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Deng C, Tang S, Huang X, Gao J, Tian J, Zhou X, Xie Y, Liao M, Mo Z, Wang Q. Identification of three novel loci of ALDH2 Gene for Serum Folate levels in a Male Chinese Population by Genome-Wide Association Study. Gene 2018; 674:121-126. [PMID: 29953918 DOI: 10.1016/j.gene.2018.06.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Serum folate is important in clinical researches and DNA synthesis and methylation. Some loci and genes that are associated with folate levels had been detected by genome-wide association studies (GWAS), such as rs1801133 in MTHFR and rs1979277 in SHMT1. Nevertheless, only a small part of variants has been clearly identified for serum folate. Hence, we conducted a GWAS to discover new inherited susceptibility and gene-environment interactions on serum folate concentration. MATERIALS AND METHODS In a healthy Chinese population of 1999 men, genotyping was performed using Illumina HumanOmni1-Quad BeadChip. Serum folate levels were measured by enzyme-linked immunosorbent assay (ELISA), pathway enrichment analysis and statistical analysis were performed by Database for Annotation, Visualization and Integrated Discovery (DAVID) and Statistic Package for Social Science (SPSS). RESULTS We validated that rs1801133 in MTHFR was significantly involved in serum folate (P = 4.21 × 10-19). Surprisingly, we discovered three novel loci rs3782886, rs671, and rs4646776 of ALDH2 gene were suggestively significantly associated with folate serum folate levels in the male population studied (P = 2.17 × 10-7, P = 3.60 × 10-7, P = 3.99 × 10-7, respectively) after adjusting for population stratification, BMI and age. Men with the AA genotype had significantly higher serum folate levels compared with men with the GG/AG genotype. But we found ALDH2 gene mutation no relation to part of environmental factors on serum folate levels. CONCLUSION In a male Chinese population, genome-wide association study discovered that three novel SNPs rs3782886, rs671 and rs4646776 of ALDH2 gene were suggestively significantly associated with serum folate levels.
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Affiliation(s)
- Caiwang Deng
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Shaomei Tang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Xiaoliang Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Jiamin Gao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Jiarong Tian
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Xianguo Zhou
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Yuanliang Xie
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Ming Liao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Department of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China.
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi Zhuang Autonomous Region 530021, China; Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Nanning, Guangxi Zhuang Autonomous Region 530021, China.
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Cummings D, Dowling KF, Silverstein NJ, Tanner AS, Eryilmaz H, Smoller JW, Roffman JL. A Cross-Sectional Study of Dietary and Genetic Predictors of Blood Folate Levels in Healthy Young Adults. Nutrients 2017; 9:nu9090994. [PMID: 28885600 PMCID: PMC5622754 DOI: 10.3390/nu9090994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/15/2017] [Accepted: 08/31/2017] [Indexed: 01/21/2023] Open
Abstract
Since 1998, the U.S. has mandated folic acid (FA) fortification of certain grain products to reduce the risk of neural tube defects. Folate intake and red blood cell (RBC) folate concentrations increased substantially post-intervention, although recent studies raise concerns about the level of ongoing benefit. This study investigated blood folate level determinants in healthy young adults, including intake of naturally occurring food folate, synthetic FA, and the interaction of naturally occurring food folate with a common missense variant in the FOLH1 gene thought to affect absorption. Participants (n = 265) completed the Diet History Questionnaire II, RBC folate testing, and were genotyped for the 484T>C FOLH1 variant. Men reported significantly greater intake of all folate sources except for supplemental FA, but RBC folate levels did not significantly differ by sex. Synthetic FA was a stronger predictor of RBC folate than naturally occurring food folate. In the largest racial group, synthetic FA and the interaction of FOLH1 genotype with naturally occurring food folate significantly predicted RBC folate, with the overall model accounting for 13.8% of the variance in RBC folate levels. Blood folate levels rely on a complex interaction of natural and synthetic folate intake as well as FOLH1 genotype.
