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Lin YF, Huang MC, Liu HC. Glycogen synthase kinase 3β gene polymorphisms may be associated with bipolar I disorder and the therapeutic response to lithium. J Affect Disord 2013; 147:401-6. [PMID: 23021822 DOI: 10.1016/j.jad.2012.08.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 01/25/2023]
Abstract
BACKGROUND Glycogen Synthase Kinase 3β (GSK-3β) is thought to be a key feature in the therapeutic mechanism of mood stabilizers (e.g., lithium). Overexpression of GSK-3β might play a role in the pathogenesis of bipolar I disorder. Within the GSK-3β gene, a promoter single nucleotide polymorphism (SNP) rs334558 was identified associated with transcriptional strength, and an intronic SNP rs6438552 was found to regulate selection of splice acceptor sites. The aim of this study is to test the association between the two polymorphisms and bipolar I disorder. METHODS We genotyped the two SNPs in 138 Taiwanese bipolar I disorder patients and 131 controls. Lithium treatment efficacy was evaluated for 83 patients who had been treated with lithium carbonate for at least 24 months. RESULTS We found no association between each of the two SNPs and the risk of bipolar I disorder. Following correction for multiple testing, CT genotype at rs6438552 was associated with an older age of onset than other genotypes (P=0.042) in female patients. Patients with genotype TT at rs334558 (P=0.044) had poorer response to lithium treatment. There was a trend that haplotype C-T increased the risk for bipolar I disorder (adjusted OR=4.22, corrected P=0.084), and patients with haplotype T-T had poorer treatment response to lithium than those with haplotype C-C. LIMITATIONS Limitations included small sample size, retrospective data collection, and a potential sampling bias. CONCLUSIONS Despite the several limitations of the study, our results suggested GSK-3β genetic variants may be associated with the risk of bipolar I disorder, age of disease onset in females, and the therapeutic response to lithium.
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Affiliation(s)
- Yen-Feng Lin
- Harvard School of Public Health, Boston, MA 02115, USA
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152
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Berenguer AG, Rosa A, Brehm A. Asthma-snapshot or motion picture? Front Genet 2013; 4:73. [PMID: 23641254 PMCID: PMC3639421 DOI: 10.3389/fgene.2013.00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/15/2013] [Indexed: 01/27/2023] Open
Affiliation(s)
| | - Alexandra Rosa
- Human Genetics Laboratory, University of MadeiraFunchal, Portugal
- Medical Sciences Unit, Life Sciences Center, University of MadeiraFunchal, Portugal
| | - António Brehm
- Human Genetics Laboratory, University of MadeiraFunchal, Portugal
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153
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Chen C, Ritland K. Lineage-specific mapping of quantitative trait loci. Heredity (Edinb) 2013; 111:106-13. [PMID: 23612690 DOI: 10.1038/hdy.2013.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/31/2023] Open
Abstract
We present an approach for quantitative trait locus (QTL) mapping, termed as 'lineage-specific QTL mapping', for inferring allelic changes of QTL evolution along with branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. Although comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage-specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkey-flower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage-specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.
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Affiliation(s)
- C Chen
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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154
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Zheng J, Gaunt TR, Day INM. Sequential sentinel SNP Regional Association Plots (SSS-RAP): an approach for testing independence of SNP association signals using meta-analysis data. Ann Hum Genet 2013; 77:67-79. [PMID: 23278391 DOI: 10.1111/j.1469-1809.2012.00737.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
Genome-Wide Association Studies (GWAS) frequently incorporate meta-analysis within their framework. However, conditional analysis of individual-level data, which is an established approach for fine mapping of causal sites, is often precluded where only group-level summary data are available for analysis. Here, we present a numerical and graphical approach, "sequential sentinel SNP regional association plot" (SSS-RAP), which estimates regression coefficients (beta) with their standard errors using the meta-analysis summary results directly. Under an additive model, typical for genes with small effect, the effect for a sentinel SNP can be transformed to the predicted effect for a possibly dependent SNP through a 2×2 2-SNP haplotypes table. The approach assumes Hardy-Weinberg equilibrium for test SNPs. SSS-RAP is available as a Web-tool (http://apps.biocompute.org.uk/sssrap/sssrap.cgi). To develop and illustrate SSS-RAP we analyzed lipid and ECG traits data from the British Women's Heart and Health Study (BWHHS), evaluated a meta-analysis for ECG trait and presented several simulations. We compared results with existing approaches such as model selection methods and conditional analysis. Generally findings were consistent. SSS-RAP represents a tool for testing independence of SNP association signals using meta-analysis data, and is also a convenient approach based on biological principles for fine mapping in group level summary data.
