51
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Genetic Risk Factors for Complex Forms of Alzheimer’s Disease. NEURODEGENER DIS 2018. [DOI: 10.1007/978-3-319-72938-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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52
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Martorell-Marugan J, Toro-Dominguez D, Alarcon-Riquelme ME, Carmona-Saez P. MetaGenyo: a web tool for meta-analysis of genetic association studies. BMC Bioinformatics 2017; 18:563. [PMID: 29246109 PMCID: PMC5732412 DOI: 10.1186/s12859-017-1990-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/06/2017] [Indexed: 11/26/2022] Open
Abstract
Background Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. Results We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. Conclusions MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/. Electronic supplementary material The online version of this article (10.1186/s12859-017-1990-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Daniel Toro-Dominguez
- Bioinformatics Unit, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Medical Genomics, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Marta E Alarcon-Riquelme
- Medical Genomics, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pedro Carmona-Saez
- Bioinformatics Unit, Centre for Genomics and Oncological Research (GENYO), Granada, Spain.
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53
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Hussein A, Askar E, Badawy A, Saad K, Zahran A, Elderwy AA. Impact of cytokine genetic polymorphisms on the risk of renal parenchymal infection in children. J Pediatr Urol 2017; 13:593.e1-593.e10. [PMID: 28716390 DOI: 10.1016/j.jpurol.2017.05.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 05/24/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Acute pyelonephritis is associated with renal scarring in up to 30% of patients. Renal scarring may cause significant long-term morbidity. The pathogenesis of acute pyelonephritis remains unclear, although it involves interaction among uroepithelium, the immune system cells, and the locally produced cytokines. That some UTI-prone children develop acute pyelonephritis, and eventually renal parenchymal scarring, suggests a genetic role. Interleukin-6, interleukin-8, chemokine receptor-1 (CXCR1), and tumor necrosis factor-alpha (TNFα), the key regulators of the host immune responses, are proteins whose secretion is controlled by genes. We postulated that functional polymorphic variants of their genes might have a role in APN susceptibility. OBJECTIVES We sought to investigate a possible association of the common functional polymorphisms in genes encoding IL-6, IL-8, CXCR1, and TNFα with the risk of APN in children. METHODS Urine culture was used to diagnose 300 children with UTI, of mean age of 51.31 ± 37.4 months (2-180 months). 99Tc-DMSA scans diagnosed 86 children with APN. Follow-up scans identified new renal scars in 18 children. Six functional single-nucleotide polymorphisms (SNPs) in genes encoding IL-6, IL-8, CXCR1, and TNFα were genotyped in all subjects (IL-6 rs1800795 (-174G/C), IL-6 rs1800796 (-572G/C), IL-8 rs2227306 (781C/T), IL8 rs4073 (-251A/T), CXCR1 rs2234671 (2607G/C), and TNFα rs1800629 (-308G/A)). RESULTS TT genotype of IL-8 -251A/T polymorphism was significantly higher in APN patients (26.7%) than those with lower UTI (11.7%, p = 0.01) and control individuals (12.2%, p = 0.002). T allele was significantly more common in APN than in lower UTI (p = 0.025) and was significantly more common in APN (46%) than in the controls (p = 0.001). Similarly, TT genotype of IL-8 781C/T polymorphism was significantly more common in APN patients (31.4%) than those with lower UTI (17.3%, p = 0.003) and the controls (14.3%, p = 0.001). T allele was significantly more common in APN (55%) than lower UTI (40%, p = 0.005) and controls (37%, p = 0.001). However, IL-8 -251A/T and +781C/T SNPs did not qualify as an independent risk for parenchymal infection (OR 1.9, 95% CI 0.68-2.6, p = 0.13 and OR 2.3, 95% CI 0.89-3.7, p = 0.091, respectively). Lower UTI did not differ from the controls. The frequency of the genotypes and alleles of IL-6, CXCR1, and TNFα SNPs did not differ significantly among the different groups of the study. CONCLUSION IL-8 -251A/T and +781C/T SNPs are associated with susceptibility to renal parenchymal infection in children and could be implicated in APN risk. However, none of these variants could clearly and independently predict this risk.
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Affiliation(s)
- Almontaser Hussein
- Pediatric Nephrology, Children's Hospital, Assiut University, Egypt; Genetic Unit, Children's Hospital, Assiut University, Egypt.
| | - Eman Askar
- Children's Hospital, Assiut University, Egypt
| | - Ahlam Badawy
- Pediatric Nephrology, Children's Hospital, Assiut University, Egypt
| | - Khaled Saad
- Children's Hospital, Assiut University, Egypt
| | - Asmaa Zahran
- Clinical Pathology, SECI, Assiut University, Egypt
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Kingsmore SF, Lindquist IE, Mudge J, Beavis WD. Genome-Wide Association Studies: Progress in Identifying Genetic Biomarkers in Common, Complex Diseases. Biomark Insights 2017. [DOI: 10.1177/117727190700200019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Novel, comprehensive approaches for biomarker discovery and validation are urgently needed. One particular area of methodologic need is for discovery of novel genetic biomarkers in complex diseases and traits. Here, we review recent successes in the use of genome wide association (GWA) approaches to identify genetic biomarkers in common human diseases and traits. Such studies are yielding initial insights into the allelic architecture of complex traits. In general, it appears that complex diseases are associated with many common polymorphisms, implying profound genetic heterogeneity between affected individuals.
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Affiliation(s)
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM 87505, U.S.A
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55
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Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H. Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline. Cancer Inform 2017. [DOI: 10.1177/117693510600200025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An important issue in current medical science research is to find the genes that are strongly related to an inherited disease. A particular focus is placed on cancer-gene relations, since some types of cancers are inherited. As bio-medical databases have grown speedily in recent years, an informatics approach to predict such relations from currently available databases should be developed. Our objective is to find implicit associated cancer-genes from biomedical databases including the literature database. Co-occurrence of biological entities has been shown to be a popular and efficient technique in biomedical text mining. We have applied a new probabilistic model, called mixture aspect model (MAM) [ 48 ], to combine different types of co-occurrences of genes and cancer derived from Medline and OMIM (Online Mendelian Inheritance in Man). We trained the probability parameters of MAM using a learning method based on an EM (Expectation and Maximization) algorithm. We examined the performance of MAM by predicting associated cancer gene pairs. Through cross-validation, prediction accuracy was shown to be improved by adding gene-gene co-occurrences from Medline to cancer-gene co-occurrences in OMIM. Further experiments showed that MAM found new cancer-gene relations which are unknown in the literature. Supplementary information can be found at http://www.bic.kyotou.ac.jp/pathway/zhusf/CancerInformatics/Supplemental2006.html
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Affiliation(s)
- Shanfeng Zhu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
| | - Yasushi Okuno
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Gozoh Tsujimoto
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Hiroshi Mamitsuka
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
- Graduate School of Pharmaceutical Sciences, Kyoto University
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56
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Association Analysis of Arsenic-Induced Straighthead in Rice ( Oryza sativa L.) Based on the Selected Population with a Modified Model. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7641362. [PMID: 28812021 PMCID: PMC5547723 DOI: 10.1155/2017/7641362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/04/2017] [Indexed: 11/17/2022]
Abstract
A rice physiological disorder makes mature panicle keep erect with empty grains termed as "straighthead." Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead. Three of them, RM263, RM169, and RM224, were consistent with a previous study. Three markers, RM475, RM263, and RM19, had a resistant allele associated with a decrease in straighthead rating (straighthead rating ≤ 4.8). In contrast, the two other marker loci RM169 and RM224 had a few susceptible alleles associated with an increase in straighthead rating (straighthead rating ≥ 8.7). Interestingly, RM475 is close to QTL "qSH-2" and "AsS" with straighthead resistance, which was reported in two studies on linkage mapping of straighthead. This finding adds to previous work and is useful for further genetic study of straighthead.