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Affiliation(s)
- Daniel Cummings
- Department of Biopsychology, Tufts University, 419 Boston Ave, Medford, MA 02155, USA.
| | - Kevin F Dowling
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | - Noah J Silverstein
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | - Alexandra S Tanner
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | - Hamdi Eryilmaz
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
| | - Joshua L Roffman
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
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Burda P, Suormala T, Heuberger D, Schäfer A, Fowler B, Froese DS, Baumgartner MR. Functional characterization of missense mutations in severe methylenetetrahydrofolate reductase deficiency using a human expression system. J Inherit Metab Dis 2017; 40:297-306. [PMID: 27743313 DOI: 10.1007/s10545-016-9987-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
5,10-Methylenetetrahydrofolate reductase (MTHFR) catalyzes the NADPH-dependent reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as the cofactor. Severe MTHFR deficiency is the most common inborn error of folate metabolism, resulting in hyperhomocysteinemia and homocystinuria. Approximately 70 missense mutations have been described that cause severe MTHFR deficiency, however, in most cases their mechanism of dysfunction remains unclear. Few studies have investigated mutational specific defects; most of these assessing only activity levels from a handful of mutations using heterologous expression. Here, we report the in vitro expression of 22 severe MTHFR missense mutations and two known single nucleotide polymorphisms (p.Ala222Val, p.Thr653Met) in human fibroblasts. Significant reduction of MTHFR activity (<20 % of wild-type) was observed for five mutant proteins that also had highly reduced protein levels on Western blot analysis. The remaining mutations produced a spectrum of enzyme activity levels ranging from 22-122 % of wild-type, while the SNPs retained wild-type-like activity levels. We found increased thermolability for p.Ala222Val and seven disease-causing mutations all located in the catalytic domain, three of which also showed FAD responsiveness in vitro. By contrast, six regulatory domain mutations and two mutations clustering around the linker region showed increased thermostability compared to wild-type protein. Finally, we confirmed decreased affinity for NADPH in individual mutant enzymes, a result previously described in primary patient fibroblasts. Our expression study allows determination of significance of missense mutations in causing deleterious loss of MTHFR protein and activity, and is valuable in detection of aberrant kinetic parameters, but should not replace investigations in native material.
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Affiliation(s)
- Patricie Burda
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland
| | - Terttu Suormala
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland
| | - Dorothea Heuberger
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland
- Division of Surgical Research, University Hospital, CH-8091, Zurich, Switzerland
| | - Alexandra Schäfer
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland
| | - Brian Fowler
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland
| | - D Sean Froese
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland.
- Radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism, University Children's Hospital, CH-8032, Zurich, Switzerland.
- Radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland.
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4
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Bueno O, Molloy AM, Fernandez-Ballart JD, García-Minguillán CJ, Ceruelo S, Ríos L, Ueland PM, Meyer K, Murphy MM. Common Polymorphisms That Affect Folate Transport or Metabolism Modify the Effect of the MTHFR 677C > T Polymorphism on Folate Status. J Nutr 2016; 146:1-8. [PMID: 26561410 DOI: 10.3945/jn.115.223685] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/13/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Although combinations of biologically relevant polymorphic variants affect folate status, most studies have focused on the effects of individual polymorphisms; however, these effects may be altered by interactions between polymorphisms. OBJECTIVE We investigated the individual and combined effects of polymorphisms that affect folate transport or metabolism on folate status. METHODS The associations between the methylenetetrahydrofolate reductase (MTHFR) 677C > T, methionine transferase reductase (MTRR) 66A > G, MTRR 524C > T, 5,10-methylenetetrahydrofolate dehydrogenase-5,10-methylenetetrahydrofolate cyclohydrolase-10-formyltetrahydrofolate