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Affiliation(s)
- Jie Zheng
- Bristol Genetic Epidemiology Laboratories, Department of Social Medicine, University of Bristol, Bristol, UK
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155
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Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 2013; 8:e60793. [PMID: 23577161 PMCID: PMC3618337 DOI: 10.1371/journal.pone.0060793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/03/2013] [Indexed: 01/11/2023] Open
Abstract
The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.
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156
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Yang HC, Liu CM, Liu YL, Chen CW, Chang CC, Fann CSJ, Chiou JJ, Yang UC, Chen CH, Faraone SV, Tsuang MT, Hwu HG. The DAO gene is associated with schizophrenia and interacts with other genes in the Taiwan Han Chinese population. PLoS One 2013; 8:e60099. [PMID: 23555897 PMCID: PMC3610748 DOI: 10.1371/journal.pone.0060099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 02/22/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Schizophrenia is a highly heritable disease with a polygenic mode of inheritance. Many studies have contributed to our understanding of the genetic underpinnings of schizophrenia, but little is known about how interactions among genes affect the risk of schizophrenia. This study aimed to assess the associations and interactions among genes that confer vulnerability to schizophrenia and to examine the moderating effect of neuropsychological impairment. METHODS We analyzed 99 SNPs from 10 candidate genes in 1,512 subject samples. The permutation-based single-locus, multi-locus association tests, and a gene-based multifactorial dimension reduction procedure were used to examine genetic associations and interactions to schizophrenia. RESULTS We found that no single SNP was significantly associated with schizophrenia. However, a risk haplotype, namely A-T-C of the SNP triplet rsDAO7-rsDAO8-rsDAO13 of the DAO gene, was strongly associated with schizophrenia. Interaction analyses identified multiple between-gene and within-gene interactions. Between-gene interactions including DAO*DISC1 , DAO*NRG1 and DAO*RASD2 and a within-gene interaction for CACNG2 were found among schizophrenia subjects with severe sustained attention deficits, suggesting a modifying effect of impaired neuropsychological functioning. Other interactions such as the within-gene interaction of DAO and the between-gene interaction of DAO and PTK2B were consistently identified regardless of stratification by neuropsychological dysfunction. Importantly, except for the within-gene interaction of CACNG2, all of the identified risk haplotypes and interactions involved SNPs from DAO. CONCLUSIONS These results suggest that DAO, which is involved in the N-methyl-d-aspartate receptor regulation, signaling and glutamate metabolism, is the master gene of the genetic associations and interactions underlying schizophrenia. Besides, the interaction between DAO and RASD2 has provided an insight in integrating the glutamate and dopamine hypotheses of schizophrenia.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chih-Min Liu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Division of Mental Health and Substance Abuse Research, National Health Research Institutes, Taipei, Taiwan
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | | | - Cathy S. J. Fann
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jen-Jie Chiou
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ueng-Cheng Yang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Houh Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Stephen V. Faraone
- Medical Genetics Research Center and Departments of Psychiatry and Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Ming T. Tsuang
- Harvard Institute of Psychiatric Epidemiology and Genetics, and Departments of Epidemiology and Psychiatry, Harvard University, Boston, Massachusetts, United States of America
- Institute of Behavioral Genomics, University of California San Diego, La Jolla, California, United States of America
| | - Hai-Gwo Hwu
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Institute of Epidemiology, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Psychology, College of Science, National Taiwan University, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