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57
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Abstract
There is a great deal of interest in personalized, individualized, or precision interventions for disease and health-risk mitigation. This is as true of nutrition-based intervention and prevention strategies as it is for pharmacotherapies and pharmaceutical-oriented prevention strategies. Essentially, technological breakthroughs have enabled researchers to probe an individual's unique genetic, biochemical, physiological, behavioral, and exposure profile, allowing them to identify very specific and often nuanced factors that an individual might possess, which may make it more or less likely that he or she responds favorably to a particular intervention (e.g., nutrient supplementation) or disease prevention strategy (e.g., specific diet). However, as compelling and intuitive as personalized nutrition might be in the current era in which data-intensive biomedical characterization of individuals is possible, appropriately and objectively vetting personalized nutrition strategies is not trivial and requires novel study designs and data analytical methods. These designs and methods must consider a very integrated use of the multiple contemporary biomedical assays and technologies that motivate them, which adds to their complexity. Single-subject or N-of-1 trials can be used to assess the utility of personalized interventions and, in addition, can be crafted in such a way as to accommodate the necessarily integrated use of many emerging biomedical technologies and assays. In this review, we consider the motivation, design, and implementation of N-of-1 trials in translational nutrition research that are meant to assess the utility of personalized nutritional strategies. We provide a number of example studies, discuss appropriate analytical methods given the complex data they generate and require, and consider how such studies could leverage integration of various biomarker assays and clinical end points. Importantly, we also consider the development of strategies and algorithms for matching nutritional needs to individual biomedical profiles and the issues surrounding them. Finally, we discuss the limitations of personalized nutrition studies, possible extensions of N-of-1 nutritional intervention studies, and areas of future research.
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Affiliation(s)
- Nicholas J Schork
- Translational Genomics Research Institute, Phoenix, Arizona 85004; .,J. Craig Venter Institute, La Jolla, California 92037; .,Departments of Psychiatry and Family Medicine and Public Health, University of California, San Diego, La Jolla, California 92037
| | - Laura H Goetz
- J. Craig Venter Institute, La Jolla, California 92037; .,Department of Surgery, Scripps Clinic Medical Group, La Jolla, California 92037.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037
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58
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Park JH, Jang H, Jung YK, Jung YL, Shin I, Cho DY, Park HG. A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosens Bioelectron 2017; 91:122-127. [DOI: 10.1016/j.bios.2016.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/21/2023]
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59
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Patil P, Peng RD, Leek JT. What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2017; 11:539-44. [PMID: 27474140 DOI: 10.1177/1745691616646366] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment.
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Affiliation(s)
- Prasad Patil
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | - Roger D Peng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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60
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MTHFR and MTHFD1 gene polymorphisms are not associated with pseudoexfoliation syndrome in South Indian population. Int Ophthalmol 2017; 38:599-606. [DOI: 10.1007/s10792-017-0498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/08/2017] [Indexed: 12/29/2022]
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61
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Cairó O. Assessing Relevance of External Cognitive Measures. Front Integr Neurosci 2017; 11:3. [PMID: 28270753 PMCID: PMC5319308 DOI: 10.3389/fnint.2017.00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Abstract
The arrival of modern brain imaging technologies has provided new opportunities for examining the biological essence of human intelligence as well as the relationship between brain size and cognition. Thanks to these advances, we can now state that the relationship between brain size and intelligence has never been well understood. This view is supported by findings showing that cognition is correlated more with brain tissues than sheer brain size. The complexity of cellular and molecular organization of neural connections actually determines the computational capacity of the brain. In this review article, we determine that while genotypes are responsible for defining the theoretical limits of intelligence, what is primarily responsible for determining whether those limits are reached or exceeded is experience (environmental influence). Therefore, we contend that the gene-environment interplay defines the intelligent quotient of an individual.
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Affiliation(s)
- Osvaldo Cairó
- Department of Computer Science, Instituto Tecnológico Autónomo de México (ITAM) Mexico City, Mexico
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62
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Genetics of inflammatory bowel disease: beyond NOD2. Lancet Gastroenterol Hepatol 2017; 2:224-234. [PMID: 28404137 DOI: 10.1016/s2468-1253(16)30111-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 01/11/2023]
Abstract
The study of the genetic underpinnings of inflammatory bowel disease has made great progress since the identification of NOD2 as a major susceptibility gene. Novel genotyping and sequencing technologies have led to the discovery of 242 common susceptibility loci, 45 of which have been fine-mapped to statistically conclusive causal variants; 50 genes associated with very-early-onset inflammatory disease have been identified. The evolving genetic architecture of inflammatory bowel disease has deepened our understanding of its pathogenesis through identification of major disease associated pathways-knowledge that has the potential to indicate novel drug targets or markers for personalised medicine. However, many causal variants have yet to be identified, and a large proportion of missing heritability still needs to be accounted for. In addition, the medical and scientific communities are probably not yet fully harnessing the power of these genetic discoveries.
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63
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Knief U, Schielzeth H, Backström N, Hemmrich‐Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W. Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations. Mol Ecol 2017; 26:1285-1305. [DOI: 10.1111/mec.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Population Ecology Friedrich Schiller University Jena 07743 Jena Germany
| | - Niclas Backström
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | | | - Michael Wittig
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Simon C. Griffith
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
- School of Biological, Earth & Environmental Sciences University of New South Wales Sydney NSW 2057 Australia
| | - Hans Ellegren
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
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64
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Oliveira-Paula GH, Lacchini R, Tanus-Santos JE. Clinical and pharmacogenetic impact of endothelial nitric oxide synthase polymorphisms on cardiovascular diseases. Nitric Oxide 2017; 63:39-51. [DOI: 10.1016/j.niox.2016.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 12/30/2022]
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65
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Pandit E, Tasleem S, Barik SR, Mohanty DP, Nayak DK, Mohanty SP, Das S, Pradhan SK. Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:552. [PMID: 28487705 PMCID: PMC5404645 DOI: 10.3389/fpls.2017.00552] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/27/2017] [Indexed: 05/05/2023]
Abstract
Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR) and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7-21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.
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66
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Shim S, Kim J, Jung W, Shin IS, Bae JM. Meta-analysis for genome-wide association studies using case-control design: application and practice. Epidemiol Health 2016; 38:e2016058. [PMID: 28092928 PMCID: PMC5309730 DOI: 10.4178/epih.e2016058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 12/18/2016] [Indexed: 01/16/2023] Open
Abstract
This review aimed to arrange the process of a systematic review of genome-wide association studies in order to practice and apply a genome-wide meta-analysis (GWMA). The process has a series of five steps: searching and selection, extraction of related information, evaluation of validity, meta-analysis by type of genetic model, and evaluation of heterogeneity. In contrast to intervention meta-analyses, GWMA has to evaluate the Hardy-Weinberg equilibrium (HWE) in the third step and conduct meta-analyses by five potential genetic models, including dominant, recessive, homozygote contrast, heterozygote contrast, and allelic contrast in the fourth step. The 'genhwcci' and 'metan' commands of STATA software evaluate the HWE and calculate a summary effect size, respectively. A meta-regression using the 'metareg' command of STATA should be conducted to evaluate related factors of heterogeneities.
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Affiliation(s)
- Sungryul Shim
- Institute for Clinical Molecular Biology Research, Soonchunhyang University Hospital, Seoul, Korea
| | - Jiyoung Kim
- Department of Radiation Oncology, Ewha Womans University School of Medicine, Seoul, Korea
| | - Wonguen Jung
- Department of Radiation Oncology, Ewha Womans University School of Medicine, Seoul, Korea
| | - In-Soo Shin
- Department of Education, Jeonju University, Jeonju, Korea
| | - Jong-Myon Bae
- Department of Preventive Medicine, Jeju National University School of Medicine, Jeju, Korea
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67
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The Functional Haplotypes of CHRM3 Modulate mRNA Expression and Associate with Bladder Cancer among a Chinese Han Population in Kaohsiung City. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4052846. [PMID: 28053981 PMCID: PMC5174173 DOI: 10.1155/2016/4052846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023]
Abstract
Bladder cancer is one of the major cancer types and both environmental factors and genetic background play important roles in its pathology. Kaohsiung is a high industrialized city in Taiwan, and here we focused on this region to evaluate the genetic effects on bladder cancer. Muscarinic acetylcholine receptor M3 (CHRM3) was reported as a key receptor in different cancer types. CHRM3 is located at 1q42-43 which was reported to associate with bladder cancer. Our study attempted to delineate whether genetic variants of CHRM3 contribute to bladder cancer in Chinese Han population in south Taiwan. Five selected SNPs (rs2165870, rs10802789, rs685550, rs7520974, and rs3738435) were genotyped for 30 bladder cancer patients and 60 control individuals and genetic association studies were performed. Five haplotypes (GTTAT, ATTGT, GCTAC, ACTAC, and ACCAC) were found significantly associated with low CHRM3 mRNA level and contributed to increased susceptibility of bladder cancer in Kaohsiung city after rigid 10000 consecutive permutation tests. To our knowledge, this is the first genetic association study that reveals the genetic contribution of CHRM3 gene in bladder cancer etiology.
