphisms in the genes involved in methionine metabolism explain only a small fraction of the heritability of tHcy levels. In a genome-wide association study, we examined the genetic determinants of tHcy using a 2-stage design. First, 283 437 single nucleotide polymorphisms (SNPs) were tested for association with tHcy in 387 persons recruited from 21 large Spanish families. Of those, 17 SNPs showed equal or stronger association with tHcy level compared with the MTHFR 677C>T SNP (beta = 0.10, P = .0001). Second, a replication analysis of these 17 SNPs was performed in patients with premature myocardial infarction (n = 1238). Novel associations were found for SNPs near the ZNF366 gene (lead SNP rs7445013; discovery stage: adjusted beta = -0.12, P = 5.30 x 10(-6), replication stage: adjusted beta = -0.13, P = .004) and the PTPRD gene (lead SNP rs973117; discovery stage: adjusted beta = 0.11, P = 5.5 x 10(-6), replication stage: adjusted beta = 0.10, P = .005). These associations were independent of known confounders, including creatinine clearance and plasma fibrinogen concentration. Our findings implicate novel pathways in homocysteine metabolism, and highlight the need for investigation of the associated genes in the etiology of vascular diseases.
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