synthetase (MTHFD1) 1958G > A, MTHFD1 -105C > T, dihydrofolate reductase (DHFR) 19-bp insertion/deletion, and solute carrier family 19A, member 1 (SLC19A1) 80G > A polymorphisms and fasting plasma folate (PF), red cell folate (RCF), and plasma total homocysteine (tHcy) were tested by ANCOVA and Cox regression analysis in 781 Spanish adults. RESULTS Folate deficiency (PF <7 nmol/L) was observed in 18.8% of the participants. Geometric mean PF (nmol/L) was lower in MTHFR 677TT (10.0; 95% CI: 9.2, 11.9) compared with 677CC (12.4; 95% CI: 11.6, 13.2; P < 0.001). RCF (nmol/L) was lower in MTHFR 677TT (652; 95% CI: 611, 695) compared with 677CC (889; 95% CI: 851, 929; P < 0.001) and in SLC19A1 80AA (776; 95% CI: 733, 822) compared with 80GG (861; 95% CI: 815, 910; P < 0.01). RCF and tHcy (μmol/L) did not differ in MTHFR + MTRR 677TT/524TT compared with 677CC/524CC: 780 (95% CI: 647, 941) compared with 853 (95% CI: 795, 915; P = 0.99) and 10.2 (95% CI: 8.4, 12.3) compared with 8.9 (95% CI: 8.5, 9.4; P = 0.99), respectively. The RR of lowest-tertile RCF (≤680 nmol/L) was 2.1 (95% CI: 1.0, 4.5) for MTHFR + MTRR 677TT/66GG compared with 677CC/66AA, 2.2 (95% CI: 1.2, 4.1) for MTHFR + MTHFD1 677TT/1958AA compared with 677CC/1958GG, 2.9 (95% CI: 1.4, 6.0) for MTHFR + MTHFD1 677TT/-105TT compared with 677CC/-105CC, and 3.5 (95% CI: 1.5, 8.1) for MTHFR + SLC19A1 677TT/80AA compared with 677CC/80GG. Confining the analysis to the MTHFR 677TT genotype, the risk of lowest-tertile RCF was reduced for MTHFR + MTRR 677TT/66GG compared with 677TT/66AA (RR: 0.5; 95% CI: 0.3, 0.9). CONCLUSIONS Folate status was lower in the MTHFR 677TT and SLC19A1 80AA genotypes compared with corresponding reference genotypes. Low folate status risk associated with the MTHFR 677TT genotype varied depending on its combination with other polymorphisms.
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Affiliation(s)
- Olalla Bueno
- Area of Preventive Medicine and Public Health, Faculty of Medicine and Health Sciences, Pere Virgili Institute for Health Research, Rovira i Virgili University, Reus, Spain; Biomedical Research Network, Pathophysiology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Anne M Molloy
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Joan D Fernandez-Ballart
- Area of Preventive Medicine and Public Health, Faculty of Medicine and Health Sciences, Pere Virgili Institute for Health Research, Rovira i Virgili University, Reus, Spain; Biomedical Research Network, Pathophysiology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Carlos J García-Minguillán
- Area of Preventive Medicine and Public Health, Faculty of Medicine and Health Sciences, Pere Virgili Institute for Health Research, Rovira i Virgili University, Reus, Spain; Biomedical Research Network, Pathophysiology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Santiago Ceruelo
- Biomedical Research Network, Pathophysiology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Madrid, Spain; Primary Health Center, El Morell, Spain
| | - Lídia Ríos
- Primary Health Center, Cambrils, Tarragona, Spain
| | - Per M Ueland
- University of Bergen, Section of Pharmacology, Department of Clinical Science, Bergen, Norway; and
| | | | - Michelle M Murphy
- Area of Preventive Medicine and Public Health, Faculty of Medicine and Health Sciences, Pere Virgili Institute for Health Research, Rovira i Virgili University, Reus, Spain; Biomedical Research Network, Pathophysiology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Madrid, Spain;
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Burda P, Schäfer A, Suormala T, Rummel T, Bürer C, Heuberger D, Frapolli M, Giunta C, Sokolová J, Vlášková H, Kožich V, Koch HG, Fowler B, Froese DS, Baumgartner MR. Insights into Severe 5,10-Methylenetetrahydrofolate Reductase Deficiency: Molecular Genetic and Enzymatic Characterization of 76 Patients. Hum Mutat 2015; 36:611-21. [DOI: 10.1002/humu.22779] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Patricie Burda
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Alexandra Schäfer
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Terttu Suormala
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Till Rummel
- Department of Pediatrics; University Hospital; Münster D-48149 Germany
| | - Céline Bürer
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Dorothea Heuberger
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Michele Frapolli
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Cecilia Giunta
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - Jitka Sokolová
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Hana Vlášková
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Hans Georg Koch
- Department of Pediatrics; University Hospital; Münster D-48149 Germany