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68
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Hernández-Tobías EA, Torres-Sánchez L, Noris G, Santana C, Samano MR, Arellano-Galindo J, Arenas-Sordo MDLL, Brooks D, Rodríguez-Ventura AL, Meraz-Ríos MA, Gómez R. PPARG-LYPLAL1 Multi-Allelic Combination Associated with Obesity and Overweight in Mexican Adolescent Females. Ethn Dis 2016; 26:477-484. [PMID: 27773974 DOI: 10.18865/ed.26.4.477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE We studied multi-loci variants to identify the contribution of six candidate genes (ADIPOQ, CDH13, LYPLAL1, MC4R, PPARG and PGC1A) in the development of obesity and overweight. DESIGN We genotyped 404 chromosomes with eleven SNPs in Mexican female adolescents, who were subdivided into two groups (obesity-overweight and normal-weight) using the World Health Organization parameters. Genomic (800 chromosomes) and ancestral (208 chromosomes) controls were included to reduce the population bias. Anthropometric measurements, biochemical parameters, and caloric intake were obtained only in the groups of Mexican female adolescents. RESULTS A positive genotype-phenotype association was found that involves the multi-allelic combination of three risk alleles (one in PPARG and two in LYPLAL1) with obesity and overweight (OR=3.1, P=.010). This combination also exhibited a significant association with waist circumference (P=.030) and triglycerides levels (P=.030). These associations were supported by a logistic regression analysis adjusted for several confounding variables. CONCLUSIONS Our data suggest the joint participation of PPARG-LYPLAL1 genes in metabolic disorders development. Hence, these genes could act as potential biomarkers in obesity and overweight. Our findings underscore the complexity of metabolic disorders and provide evidence about the importance of multi-loci analysis to study complex diseases.
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Affiliation(s)
| | | | - Gino Noris
- Laboratorio BIMODI (Biología Molecular Diagnóstica), Querétaro, Qro., México
| | - Carla Santana
- Laboratorio BIMODI (Biología Molecular Diagnóstica), Querétaro, Qro., México
| | - María Reyna Samano
- Departamento de Nutrición y Bioprogramación, Instituto Nacional de Perinatología, México, D.F., México
| | | | | | - Daniel Brooks
- Departamento de Toxicología, Cinvestav-IPN, México D.F., México; Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, México D.F., México
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Ye C, Hu Z, Wu E, Yang X, Buford UJ, Guo Z, Saveanu RV. Two SNAP-25 genetic variants in the binding site of multiple microRNAs and susceptibility of ADHD: A meta-analysis. J Psychiatr Res 2016; 81:56-62. [PMID: 27380186 DOI: 10.1016/j.jpsychires.2016.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/23/2016] [Accepted: 06/10/2016] [Indexed: 12/14/2022]
Abstract
The aim of this meta-analysis is to assess the associations between two most widely investigated polymorphisms (rs3746544 and rs1051312) in the 3'UTR of the SNAP-25 gene and susceptibility of ADHD. Two investigators selected related studies and assessed methodological quality independently. Six studies were included in this meta-analysis for a total of 715 cases and 655 controls. There is no apparent association between rs3746544 polymorphisms and risk of ADHD. However, subgroup analysis based on ethnicity demonstrated a strong association between rs3746544 polymorphism and ADHD in the subset of Asian participants, but not among Caucasians. Compared to the T allele, the allele G was associated with a significantly decreased risk of developing ADHD in the Asian population (odds ratio (OR) = 0.70, 95% confidence interval (CI) = 0.52-0.95, p = 0.02). The association between the TT genotype and ADHD risk was also significantly increased as compared to G/T (OR = 1.56, 95% CI = 1.00-2.44, p = 0.05) and the dominant genetic model (GG + GT vs. TT: OR = 1.51, 95% CI = 1.07-2.13, p = 0.02). For the rs1051312 SNP, being homozygous for the minor allele (C/C) was associated with a 3.66 higher odds of ADHD as compared to cases homozygous for the major allele (T/T) (95% CI = 1.64-8.13, p = 0.001), and 3.57 higher odds as compared to heterozygous (C/T) carriers (95% CI = 2.01-12.90, p < 0.001). Our results suggest that the polymorphisms rs3746544 and rs1051312 may increase the odds of developing ADHD. Additional studies are needed to confirm these findings.
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Affiliation(s)
- Chuanzhong Ye
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine/Jackson Health System, 1695 NW 9th Ave, 33136, United States.
| | - Zhijian Hu
- Department of Epidemiology and Health Statistics, Fujian Medical University, 1 Xue Yuan Road University Town, Fujian, 350108, China
| | - Evan Wu
- Department of Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14th St, Miami, FL, 33136, United States
| | - Xiaolu Yang
- Department of Epidemiology and Health Statistics, Fujian Medical University, 1 Xue Yuan Road University Town, Fujian, 350108, China
| | - Ushimbra J Buford
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine/Jackson Health System, 1695 NW 9th Ave, 33136, United States
| | - Zhihong Guo
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine/Jackson Health System, 1695 NW 9th Ave, 33136, United States
| | - Radu V Saveanu
- Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine/Jackson Health System, 1695 NW 9th Ave, 33136, United States
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Kandt J, Cheshire JA, Longley PA. Regional surnames and genetic structure in Great Britain. TRANSACTIONS (INSTITUTE OF BRITISH GEOGRAPHERS : 1965) 2016; 41:554-569. [PMID: 27708455 PMCID: PMC5032893 DOI: 10.1111/tran.12131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 06/06/2023]
Abstract
Following the increasing availability of DNA-sequenced data, the genetic structure of populations can now be inferred and studied in unprecedented detail. Across social science, this innovation is shaping new bio-social research agendas, attracting substantial investment in the collection of genetic, biological and social data for large population samples. Yet genetic samples are special because the precise populations that they represent are uncertain and ill-defined. Unlike most social surveys, a genetic sample's representativeness of the population cannot be established by conventional procedures of statistical inference, and the implications for population-wide generalisations about bio-social phenomena are little understood. In this paper, we seek to address these problems by linking surname data to a censored and geographically uneven sample of DNA scans, collected for the People of the British Isles study. Based on a combination of global and local spatial correspondence measures, we identify eight regions in Great Britain that are most likely to represent the geography of genetic structure of Great Britain's long-settled population. We discuss the implications of this regionalisation for bio-social investigations. We conclude that, as the often highly selective collection of DNA and biomarkers becomes a more common practice, geography is crucial to understanding variation in genetic information within diverse populations.
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Affiliation(s)
- Jens Kandt
- Department of GeographyUniversity College LondonLondonWC1E 6BT
| | | | - Paul A Longley
- Department of GeographyUniversity College LondonLondonWC1E 6BT
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Bernhard RM, Chaponis J, Siburian R, Gallagher P, Ransohoff K, Wikler D, Perlis RH, Greene JD. Variation in the oxytocin receptor gene (OXTR) is associated with differences in moral judgment. Soc Cogn Affect Neurosci 2016; 11:1872-1881. [PMID: 27497314 PMCID: PMC5141955 DOI: 10.1093/scan/nsw103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/02/2016] [Accepted: 07/21/2016] [Indexed: 11/13/2022] Open
Abstract
Moral judgments are produced through the coordinated interaction of multiple neural systems, each of which relies on a characteristic set of neurotransmitters. Genes that produce or regulate these neurotransmitters may have distinctive influences on moral judgment. Two studies examined potential genetic influences on moral judgment using dilemmas that reliably elicit competing automatic and controlled responses, generated by dissociable neural systems. Study 1 (N = 228) examined 49 common variants (SNPs) within 10 candidate genes and identified a nominal association between a polymorphism (rs237889) of the oxytocin receptor gene (OXTR) and variation in deontological vs utilitarian moral judgment (that is, judgments favoring individual rights vs the greater good). An association was likewise observed for rs1042615 of the arginine vasopressin receptor gene (AVPR1A). Study 2 (N = 322) aimed to replicate these findings using the aforementioned dilemmas as well as a new set of structurally similar medical dilemmas. Study 2 failed to replicate the association with AVPR1A, but replicated the OXTR finding using both the original and new dilemmas. Together, these findings suggest that moral judgment is influenced by variation in the oxytocin receptor gene and, more generally, that single genetic polymorphisms can have a detectable effect on complex decision processes.
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Affiliation(s)
- Regan M Bernhard
- Department of Psychology, Harvard University, 02138, Cambridge, MA, USA
| | - Jonathan Chaponis
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, 02114, Boston MA, USA
| | - Richie Siburian
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, 02114, Boston MA, USA
| | - Patience Gallagher
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, 02114, Boston MA, USA
| | | | - Daniel Wikler
- Department of Global Health and Population, Harvard School of Public Health, 02115, Boston, MA, USA
| | - Roy H Perlis
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, 02114, Boston MA, USA.,Center for Experimental Drugs and Diagnostics, Massachusetts General Hospital and Harvard Medical School, 02114, Boston, MA, USA
| | - Joshua D Greene
- Department of Psychology, Harvard University, 02138, Cambridge, MA, USA
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Pradhan SK, Barik SR, Sahoo A, Mohapatra S, Nayak DK, Mahender A, Meher J, Anandan A, Pandit E. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice. PLoS One 2016; 11:e0160027. [PMID: 27494320 PMCID: PMC4975506 DOI: 10.1371/journal.pone.0160027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/12/2016] [Indexed: 11/23/2022] Open
Abstract
Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.