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157
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McKay GJ, Savage DA, Patterson CC, Lewis G, McKnight AJ, Maxwell AP. Association analysis of dyslipidemia-related genes in diabetic nephropathy. PLoS One 2013; 8:e58472. [PMID: 23555584 PMCID: PMC3608831 DOI: 10.1371/journal.pone.0058472] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/05/2013] [Indexed: 01/13/2023] Open
Abstract
Type 1 diabetes (T1D) increases risk of the development of microvascular complications and cardiovascular disease (CVD). Dyslipidemia is a common risk factor in the pathogenesis of both CVD and diabetic nephropathy (DN), with CVD identified as the primary cause of death in patients with DN. In light of this commonality, we assessed single nucleotide polymorphisms (SNPs) in thirty-seven key genetic loci previously associated with dyslipidemia in a T1D cohort using a case-control design. SNPs (n = 53) were genotyped using Sequenom in 1467 individuals with T1D (718 cases with proteinuric nephropathy and 749 controls without nephropathy i.e. normal albumin excretion). Cases and controls were white and recruited from the UK and Ireland. Association analyses were performed using PLINK to compare allele frequencies in cases and controls. In a sensitivity analysis, samples from control individuals with reduced renal function (estimated glomerular filtration rate<60 ml/min/1.73 m2) were excluded. Correction for multiple testing was performed by permutation testing. A total of 1394 samples passed quality control filters. Following regression analysis adjusted by collection center, gender, duration of diabetes, and average HbA1c, two SNPs were significantly associated with DN. rs4420638 in the APOC1 region (odds ratio [OR] = 1.51; confidence intervals [CI]: 1.19–1.91; P = 0.001) and rs1532624 in CETP (OR = 0.82; CI: 0.69–0.99; P = 0.034); rs4420638 was also significantly associated in a sensitivity analysis (P = 0.016) together with rs7679 (P = 0.027). However, no association was significant following correction for multiple testing. Subgroup analysis of end-stage renal disease status failed to reveal any association. Our results suggest common variants associated with dyslipidemia are not strongly associated with DN in T1D among white individuals. Our findings, cannot entirely exclude these key genes which are central to the process of dyslipidemia, from involvement in DN pathogenesis as our study had limited power to detect variants of small effect size. Analysis in larger independent cohorts is required.
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Affiliation(s)
- Gareth J McKay
- Nephrology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.
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158
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Human leukocyte antigen class I alleles and haplotypes associated with primary hepatocellular carcinoma in persistent HBV-infected patients. Hum Immunol 2013; 74:758-63. [PMID: 23459080 DOI: 10.1016/j.humimm.2013.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 01/18/2013] [Accepted: 02/19/2013] [Indexed: 01/04/2023]
Abstract
Many studies have shown that Human leukocyte antigen (HLA) class I alleles are associated with the development of various cancers. However, its role in hepatocellular carcinoma (HCC) is still unknown. To investigate whether HLA class I allelic polymorphism is related to the development of hepatitis B virus(HBV)-associated HCC, a total of 326 HBV-infected patients (138 individuals with HCC and 188 well-matched controls without HCC) were enrolled in this study. HLA-A, -B, and -C were genotyped by polymerase chain reaction-sequencing based typing (PCR-SBT) method. We identified HLA-B(∗)35:01:01G as a risk factor for HBV-related HCC development independent of our previous findings in HLA region (OR, 12.04; p, 0.0028; pc, 0.04). HLA-A(∗)11:01:01G, B(∗)58:01:01G, C(∗)03:02:01G and some of their extended haplotypes were found as potential susceptible factors for HCC development. HLA-B(∗)46:01:01G and some of its extended haplotypes were found as potential protective factors for HCC development. Our results support that specific HLA class I alleles and haplotypes may affect the risk of HBV-related HCC development. The findings may help to determine better approaches for prevention and treatment of HCC in these patients.