- Klinikum für Kinder- und Jugendmedizin; Klinikum Braunschweig; Braunschweig D-38118 Germany
| | - Brian Fowler
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
| | - D. Sean Froese
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases, University of Zurich; Switzerland
| | - Matthias R. Baumgartner
- Division of Metabolism and Children's Research Center; University Children's Hospital; Zurich CH-8032 Switzerland
- radiz - Rare Disease Initiative Zurich; Clinical Research Priority Program for Rare Diseases, University of Zurich; Switzerland
- Zurich Center for Integrative Human Physiology; University of Zurich; Switzerland
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6
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Sukla KK, Tiwari PK, Kumar A, Raman R. Low birthweight (LBW) and neonatal hyperbilirubinemia (NNH) in an Indian cohort: association of homocysteine, its metabolic pathway genes and micronutrients as risk factors. PLoS One 2013; 8:e71587. [PMID: 23936521 PMCID: PMC3735579 DOI: 10.1371/journal.pone.0071587] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/01/2013] [Indexed: 11/21/2022] Open
Abstract
Background & Aims Indian subcontinent has the highest child mortality rates along with a very high frequency of low birthweight (LBW). Folate and vitamin B12 (Vit-B12) are necessary during foetal development and their deficiency prevalence in Indians is very high. The objective of the present paper is to assess whether foetal homocysteine (Hcy)/folate metabolic pathway genes, their cofactors and homocysteine level independently (or collectively) predispose children to Low birth weight. Methods Cord blood was collected for the study. Frequency of 5 SNPs in 4-Hcy-pathway genes, and levels of Hcy, Vit-B12 and folate were evaluated. Results Of the 421 newborns recruited for the study, 38% showed low birth weight (<2.5kg) and 16% were preterm babies. 101 neonates developed neonatal hyperbilirubinemia (NNH). High prevalence of Vit-B12 (65%) and folate (27%) deficiency was observed in newborns along with hyperhomocystinemia (hypHcy-25%). Preterm delivery, micronutrient deficiency, hypHcy and MTHFR 677T SNP are associated as risk factor while G allele of TCN2 C776G is protective against LBW. MTHFR 677T allele and folate deficiency are also independent risk factors for NNH. Conclusion We record the highest incidence of Vit-B12, folate deficiency and elevated Hcy levels, of all the studies so far reported on neonates. These together with MTHFR 677T are potential risk factors for LBW. Association of impaired folate/Hcy metabolism with NNH is reported for the first time and the possible way of interaction is discussed. It appears that proper nutritional management during pregnancy would reduce the risk of complex clinical outcomes.
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Affiliation(s)
- Krishna Kishore Sukla
- Cytogenetics Laboratory, Department of Zoology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Centre for Genetic Disorders, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Pankaj Kumar Tiwari
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok Kumar
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rajiva Raman
- Cytogenetics Laboratory, Department of Zoology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Centre for Genetic Disorders, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- * E-mail:
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Wagner MJ. Rare-variant genome-wide association studies: a new frontier in genetic analysis of complex traits. Pharmacogenomics 2013; 14:413-24. [DOI: 10.2217/pgs.13.36] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies have, in the last few years, identified thousands of common genetic variants associated with common complex traits and diseases, implicating many genes not previously known to be involved in the biology of those traits. However, these variants have so far explained little of the population variance in trait values or disease susceptibility. As large-scale genome sequencing efforts have revealed the extent of genetic variation at the low end of the frequency range in human populations, the effects of rare variants have been proposed as an explanation of the ‘missing genetic variance.’ Improved technologies for genotyping rare variants, including inexpensive whole-genome and whole-exome sequencing and rare-variant genotyping chips, coupled with novel analytical methods, are making genome-wide scans for the effects of rare variants possible, and seem likely to usher in a new era in the genetic analysis of complex traits.
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Affiliation(s)
- Michael J Wagner
- Institute for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7361, USA
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