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Affiliation(s)
- Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Saumya Ranjan Barik
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Ambika Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Sudipti Mohapatra
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Deepak Kumar Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Anumalla Mahender
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Jitandriya Meher
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
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Nicoletti A, Messina S, Bruno E, Mostile G, Quattrocchi G, Raciti L, Dibilio V, Cappellani R, D'Amico E, Sciacca G, Lo Fermo S, Paradisi V, Patti F, Zappia M. Risk factors in multiple sclerosis: a population-based case-control study in Sicily. Background and methods. Neurol Sci 2016; 37:1931-1937. [PMID: 27488302 DOI: 10.1007/s10072-016-2685-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Incidence of multiple sclerosis (MS) has steeply increased over time during the last 30 years in the city of Catania. We carried out a population-based case-control study to evaluate the possible role of both environmental and genetic factors. From 1975 to 2004 in Catania, 367 MS patients diagnosed according to the Poser's criteria had the onset of disease. A sample of MS patients was randomly selected from this incident cohort. Three controls matched by age and sex were randomly selected from the rosters of 14 GPs. Controls were proportionally selected according to the distribution by municipality of the target population using a multistage sampling methods. All cases and controls underwent a face-to-face interview to record information concerning environmental factors and a blood sample was taken for serological and genetic analysis. 164 MS patients (64 % women; mean age of 46.4 ± 10.7) and 481 controls (69 % women; mean age of 47.7 ± 14.8) were enrolled in the study. The distribution of the whole population and the selected controls by municipalities was similar. A blood sample was taken from 150 MS cases and from 337 controls. At the end of the enrolment, we obtained a representative sample of the MS cases and population controls avoiding possible selection bias. Participation rate was very high also concerning the collection of biological specimens.
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Affiliation(s)
- Alessandra Nicoletti
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Silvia Messina
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Elisa Bruno
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Giovanni Mostile
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Graziella Quattrocchi
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Loredana Raciti
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Valeria Dibilio
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Roberto Cappellani
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Emanuele D'Amico
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Giorgia Sciacca
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Salvatore Lo Fermo
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Vincenza Paradisi
- Italian Society of General Medicine (SIMG)-Catania Municipality Section, Catania, Italy
| | - Francesco Patti
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Mario Zappia
- Department GF Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy.
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Rincker K, Lipka AE, Diers BW. Genome-Wide Association Study of Brown Stem Rot Resistance in Soybean across Multiple Populations. THE PLANT GENOME 2016; 9. [PMID: 27898824 DOI: 10.3835/plantgenome2015.08.0064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/15/2015] [Indexed: 05/07/2023]
Abstract
Genetic resistance to brown stem rot (BSR) of soybean [ (L.) Merr.], caused by (Allington & D.W. Chamb.) T.C. Harr. & McNew, has been identified and mapped with biparental populations. Although nearly 400 accessions have been identified with BSR resistance, this trait has been mapped in only 12 sources, and just two, PI84946-2 and PI88788, have been used to develop BSR resistant cultivars. Thus, there is a serious need to improve our knowledge of the genetic basis of BSR resistance in soybean so that resistance genes in cultivars can be diversified and markers close to resistance genes can be identified and used in marker-assisted selection (MAS). To this end, we conducted a genome-wide association study (GWAS) to identify novel genomic loci associated with BSR resistance and to gain further insight into a previously reported chromosome 16 region containing BSR resistance () genes. A total of 52,041 single-nucleotide polymorphisms (SNPs) were tested for association with BSR in a set of 4735 accessions from four diversity panels evaluated for resistance from 1989 to 2003. Using a unified mixed linear model and stepwise model selection, we refined the signals within the interval on chromosome 16 by finding associations that explain a substantial proportion of the total variation of BSR resistance. In combination with significant GWAS signals found elsewhere in the genome, our study will aid efforts to improve BSR resistance by providing new targets for MAS.
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Anstee QM, Seth D, Day CP. Genetic Factors That Affect Risk of Alcoholic and Nonalcoholic Fatty Liver Disease. Gastroenterology 2016; 150:1728-1744.e7. [PMID: 26873399 DOI: 10.1053/j.gastro.2016.01.037] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies and candidate gene studies have informed our understanding of factors contributing to the well-recognized interindividual variation in the progression and outcomes of alcoholic liver disease and nonalcoholic fatty liver disease. We discuss the mounting evidence for shared modifiers and common pathophysiological processes that contribute to development of both diseases. We discuss the functions of proteins encoded by risk variants of genes including patatin-like phospholipase domain-containing 3 and transmembrane 6 superfamily member 2, as well as epigenetic factors that contribute to the pathogenesis of alcoholic liver disease and nonalcoholic fatty liver disease. We also discuss important areas of future genetic research and their potential to affect clinical management of patients.
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Affiliation(s)
- Quentin M Anstee
- Liver Research Group, Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom.
| | - Devanshi Seth
- Centenary Institute of Cancer Medicine, Royal Prince Alfred Hospital, Camperdown, Australia; Drug Health Services, Royal Prince Alfred Hospital, Camperdown, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia
| | - Christopher P Day
- Liver Research Group, Institute of Cellular Medicine, The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Power considerations for λ inflation factor in meta-analyses of genome-wide association studies. Genet Res (Camb) 2016; 98:e9. [PMID: 27193946 DOI: 10.1017/s0016672316000069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genomic control (GC) approach is extensively used to effectively control false positive signals due to population stratification in genome-wide association studies (GWAS). However, GC affects the statistical power of GWAS. The loss of power depends on the magnitude of the inflation factor (λ) that is used for GC. We simulated meta-analyses of different GWAS. Minor allele frequency (MAF) ranged from 0·001 to 0·5 and λ was sampled from two scenarios: (i) random scenario (empirically-derived distribution of real λ values) and (ii) selected scenario from simulation parameter modification. Adjustment for λ was considered under single correction (within study corrected standard errors) and double correction (additional λ corrected summary estimate). MAF was a pivotal determinant of observed power. In random λ scenario, double correction induced a symmetric power reduction in comparison to single correction. For MAF 1·2 and MAF >5%. Our results provide a quick but detailed index for power considerations of future meta-analyses of GWAS that enables a more flexible design from early steps based on the number of studies accumulated in different groups and the λ values observed in the single studies.
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Kita-Milczarska K, Sieminska A, Jassem E. Association Between CHRNA3 and CHRNA5 Nicotine Receptor Subunit Gene Variants and Nicotine Dependence in an Isolated Populationof Kashubians in Poland. Med Sci Monit 2016; 22:1442-50. [PMID: 27127891 PMCID: PMC4915318 DOI: 10.12659/msm.895907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background Genome-wide and allelic association studies have shown the contribution of CHRNA5-A3-B4 nicotinic receptor subunit gene cluster within chromosome 15 to nicotine dependence (ND). While an association between several single-nucleotide polymorphisms (SNPs) at that locus and smoking quantity (cigarettes per day; CPD) has been well recognized, there are some inconsistencies in demonstrating the influence of these SNPs on other ND phenotypes. This uncertainty motivated us to examine the association of 3 selected SNPs (CHRNA3 rs1051730, rs6495308, and CHRNA5 rs55853898) with ND in an isolated population of Kashubians from Poland. Material/Methods The study sample consisted of 788 current daily smokers. ND was assessed by CPD, the Fagerstrom Test for Nicotine Dependence (FTND), its brief version - Heavy Smoking Index (HSI), and time to first cigarette after waking (TTF). The correlation between studied SNPs and dichotomized values of ND measures was assessed in the regression analysis. Bonferroni corrected p-value of 0.017 was set for a type 1 error. Results We found a robust association between risk allele A of rs1051730 and CPD >10 (odds ratio (OR)=1.77, 95% confidence interval (CI): 1.20–2.59, p=0.004), and a weak association, which did not survive correction for multiple testing, with FTND ≥4. No associations between studied SNPs and HSI or TTF were demonstrated. Conclusions Our findings confirm that rs1051730 influences ND phenotype, as defined by CPD.