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159
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Guo S, Li X, Gao M, Li Y, Song B, Niu W. The relationship between XRCC1 and XRCC3 gene polymorphisms and lung cancer risk in northeastern Chinese. PLoS One 2013; 8:e56213. [PMID: 23409158 PMCID: PMC3568083 DOI: 10.1371/journal.pone.0056213] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 01/10/2013] [Indexed: 11/23/2022] Open
Abstract
Background The prevalence of lung cancer in China will be the world's highest if allowed to proceed uncurbed. To unravel its genetic underpinnings, we sought to investigate the association of three well-characterized nonsynonymous polymorphisms in XRCC1 (Arg194Trp and Arg399Gln) and XRCC3 (Thr241Met) genes with lung cancer risk in northeastern Chinese. Methodology/Principal Findings This study was hospital-based in design, encompassing 684 patients with lung cancer and 604 cancer-free controls. Genotyping was performed using the PCR-LDR (ligase detection reactions) method. Data were analyzed by R language and multifactor dimensionality reduction (MDR) software. Single-locus analysis identified significance in genotype distributions of polymorphism Arg194Trp (P = 0.002) and Arg399Gln (P = 0.017), and in allele distributions of Thr241Met (P = 0.005). Carriers of 399Gln/Gln genotype conferred a 147% increased risk relative to the non-carriers (odds ratio (OR): 2.47; 95% confidence interval (95% CI): 1.48–4.13; P<0.001). For Thr241Met, significance persisted under allelic (OR = 1.63; 95% CI: 1.14–2.33; P = 0.005), additive (OR = 1.64; 95% CI: 1.16–2.32; P = 0.005) and dominant (OR = 1.67; 95% CI: 1.17–2.38; P = 0.004) models. However, common allele combinations were comparable in frequency between patients and controls. In interaction analysis, the overall best MDR model included Arg399Gln and Thr241Met polymorphisms, with a maximal testing accuracy of 63.18% and a maximal cross-validation consistency of 10 out of 10 (P = 0.0175). Conclusions Our study significantly demonstrated an independent and synergistic contribution of XRCC1 Arg399Gln and XRCC3 Thr241Met polymorphisms to lung cancer susceptibility in northeastern Chinese.
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Affiliation(s)
- Shujie Guo
- State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaobo Li
- State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Gao
- Department of Respiratory Medicine, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuqiong Li
- State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bei Song
- State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenquan Niu
- State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
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160
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Gu L, Su L, Chen Q, Xie J, Yan Y, Wu G, Tan J, Liang B, Dou W, Chen W, Wu P, Wang J, Tang N. Association between the single-nucleotide polymorphism rs12425791 and ischemic stroke in Chinese populations: new data and meta-analysis. Int J Neurosci 2013; 123:359-65. [PMID: 23270316 DOI: 10.3109/00207454.2012.761217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Two single-nucleotide polymorphisms rs11833579 and rs12425791 located on chromosome 12p13 were reported to be associated with ischemic stroke in Caucasians. In the present study, we investigated whether the single-nucleotide polymorphism rs12425791 was associated with ischemic stroke in Chinese populations. METHODS We carried out a case-control study examining a total of 166 Guangxi Han patients with ischemic stroke and 192 healthy controls. We also performed a meta-analysis of the data from our study and those from published studies to investigate whether an association between rs12425791 and ischemic stroke could be detected in Chinese populations. RESULTS There was no statistically significant association between the single-nucleotide polymorphism rs12425791 and ischemic stroke in the Guangxi Han population. Our meta-analysis also found no significant association between rs12425791 and ischemic stroke in Chinese populations [allelic model odds ratio (OR) = 1.01, 95% confidence interval (CI), 0.96-1.07; dominant model OR = 1.01, 95%CI, 0.94-1.10; recessive model OR = 1.00, 95%CI, 0.86-1.17]. CONCLUSIONS The single-nucleotide polymorphism rs12425791 does not confer a substantial risk for ischemic stroke in Chinese populations.
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Affiliation(s)
- Lian Gu
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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161
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Zoldoš V, Horvat T, Lauc G. Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies. Curr Opin Chem Biol 2013; 17:34-40. [DOI: 10.1016/j.cbpa.2012.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/29/2012] [Accepted: 12/02/2012] [Indexed: 01/28/2023]
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162
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Lu X, Wang H, Liu B, Xiang J. Three EST-SSR markers associated with QTL for the growth of the clam Meretrix meretrix revealed by selective genotyping. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:16-25. [PMID: 22538932 DOI: 10.1007/s10126-012-9453-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/04/2012] [Indexed: 05/31/2023]
Abstract
The clam Meretrix meretrix is a member of widely cultured, commercially important clams. A marker-trait association analysis was performed using expressed sequence tag (EST) simple sequence repeat (SSR) markers for marker-assisted selection in M. meretrix. Three markers, MM1272, MM2034, and MM7721, were found to be significantly associated with quantitative trait loci (QTLs) controlling shell length (P < 0.0001) in clams of a fast-growing population (JSF) and a control population (JSC). The 144-bp allele of MM1272, the 154-bp allele of MM2034, and the 152- and 165-bp alleles of MM7721 showed a significantly higher frequency in the JSF population (17.65, 36.41, 28.67, and 29.33 %) than in the JSC population (4.65, 8.33, 3.47, and 5.56 %). The three markers showed lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes in JSF than in JSC population. The three markers have been further confirmed in the high and low tails of another population (09G₃SPSB); similarly, lower values for the number of alleles and observed heterozygosity as well as a higher proportion of homozygotes were found in 09G₃SPSB(H). The putative functions of the three gene fragments containing MM1272, MM2034, and MM7721 also suggested that the three SSR-containing genes might be involved in growth of M. meretrix. All the results suggest that the three EST-SSR markers associated with growth QTLs would be useful for marker-assisted selection in M. meretrix breeding.