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Affiliation(s)
| | - Alicja Sieminska
- Department of Allergology and Pneumonology, Medical University of Gdańsk, Gdańsk, Poland
| | - Ewa Jassem
- Department of Allergology and Pneumonology, Medical University of Gdańsk, Gdańsk, Poland
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Hassani M, Saliminejad K, Heidarizadeh M, Kamali K, Memariani T, Khorram Khorshid HR. Association study of Glutathione S-Transferase polymorphisms and risk of endometriosis in an Iranian population. Int J Reprod Biomed 2016. [DOI: 10.29252/ijrm.14.4.241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Serum level and polymorphisms of retinol-binding protein-4 and risk for gestational diabetes mellitus: a meta-analysis. BMC Pregnancy Childbirth 2016; 16:52. [PMID: 26975349 PMCID: PMC4791876 DOI: 10.1186/s12884-016-0838-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/03/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Retinol-binding protein-4 (RBP4) has been reported to be potentially involved in the pathogenesis of gestational diabetes mellitus (GDM); however, the findings are inconsistent. Our aims were to review the studies that investigated the association of serum levels and polymorphisms of RBP4 with GDM risk, and to provide recommendations for future research. METHODS The databases PubMed, EBSCO, ScienceDirect, and Web of Knowledge were searched up to October 2015 to find out studies evaluating the relationship between serum RBP4 level/ RBP4 polymorphisms and GDM risk. In the meta-analysis of serum RBP4 levels the key inclusion was that studies were designed as BMI-matched studies or had observed non-significant differences in BMI between cases and controls. RESULTS Fourteen case-control studies (647 cases and 620 controls) reporting the association between serum RBP4 level and GDM risk, and three studies (1012 cases and 1605 controls) investigating the association between RBP4 polymorphisms and GDM risk were involved. Our results showed that high serum RBP4 levels represent a risk factor for GDM (pooled standardized mean difference =0.758, 95% confidence interval [0.387, 1.128]). The results of subgroup analyses based on "gestational age at blood sampling" or "diagnostic criteria" are consistent with the overall results. However, the postpartum subgroup and "before 24 weeks" subgroup both only include one article and indicate no association between serum RBP4 level and GDM risk. The meta-analysis on the association between rs3758539 polymorphism and GDM risk shows that RBP4 rs3758539 polymorphism is not associated with the development of GDM. CONCLUSIONS The results of this meta-analysis support the hypothesis that RBP4 is a modest independent risk factor for GDM (i.e., nonobese patients with GDM might express RBP4 at abnormal levels). The serum RBP4 level is associated with the risk of GDM. However, the association in the first-trimester and postpartum period should be validated by further research. The association between RBP4 rs3758539 polymorphism and GDM risk was not confirmed.
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Gender bias in individual radiosensitivity and the association with genetic polymorphic variations. Radiother Oncol 2016; 119:236-43. [PMID: 26987471 DOI: 10.1016/j.radonc.2016.02.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 12/08/2015] [Accepted: 02/29/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE To assess the extent of variation in radiosensitivity between individuals, gender-related dissimilarity and impact on the association with single nucleotide polymorphisms (SNPs). MATERIALS AND METHODS Survival curves of 152 fibroblast cell strains derived from both gender were generated. Individual radiosensitivity was characterized by the surviving fraction at 2Gy (SF2). SNPs in 10 radiation responsive genes were genotyped by direct sequencing. RESULTS The wide variation in SF2 (0.12-0.50; mean=0.33) was significantly associated with 3 SNPs: TP53 G72C (P=0.007), XRCC1 G399A (P=0.002) and ATM G1853A (P=0.01). Females and males differed significantly in radiosensitivity (P=0.004) that impacted genetic association where only XRCC1 remained significant in both gender (P<0.05). Meanwhile, discordant association was observed for TP53 that was significant in females (P=0.012) and ATM that was significant in males (P=0.0006). When gender-specific SF2-mean (0.31 and 0.35 for females and males; respectively) was considered, further discordance was observed where XRCC1 turned out not to be associated with radiosensitivity in males (P>0.05). CONCLUSIONS Although the variation in individual radiosensitivity was associated with certain SNPs, gender bias for both endpoints was evident. Therefore, assessing the risk of radiation exposure in females and males should be considered separately in order to achieve the ultimate goal of personalized radiation medicine.
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Fontanesi L, Scotti E, Speroni C, Buttazzoni L, Russo V. A selective genotyping approach identifies single nucleotide polymorphisms in porcine chromosome 2 genes associated with production and carcass traits in Italian heavy pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2011.e15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Garatachea N, Marín PJ, Santos-Lozano A, Sanchis-Gomar F, Emanuele E, Lucia A. The ApoE gene is related with exceptional longevity: a systematic review and meta-analysis. Rejuvenation Res 2016; 18:3-13. [PMID: 25385258 DOI: 10.1089/rej.2014.1605] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The objective of this meta-analysis was to determine the association of the apolipoprotein E (ApoE) gene with exceptional longevity (EL) (i.e., reaching 100+ years) by identifying possible unequal distribution of alleles/genotypes in the common variants ε2, ε3, and ε4 among centenarians and younger population. The association of ApoE with EL was analyzed in a total of 2776 centenarians (cases) and 11,941 younger controls (from 13 case-control studies) using the chi-squared test with the Yates correction. We conducted combined and separate analyses for all ethnic groups studied in the literature (Caucasian and Asian). The main result for all ethnic groups combined was that the likelihood of reaching EL was negatively associated with ε4 allele carriage [pooled odds ratio (OR)=0.43; 95% confidence interval (CI) 0.36, 0.50; p<0.001] and with ε4/ε4 (OR=0.18; 95% CI 0.08, 0.39; p<0.001), ε3/ε4 (OR=0.44; 95% CI 0.37, 0.53; p<0.001) and ε2/ε4 genotypes (OR=0.48; 95% CI 0.31, 0.74; p<0.001). In contrast, the ε2/ε3 genotype was positively associated with EL (OR=1.35; 95% CI 1.06, 1.72; p=0.017). When compared with the ε3 allele, the ε2 allele was not associated with increased odds of EL (OR=1.08; 95% CI 0.77, 1.50, p=0.660). The present meta-analysis confirms that, besides its previously documented influence on Alzheimer's and cardiovascular disease risk, the ApoE gene is associated with the likelihood of reaching EL.
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Affiliation(s)
- Nuria Garatachea
- 1 Faculty of Health and Sport Science, University of Zaragoza , Huesca, Spain
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85
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Martinucci I, Blandizzi C, de Bortoli N, Bellini M, Antonioli L, Tuccori M, Fornai M, Marchi S, Colucci R. Genetics and pharmacogenetics of aminergic transmitter pathways in functional gastrointestinal disorders. Pharmacogenomics 2016; 16:523-39. [PMID: 25916523 DOI: 10.2217/pgs.15.12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Functional gastrointestinal disorders (FGIDs) are highly prevalent syndromes, without evident underlying organic causes. Their pathogenesis is multifactorial in nature, with a combination of environmental and genetic factors contributing to their clinical manifestations, for which most of current treatments are not satisfactory. It is acknowledged that amine mediators (noradrenaline, dopamine and serotonin) play pivotal regulatory actions on gut functions and visceral sensation. In addition, drugs of therapeutic interest for FGIDs act on these transmitter pathways. The present article reviews current knowledge on the impact of genetics and pharmacogenetics of aminergic pathways on FGID pathophysiology, clinical presentations, symptom severity and medical management, in an attempt of highlighting the most relevant evidence and point out issues that should be addressed in future investigations.
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Affiliation(s)
- Irene Martinucci
- Gastroenterology Unit, Department of Translational Research & New Technologies in Medicine, University of Pisa, Via Paradisa 2, I-56124 Pisa, Italy
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86
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Significant association of GRM7 and GRM8 genes with schizophrenia and major depressive disorder in the Han Chinese population. Eur Neuropsychopharmacol 2016; 26:136-146. [PMID: 26655190 DOI: 10.1016/j.euroneuro.2015.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/06/2015] [Accepted: 05/12/2015] [Indexed: 01/14/2023]
Abstract
Metabotropic glutamate receptor type 7 (GRM7) and type 8 (GRM8) are involved in the neurotransmission of glutamate which is supposed to play an important role in the development of schizophrenia (SCZ) and major depressive disorders (MDD). We designed this study to investigate whether common DNA variants or their genetic interactions within GRM7 and GMR8 genes were associated with these disorders in the Han Chinese population. Fourteen SNPs in GRM7 and GRM8 were selected within a sample set comprising 1235 SCZ patients, 1045 MDD patients and 1235 normal controls. Significant association in SCZ case-control subjects was observed for rs2229902 (permutated Pallele=0.0005, OR=1.492 [95% CI=1.231-1.807]) and rs9870680 (permutated Pallele=0.0023, OR=1.262 [95% CI=1.116-1.426]) in GRM7 and rs2237781 (permutated Pallele=0.0027, OR=1.346 [95% CI=1.149-1.575]) in GRM8. Association analysis for MDD case-control subjects revealed positive results in rs779706 (permutated Pallele=0.0099, OR=1.237 [95% CI=1.093-1.399]) of GRM7 and in rs1361995 (permutated Pallele=0.0017, OR=1.488 [95% CI=1.215-1.823]) of GRM8. Moreover, a three-locus model, constituted by polymorphisms in GRM7 and GRM8 significantly correlated with MDD in the gene-gene interaction analysis. Meta-analysis and haplotype analysis further confirmed our significant results. We demonstrated the genetic association of GRM7 and GRM8 with SCZ and MDD in the Han Chinese population. We also found susceptibility interactive effects of these two genes with both psychiatric disorders, which might provide new insights into the etiology of them.
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87
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Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach. Genetics 2015; 202:411-26. [PMID: 26661113 DOI: 10.1534/genetics.115.179507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 11/19/2015] [Indexed: 01/08/2023] Open
Abstract
Genome-wide data with millions of single-nucleotide polymorphisms (SNPs) can be highly correlated due to linkage disequilibrium (LD). The ultrahigh dimensionality of big data brings unprecedented challenges to statistical modeling such as noise accumulation, the curse of dimensionality, computational burden, spurious correlations, and a processing and storing bottleneck. The traditional statistical approaches lose their power due to [Formula: see text] (n is the number of observations and p is the number of SNPs) and the complex correlation structure among SNPs. In this article, we propose an integrated distance correlation ridge regression (DCRR) approach to accommodate the ultrahigh dimensionality, joint polygenic effects of multiple loci, and the complex LD structures. Initially, a distance correlation (DC) screening approach is used to extensively remove noise, after which LD structure is addressed using a ridge penalized multiple logistic regression (LRR) model. The false discovery rate, true positive discovery rate, and computational cost were simultaneously assessed through a large number of simulations. A binary trait of Arabidopsis thaliana, the hypersensitive response to the bacterial elicitor AvrRpm1, was analyzed in 84 inbred lines (28 susceptibilities and 56 resistances) with 216,130 SNPs. Compared to previous SNP discovery methods implemented on the same data set, the DCRR approach successfully detected the causative SNP while dramatically reducing spurious associations and computational time.
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88
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Millard LAC, Davies NM, Timpson NJ, Tilling K, Flach PA, Davey Smith G. MR-PheWAS: hypothesis prioritization among potential causal effects of body mass index on many outcomes, using Mendelian randomization. Sci Rep 2015; 5:16645. [PMID: 26568383 PMCID: PMC4644974 DOI: 10.1038/srep16645] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 10/16/2015] [Indexed: 01/03/2023] Open
Abstract
Observational cohort studies can provide rich datasets with a diverse range of phenotypic variables. However, hypothesis-driven epidemiological analyses by definition only test particular hypotheses chosen by researchers. Furthermore, observational analyses may not provide robust evidence of causality, as they are susceptible to confounding, reverse causation and measurement error. Using body mass index (BMI) as an exemplar, we demonstrate a novel extension to the phenome-wide association study (pheWAS) approach, using automated screening with genotypic instruments to screen for causal associations amongst any number of phenotypic outcomes. We used a sample of 8,121 children from the ALSPAC dataset, and tested the linear association of a BMI-associated allele score with 172 phenotypic outcomes (with variable sample sizes). We also performed an instrumental variable analysis to estimate the causal effect of BMI on each phenotype. We found 21 of the 172 outcomes were associated with the allele score at an unadjusted p < 0.05 threshold, and use Bonferroni corrections, permutation testing and estimates of the false discovery rate to consider the strength of results given the number of tests performed. The most strongly associated outcomes included leptin, lipid profile, and blood pressure. We also found novel evidence of effects of BMI on a global self-worth score.
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Affiliation(s)
- Louise A C Millard
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol.,Intelligent Systems Laboratory, Department of Computer Science, University of Bristol, UK
| | - Neil M Davies
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol
| | - Nic J Timpson
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol
| | - Kate Tilling
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol
| | - Peter A Flach
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol.,Intelligent Systems Laboratory, Department of Computer Science, University of Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol
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89
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Oliveira-Paula GH, Lacchini R, Tanus-Santos JE. Endothelial nitric oxide synthase: From biochemistry and gene structure to clinical implications of NOS3 polymorphisms. Gene 2015; 575:584-99. [PMID: 26428312 DOI: 10.1016/j.gene.2015.09.061] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/10/2015] [Accepted: 09/22/2015] [Indexed: 02/07/2023]
Abstract
Nitric oxide (NO) is an important vasodilator with a well-established role in cardiovascular homeostasis. While mediator is synthesized from L-arginine by neuronal, endothelial, and inducible nitric oxide synthases (NOS1,NOS3 and NOS2 respectively), NOS3 is the most important isoform for NO formation in the cardiovascular system. NOS3 is a dimeric enzyme whose expression and activity are regulated at transcriptional, posttranscriptional,and posttranslational levels. The NOS3 gene, which encodes NOS3, exhibits a number of polymorphic sites including single nucleotide polymorphisms (SNPs), variable number of tandem repeats (VNTRs), microsatellites, and insertions/deletions. Some NOS3 polymorphisms show functional effects on NOS3 expression or activity, thereby affecting NO formation. Interestingly, many studies have evaluated the effects of functional NOS3 polymorphisms on disease susceptibility and drug responses. Moreover, some studies have investigated how NOS3 haplotypes may impact endogenous NO formation and disease susceptibility. In this article,we carried out a comprehensive review to provide a basic understanding of biochemical mechanisms involved in NOS3 regulation and how genetic variations in NOS3 may translate into relevant clinical and pharmacogenetic implications.
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Affiliation(s)
- Gustavo H Oliveira-Paula
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Jose E Tanus-Santos
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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90
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Abstract
Sickle cell disease and β thalassemia are common severe diseases with little effective pathophysiologically-based treatment. Their phenotypic heterogeneity prompted genomic approaches to identify modifiers that ultimately might be exploited therapeutically. Fetal hemoglobin (HbF) is the major modulator of the phenotype of the β hemoglobinopathies. HbF inhibits deoxyHbS polymerization and in β thalassemia compensates for the reduction of HbA. The major success of genomics has been a better understanding the genetic regulation of HbF by identifying the major quantitative trait loci for this trait. If the targets identified can lead to means of increasing HbF to therapeutic levels in sufficient numbers of sickle or β-thalassemia erythrocytes, the pathophysiology of these diseases would be reversed. The availability of new target loci, high-throughput drug screening, and recent advances in genome editing provide the opportunity for new approaches to therapeutically increasing HbF production.
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Affiliation(s)
- Duyen A Ngo
- Department of Medicine, Boston University School of Medicine, 820 Harrison Ave., FGH 1st Floor, Boston, MA, 02118, USA.
| | - Martin H Steinberg
- Departments of Medicine, Pediatrics, Pathology and Laboratory Medicine, Boston University School of Medicine, 72 E. Concord Street, Boston, MA, 02118, USA.
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91
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García-Ortiz L, Gutiérrez-Salinas J, Guerrero-Muñiz S, Chima-Galán MDC, Sánchez-Hernández J. [Intracranial aneurysms and their clinical and genetic behaviour]. CIR CIR 2015; 83:467-72. [PMID: 26188706 DOI: 10.1016/j.circir.2015.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/08/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Intracranial aneurysms are abnormal dilations of the cerebral arteries of unknown origin. However, some genes have been linked to their formation, as in the case of NOS3 gene which encodes the endothelial nitric oxide synthase responsible for producing nitric oxide. Several polymorphisms in this gene, in association with a variable number tandem repeat located in intron 4 from eNOS4 gene, can influence the formation of aneurysms. Therefore, the purpose of this study is to determine the genotype frequencies of eNOS3 and eNOS4 genes, and their relationship with intracranial aneurysms. MATERIAL AND METHODS A prospective case-control study was performed on 79 cases with ruptured intracranial aneurysm and 93 healthy controls. DNA was obtained from all subjects for the study of the eNOS3 and eNOS4 genes by molecular techniques. RESULTS The GG genotype of eNOS3 gene showed the largest number of patients (n=29) with a large aneurysm. While the intracranial aneurysms of medium size were found in a higher percentage (50%) in patients with genotype GT. In terms of patient outcomes, it was observed that those with genotype GG had the highest percentage (43.13%) recovery, compared to genotype GT (27.27%). CONCLUSIONS The present study shows that there is a tendency of an association between genotypes of eNOS3 gene with the mean size of the aneurysm, as well as clinical sequelae of the disease in patients with intracranial aneurysms.