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Affiliation(s)
- Xia Lu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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163
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Aljasir B, Ioannidis JPA, Yurkiewich A, Moher D, Higgins JPT, Arora P, Little J. Assessment of systematic effects of methodological characteristics on candidate genetic associations. Hum Genet 2013; 132:167-78. [PMID: 23095857 DOI: 10.1007/s00439-012-1237-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/08/2012] [Indexed: 12/30/2022]
Abstract
Candidate genetic association studies have been found to have a low replication rate in the past. Here, we aimed to assess whether aspects of reported methodological characteristics in genetic association studies may be related to the magnitude of effects observed. An observational, literature-based investigation of 511 case-control studies of genetic association studies indexed in 2007, was undertaken. Meta-regression analyses were used to assess the relationship between 23 reported methodological characteristics and the magnitude of genetic associations. The 511 studies had been conducted in 52 countries and were published in 220 journals (median impact factor 5.1). The multivariate meta-regression model of methodological characteristics plus disease category accounted for 17.2 % of the between-study variance in the magnitude of the reported genetic associations. Our findings are consistent with the view that better conducted and better reported genetic association research may lead to less inflated results.
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Affiliation(s)
- Badr Aljasir
- Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, ON, Canada
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164
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Pishva SR, Vasudevan R, Etemad A, Heidari F, Komara M, Ismail P, Othman F, Karimi A, Sabri MR. Analysis of MTHFR and MTRR Gene Polymorphisms in Iranian Ventricular Septal Defect Subjects. Int J Mol Sci 2013; 14:2739-52. [PMID: 23358257 PMCID: PMC3588012 DOI: 10.3390/ijms14022739] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 01/04/2013] [Accepted: 01/13/2013] [Indexed: 01/04/2023] Open
Abstract
Ventricular septal defect (VSD) is one of the most common types of congenital heart defects (CHD). There are vivid multifactorial causes for VSD in which both genetic and environmental risk factors are consequential in the development of CHD. Methionine synthase reductase (MTRR) and methylenetetrahydrofolate reductase (MTHFR) are two of the key regulatory enzymes involved in the metabolic pathway of homocysteine. Genes involved in homocysteine/folate metabolism may play an important role in CHDs. In this study; we determined the association of A66G and C524T polymorphisms of the MTRR gene and C677T polymorphism of the MTHFR gene in Iranian VSD subjects. A total of 123 children with VSDs and 125 healthy children were included in this study. Genomic DNA was extracted from the buccal cells of all the subjects. The restriction fragment length polymorphism polymerase chain reaction (PCR-RFLP) method was carried out to amplify the A66G and C524T polymorphism of MTRR and C677T polymorphism of MTHFR genes digested with Hinf1, Xho1 and Nde1 enzymes, respectively. The genotype frequencies of CC, CT and TT of MTRR gene among the studied cases were 43.1%, 40.7% and 16.3%, respectively, compared to 52.8%, 43.2% and 4.0%, respectively among the controls. For the MTRR A66G gene polymorphism, the genotypes frequencies of AA, AG and GG among the cases were 33.3%, 43.9% and 22.8%, respectively, while the frequencies were 49.6%, 42.4% and 8.0%, respectively, among control subjects. The frequencies for CC and CT genotypes of the MTHFR gene were 51.2% and 48.8%, respectively, in VSD patients compared to 56.8% and 43.2% respectively, in control subjects. Apart from MTHFR C677T polymorphism, significant differences were noticed (p < 0.05) in C524T and A66G polymorphisms of the MTRR gene between cases and control subjects.