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Affiliation(s)
- Liliana García-Ortiz
- División de Medicina Genómica, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, México, D.F., México.
| | - José Gutiérrez-Salinas
- Laboratorio de Bioquímica y Medicina Experimental, División de Investigación Biomédica, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, México, D.F., México
| | - Salvador Guerrero-Muñiz
- Cirugía Cerebro Vascular, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, México, D.F., México
| | - María del Carmen Chima-Galán
- División de Medicina Genómica, Centro Médico Nacional 20 de Noviembre, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, México, D.F., México
| | - Jonathan Sánchez-Hernández
- Licenciatura en Química, Facultad de Estudios Superiores Cuautitlán-Universidad Nacional Autónoma de México, Cuautitlán, Estado de México, México
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92
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Samochowiec J, Samochowiec A, Puls I, Bienkowski P, Schott BH. Genetics of alcohol dependence: a review of clinical studies. Neuropsychobiology 2015; 70:77-94. [PMID: 25359488 DOI: 10.1159/000364826] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 05/24/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS Alcohol dependence is a common severe psychiatric disorder with a multifactorial etiology. Since the completion of the human genome project and with the increased availability of high-throughput genotyping, multiple genetic risk factors for substance-related disorders, including alcohol dependence, have been identified, but not all results could be replicated. METHODS We systematically review the clinical literature on genetic risk factors for alcohol dependence and alcohol-related phenotypes, including candidate gene-based studies, linkage studies and genome-wide association studies (GWAS). RESULTS Irrespectively of the methodology employed, the most robust findings regarding genetic risk factors for alcohol dependence concern genetic variations that affect alcohol metabolism. GWAS confirm the importance of the alcohol dehydrogenase gene cluster on chromosome 4 in the genetic risk for alcohol dependence with multiple variants that exert a small, but cumulative influence. A single variant with strong influence on individual risk is the aldehyde dehydrogenase 2 ALDHD2*2 variant common in Asian populations. Other robust associations have been found with previously uncharacterized genes like KIAA0040, and such observations can lead to the identification of thus far unknown signaling pathways. Converging evidence also points to a role of glutamatergic, dopaminergic and serotonergic neurotransmitter signaling in the risk for alcohol dependence, but effects are small, and gene-environment interactions further increase the complexity. CONCLUSION With few exceptions like ALDH2*2, the contribution of individual genetic variants to the risk for alcohol-related disorders is small. However, the concentration of risk variants within neurotransmitter signaling pathways may help to deepen our understanding of the underlying pathophysiology and thereby contribute to develop novel therapeutic strategies.
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Affiliation(s)
- Jerzy Samochowiec
- Department of Psychiatry, Pomeranian Medical University, Szczecin, Poland
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93
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An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions. BIOMED RESEARCH INTERNATIONAL 2015; 2015:524821. [PMID: 26236727 PMCID: PMC4509494 DOI: 10.1155/2015/524821] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/30/2014] [Accepted: 01/02/2015] [Indexed: 12/22/2022]
Abstract
SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.
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94
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Liu Y, Geng PL, Yan FQ, Chen T, Wang W, Tang XD, Zheng JC, Wu WP, Wang ZF. C-reactive Protein -717A>G and -286C>T>A Gene Polymorphism and Ischemic Stroke. Chin Med J (Engl) 2015; 128:1666-70. [PMID: 26063371 PMCID: PMC4733752 DOI: 10.4103/0366-6999.158371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Inflammation plays a pivotal role in the formation and progression of ischemic stroke. Recently, more and more epidemiological studies have focused on the association between C-reactive protein (CRP) −717A > G and −286C > T > A genetic polymorphisms and ischemic stroke. However, the findings of these researches are not conclusive. Methods: We performed a meta-analysis to determine whether these two polymorphisms are associated with the risk of ischemic stroke. Eligible studies were identified from the database of PubMed, Medline, Embase, Web of Science, CNKI, Weipu, and Wanfang. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the association. Results: Four articles were included in our study, including 1926 cases and 2678 controls for −717A > G polymorphism, 652 cases and 1103 controls for −286C > T > A polymorphism. The results of meta-analysis showed that single nucleotide polymorphism (SNP) −717A > G was not significantly associated with the risk of ischemic stroke (GG vs. AA, OR = 1.12, 95% CI = 0.83–1.50, P = 0.207; GG + GA vs. AA, OR = 1.04, 95% CI = 0.93–1.17, P = 0.533; GG vs. GA + AA, OR = 1.10, 95% CI = 0.82–1.47, P = 0.220). Meta-analysis of SNP − 286C > T > A also demonstrated no statistical evidence of a significant association with the risk of ischemic stroke (AA vs. CC, OR = 0.86, 95% CI = 0.59–1.25, P = 0.348; AA vs. CC, OR = 0.92, 95% CI = 0.80–1.06, P = 0.609; AA vs. CC, OR = 0.89, 95% CI = 0.62–1.30, P = 0.374). Conclusions: This meta-analysis demonstrated little evidence to support a role of CRP gene −717A > G, −286C > T > A polymorphisms in ischemic stroke predisposition. However, to draw comprehensive and more reliable conclusions, further larger studies are needed to validate the association between CRP gene polymorphisms and ischemic stroke in various ethnic groups.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhen-Fu Wang
- Department of Nanlou Neurology, The General Hospital of PLA, Beijing 100853, China
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95
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Saliminejad K, Saket M, Kamali K, Memariani T, Khorram Khorshid HR. DNA repair gene XRCC1 and XRCC4 variations and risk of endometriosis: an association study. Gynecol Obstet Invest 2015; 80:85-8. [PMID: 26088159 DOI: 10.1159/000366444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/06/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND Endometriosis is a polygenic and multifactorial disease. DNA damage plays a major role in mutagenesis, carcinogenesis and aging and is usually repaired by the action of several DNA repair enzymes. We investigated the association of the common variations of the DNA repair genes XRCC1 and XRCC4 with susceptibility to endometriosis in an Iranian population. METHODS In total, 160 patients with endometriosis (stages I-IV) and 174 healthy women were included in this case-control study. Genotyping of XRCC1 codon 399 as well as of XRCC4 -1394T/G, codon 247 and intron 3 insertion/deletion variations was performed using restriction fragment length polymorphism analysis of PCR-amplified fragments. RESULTS The XRCC4 -1394TG genotype frequency was significantly lower (p = 0.005) in the patients (9.4%) than in the controls (21.1%). The frequency of the -1394G allele was significantly lower (p < 0.0001) in the patients (6.6%) than in the controls (19.0%). There were no statistically significant differences in the genotype and allele frequencies of the XRCC1 codon 399, XRCC4 codon 247 and XRCC4 intron 3 insertion/deletion polymorphisms between the cases and controls. CONCLUSIONS The XRCC4 -1394T/G polymorphism was associated with susceptibility to endometriosis in an Iranian population.
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Affiliation(s)
- Kioomars Saliminejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Lindner MD, Nakamura RK. Examining the Predictive Validity of NIH Peer Review Scores. PLoS One 2015; 10:e0126938. [PMID: 26039440 PMCID: PMC4454673 DOI: 10.1371/journal.pone.0126938] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/30/2015] [Indexed: 11/19/2022] Open
Abstract
The predictive validity of peer review at the National Institutes of Health (NIH) has not yet been demonstrated empirically. It might be assumed that the most efficient and expedient test of the predictive validity of NIH peer review would be an examination of the correlation between percentile scores from peer review and bibliometric indices of the publications produced from funded projects. The present study used a large dataset to examine the rationale for such a study, to determine if it would satisfy the requirements for a test of predictive validity. The results show significant restriction of range in the applications selected for funding. Furthermore, those few applications that are funded with slightly worse peer review scores are not selected at random or representative of other applications in the same range. The funding institutes also negotiate with applicants to address issues identified during peer review. Therefore, the peer review scores assigned to the submitted applications, especially for those few funded applications with slightly worse peer review scores, do not reflect the changed and improved projects that are eventually funded. In addition, citation metrics by themselves are not valid or appropriate measures of scientific impact. The use of bibliometric indices on their own to measure scientific impact would likely increase the inefficiencies and problems with replicability already largely attributed to the current over-emphasis on bibliometric indices. Therefore, retrospective analyses of the correlation between percentile scores from peer review and bibliometric indices of the publications resulting from funded grant applications are not valid tests of the predictive validity of peer review at the NIH.