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Affiliation(s)
- Seyyed Reza Pishva
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
| | - Ramachandran Vasudevan
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
- School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, Selangor 46150, Darul Ehsan, Malaysia
| | - Ali Etemad
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
| | - Farzad Heidari
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
| | - Makanko Komara
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
| | - Patimah Ismail
- Genetic Research Group, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mails: (S.R.P.); (R.V.); (A.E.); (F.H.); (M.K.)
| | - Fauziah Othman
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia; E-Mail:
| | - Abdollah Karimi
- Pediatric Infectious Research Centre, Mofid Children Hospital, Shariati St, Tehran 15468, Iran; E-Mail:
| | - Mohammad Reza Sabri
- Pediatric Heart Centre, Isfahan Medical University, Isfahan 73461, Iran; E-Mail:
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Sequence variations in OsAGPase significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.). Genet Res (Camb) 2013; 94:179-89. [PMID: 22950899 DOI: 10.1017/s0016672312000390] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A-G) was significantly associated with increased AC (P<0·001, R(2)=15·6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001, R(2)=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.
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166
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Baxter AG, Jordan MA. From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. Rev Diabet Stud 2012; 9:201-23. [PMID: 23804261 DOI: 10.1900/rds.2012.9.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.
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Affiliation(s)
- Alan G Baxter
- Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville QLD 4811, Australia.
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167
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Jin W, Su X, Xu M, Liu Y, Shi J, Lu L, Niu W. Interactive association of five candidate polymorphisms in Apelin/APJ pathway with coronary artery disease among Chinese hypertensive patients. PLoS One 2012; 7:e51123. [PMID: 23226564 PMCID: PMC3513301 DOI: 10.1371/journal.pone.0051123] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022] Open
Abstract
Background Via sequencing the genes of apelin/angiotensin receptor-like 1 (apelin/APJ) pathway, we have recently identified and validated four common polymorphisms (rs3761581, rs56204867, rs7119375, and rs10501367) implicated in the development of hypertension. Extending these findings, we, in Chinese hypertensive patients, sought to investigate the association of these four polymorphisms and one additional promising candidate (rs9943582) from this pathway with the risk of developing coronary artery disease (CAD). Methodology/Principal Findings Genotypes were obtained from 994 sporadic CAD patients and 708 age- and sex-matched controls. All participants were hypertensives and angiographically-confirmed. Data were analyzed by Haplo.Stats and multifactor dimensionality reduction (MDR) softwares. Genotype distributions of five examined polymorphisms satisfied Hardy-Weinberg equilibrium in controls of both genders. Single-locus analyses exhibited no significant differences in the genotype/allele frequencies of examined polymorphisms between CAD patients and controls (P>0.05), even after controlling traditional cardiovascular confounders. In haplotype analyses, low-penetrance haplotype G-A (in order of rs56204867 and rs3761581 from apelin gene) was significantly overrepresented in controls (1.73%) relative to in CAD patients (0.4%) in males (P = 0.047). Further interaction analyses suggested an overall best MDR model including rs3761581 in males (P = 0.0408) and including rs7119375 and rs9943582 in females (P<0.0001), which were further substantiated in the classical logistical regression model. Conclusions Our findings demonstrated a contributive role of low-penetrance haplotype in apelin gene on CAD in males, and more importantly, interactive effects of genetic defects in apelin/APJ pathway might confer a potential risk in Chinese hypertensive patients.
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Affiliation(s)
- Wei Jin
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuxiu Su
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Liu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyi Shi
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenquan Niu
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Hypertension, Shanghai, China
- * E-mail:
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168
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Menke V, Van Zoest KPM, Moons LMG, Pot RGJ, Siersema PD, Kuipers EJ, Kusters JG. Myo9B is associated with an increased risk of Barrett's esophagus and esophageal adenocarcinoma. Scand J Gastroenterol 2012; 47:1422-8. [PMID: 22954106 DOI: 10.3109/00365521.2012.722673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Reflux esophagitis (RE) and Barrett's esophagus (BE) are predisposing factors for development of esophageal adenocarcinoma (EAC), the solid tumor with the fastest rising incidence in the Western world. This RE-BE-EAC cascade involves multiple host factors and consequently multiple genes. Polymorphisms in the 3' region of myosin IXB (Myo9B) are associated with chronic inflammatory gastrointestinal disorders like celiac disease and ulcerative colitis, assuming that variation in Myo9B influences the intestinal permeability. AIM To determine esophageal expression and the genetic variation of the Myo9B gene in the RE-BE-EAC cascade. METHODS DNA from 886 Caucasian participants (198 non-reflux controls, 305 RE, 254 BE, 129 EAC) was collected for the determination of the Myo9B gene polymorphism (rs2305764). Esophageal Myo9B expression was determined on biopsies from normal, RE, BE and EAC epithelium. RESULTS Genotype G/G was more common in BE (p = 0.032) and EAC (p = 0.046), but not in RE (p = 0.126) compared with the control group. Cytoplasmic Myo9B expression was determined in RE, BE and EAC, but most prominent in epithelial cells of BE and EAC. CONCLUSIONS Genetic variation of Myo9B may play a role in the etiology of BE and EAC by increasing the permeability of the epithelial barrier.