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Affiliation(s)
- Mark D. Lindner
- Center for Scientific Review, National Institutes of Health, 6701 Rockledge Dr., Bethesda, Maryland, United States of America
| | - Richard K. Nakamura
- Center for Scientific Review, National Institutes of Health, 6701 Rockledge Dr., Bethesda, Maryland, United States of America
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Hussein A, Elderwy AA, Askar E, Afifi N, Askar G, Metwalley KA, Alsaeid M. Impact of common functional polymorphisms in renin angiotensin system genes on the risk of renal parenchymal scarring following childhood urinary tract infection. J Pediatr Urol 2015; 11:152.e1-7. [PMID: 25939993 DOI: 10.1016/j.jpurol.2015.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pathogenesis of renal parenchymal scarring (RPS) after acute pyelonephritis (APN) is unclear. The risk of RPS varies markedly among individuals, suggesting a genetic role. OBJECTIVE To investigate a possible role of common polymorphisms in renin angiotensin system genes in APN-associated RPS in children. PATIENTS AND METHODS This study included 104 APN children and 300 controls. APN was diagnosed by urine culture and typical findings on 99Tc-DMSA scans. Voiding cystourethrogram tested the presence of vesicoureteral reflux (VUR). Follow-up DMSA scans were performed 4-6 months later to identify new RPS. Angiotensin converting enzyme gene I/D, angiotensin II receptor type-1 A1166C and angiotensinogen M235T polymorphisms were genotyped. RESULTS New RPS developed in 44.2% (46/104) of children with APN. VUR was diagnosed in 35.6% (37/104) of APN cases. RPS developed in 73% of cases of VUR. The D allele of ACE gene I/D polymorphism was significantly more common in APN cases with RPS (73.91%) than non-RPS (58.6%) and controls (54.5%) (p = 0.021, p = 0.002, respectively). The AGTR-1 A1166C A allele was significantly more common in VUR than the non-reflux children (91.9% versus 76.1%; p = 0.005). VUR, in contrast to the D allele (OR 6.1, 95% CI 0.878-19.7; p = 0.05), was an independent risk factor for RPS. DISCUSSION ACE gene D allele is associated with a twofold increase in RPS risk, which could be a result of a functional effect to increase tissue levels and activity of ACE during APN. However, D allele failed to qualify as an independent risk and its RPS association could be dependent on other co-factors, such as TGFβ1 activation, or the D-allele might link with recently discovered functional polymorphisms at the 5' end of the ACE gene. Although VUR is an independent risk for RPS, it is not clear whether this is due to exposure of the kidneys to infected urine, or VUR-associated dysplasia. In contrast with published literature, we noted higher rates of RPS and high-grade VUR, suggesting a more aggressive VUR course or local unawareness of APN. Our study has its limitations; the small number of VUR children, and the clinical and ethical difficulties of testing VCUG and DMSA in controls. CONCLUSIONS ACE gene D allele is associated with, but cannot independently predict, RPS in children. VUR is an independent risk for post-pyelonephritic scarring. AGTR-1 1166A/C polymorphism is associated with occurrence, but not progression, of VUR.
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Affiliation(s)
- Almontaser Hussein
- Children Hospital, Assiut University, Egypt; Division of Pediatric Nephrology, Center for Children and Adolescent Medicine, University of Heidelberg, Germany.
| | | | - Eman Askar
- Children Hospital, Assiut University, Egypt.
| | - Noha Afifi
- Department of Microbiology and Immunology, Assiut University, Egypt
| | - Gamal Askar
- Children Hospital, Assiut University, Egypt.
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G-protein beta 3 subunit polymorphisms and essential hypertension: a case-control association study in northern Han Chinese. JOURNAL OF GERIATRIC CARDIOLOGY : JGC 2015; 12:127-34. [PMID: 25870615 PMCID: PMC4394327 DOI: 10.11909/j.issn.1671-5411.2015.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/19/2014] [Accepted: 12/17/2014] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To explore the association between the three polymorphisms [ C825T, C1429T and G(-350)A] of the gene encoding the G protein beta 3 subunit (GNB3) and hypertension by performing a case-control study in the northern Han Chinese population. METHODS We recruited 731 hypertensive patients and 673 control subjects (the calculated power value was > 0.8). Genotyping was performed to identify C825T, C1429T and G(-350)A polymorphisms using the TaqMan assay. Comparisons of allelic and genotypic frequencies between cases and controls were made by using the chi-square test. Logistic regression analyses were performed to investigate the relationships between the three polymorphisms of GNB3 gene under different genetic models (additive, dominant and recessive models). RESULTS The genotype distribution and allele frequencies of C825T, C1429T and G(-350)A polymorphisms did not differ significantly between hypertensive patients and control subjects, either when the full sample was assessed, or when the sample was stratified by gender. No significant association was observed between C825T, C1429T and G(-350)A polymorphisms and the risk of essential hypertension in any genetic model. Linkage disequilibrium was only detected between C825T and C1429T polymorphisms. Haplotype analyses observed that none of the three estimated haplotypes significantly increased the risk of hypertension. CONCLUSIONS Our study suggested that the GNB3 gene polymorphisms [C825T, C1429T and G(-350)A] were not significantly associated with essential hypertension in northern Han Chinese population.
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99
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Lee YH. Meta-analysis of genetic association studies. Ann Lab Med 2015; 35:283-7. [PMID: 25932435 PMCID: PMC4390695 DOI: 10.3343/alm.2015.35.3.283] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/02/2014] [Accepted: 03/04/2015] [Indexed: 02/05/2023] Open
Abstract
The object of this review is to help readers to understand meta-analysis of genetic association study. Genetic association studies are a powerful approach to identify susceptibility genes for common diseases. However, the results of these studies are not consistently reproducible. In order to overcome the limitations of individual studies, larger sample sizes or meta-analysis is required. Meta-analysis is a statistical tool for combining results of different studies on the same topic, thus increasing statistical strength and precision. Meta-analysis of genetic association studies combines the results from independent studies, explores the sources of heterogeneity, and identifies subgroups associated with the factor of interest. Meta-analysis of genetic association studies is an effective tool for garnering a greater understanding of complex diseases and potentially provides new insights into gene-disease associations.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
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100
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Shaaban HH, Mohy AM, Abdel-Razek ARA, Wahab AA. Interleukin-18 -607C/A gene polymorphism in Egyptian asthmatic children. Mol Diagn Ther 2015; 18:427-34. [PMID: 24711060 DOI: 10.1007/s40291-014-0097-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Asthma is a multifactorial respiratory disease determined by interactions of multiple disease susceptibility genes and environmental factors. Interleukin (IL)-18 is an important cytokine for initiating and perpetuating the catabolic and inflammatory response in allergic asthma. A number of single nucleotide polymorphisms that influence IL-18 production are found in the gene promoter region. OBJECTIVES The aim of this study was to investigate the association of IL-18 -607C/A promoter polymorphism with asthma and whether this polymorphism influenced the severity of asthma in affected children. The influence of this promoter gene polymorphism on total serum IgE level in studied subjects was also investigated. SUBJECTS AND METHODS This study was carried out at the Allergy Clinic of Abu El Reesh Children's Hospital at Cairo University, Egypt. This study included 40 asthmatic children, subdivided into four groups according to different degrees of asthma severity, and 20 apparently healthy subjects as the control group. All cases were subjected to history taking, clinical examination, and the following laboratory investigations: complete blood count, total serum IgE level assay by ELISA and genomic DNA extraction, and analysis for IL-18 -607C/A promoter gene polymorphism using the PCR-RFLP (restriction fragment length polymorphism) technique. RESULTS In the present study the IL-18 -607AA genotype frequency was higher in cases (22.5 %) than in the control group (15 %); however, the difference was not statistically significant (p = 0.773). No statistically significant difference between the degree of asthma severity and IL-18 -607C/A polymorphism was found (p = 0.489). No significant association could be detected upon comparing the frequencies of C and A alleles among the two studied groups (p = 0.366). Also, no significant differences were demonstrated for the allele frequencies when the intermittent with mild [odds ratio (OR) = 2.72, 95 % CI 1.03-2.33, p = 0.067], intermittent with moderate, and severe (OR = 2.8, 95 % CI 1.01-8.5, p = 0.066) asthma groups were compared. The median value of the total serum IgE level in asthmatic cases with the mutant genotype (AA) was significantly higher [360 IU/L (96.6-1,340 IU/L)] than in the control group [119 IU/L (70.6-158.9 IU/L)] (p = 0.033). CONCLUSION No significant statistical difference was encountered regarding the distribution of IL-18 -607C/A genotypes and allele frequencies in asthma patients and healthy controls. Also, there were no significant associations between asthma severity and different genotypes or alleles. The median value of the total serum IgE level in asthmatic cases with the mutant genotype (AA) was significantly higher than in the control group. Thus, IL-18 -607AA genotype frequency might be related to higher total serum IgE.
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