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Affiliation(s)
- Vivianda Menke
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
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169
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Tejera P, Meyer NJ, Chen F, Feng R, Zhao Y, O'Mahony DS, Li L, Sheu CC, Zhai R, Wang Z, Su L, Bajwa E, Ahasic AM, Clardy PF, Gong MN, Frank AJ, Lanken PN, Thompson BT, Christie JD, Wurfel MM, O'Keefe GE, Christiani DC. Distinct and replicable genetic risk factors for acute respiratory distress syndrome of pulmonary or extrapulmonary origin. J Med Genet 2012; 49:671-80. [PMID: 23048207 DOI: 10.1136/jmedgenet-2012-100972] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The role of genetics in the development of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) from direct or indirect lung injury has not been specifically investigated. The aim of this study was to identify genetic variants contributing to ALI/ARDS from pulmonary or extrapulmonary causes. METHODS We conducted a multistage genetic association study. We first performed a large-scale genotyping (50K ITMAT-Broad_CARe Chip) in 1717 critically ill Caucasian patients with either pulmonary or extrapulmonary injury, to identify single nucleotide polymorphisms (SNPs) associated with the development of ARDS from direct or indirect insults to the lung. Identified SNPs (p≤0.0005) were validated in two separated populations (Stage II), with trauma (Population I; n=765) and pneumonia/pulmonary sepsis (Population II; n=838), as causes for ALI/ARDS. Genetic variants replicating their association with trauma related-ALI in Stage II were validated in a second trauma-associated ALI population (n=224, Stage III). RESULTS In Stage I, non-overlapping SNPs were significantly associated with ARDS from direct/indirect lung injury, respectively. The association between rs1190286 (POPDC3) and reduced risk of ARDS from pulmonary injury was validated in Stage II (p<0.003). SNP rs324420 (FAAH) was consistently associated with increased risk of ARDS from extrapulmonary causes in two independent ALI-trauma populations (p<0.006, Stage II; p<0.05, Stage III). Meta-analysis confirmed these associations. CONCLUSIONS Different genetic variants may influence ARDS susceptibility depending on direct versus indirect insults. Functional SNPs in POPDC3 and FAAH genes may be driving the association with direct and indirect ALI/ARDS, respectively.
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Affiliation(s)
- Paula Tejera
- Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA
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170
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Harnessing Nutrigenomics: Development of web-based communication, databases, resources, and tools. GENES AND NUTRITION 2012; 1:5-11. [PMID: 18850216 DOI: 10.1007/bf02829931] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 02/10/2006] [Indexed: 10/22/2022]
Abstract
Nutrient - gene interactions are responsible for maintaining health and preventing or delaying disease. Unbalanced diets for a given genotype lead to chronic diseases such as obesity, diabetes, cardiovascular, and are likely to contribute to increased severity and/or early-onset of many age-related diseases. Many nutrition and many genetic studies still fail to properly include both variables in the design, execution, and analyses of human, laboratory animal, or cell culture experiments. The complexity ofnutrient-gene interactions has led to the realization that strategic international alliances are needed to improve the completeness of nutrigenomic studies - a task beyond the capabilities of a single laboratory team. Eighty-eight researchers from 22 countries recently outlined the issues and challenges for harnessing the nutritional genomics for public and personal health. The next step in the process of forming productive international alliances is the development of a virtual center for organizing collaborations and communications that foster resources sharing, best practices improvements, and creation of databases. We describe here plans and initial efforts of creating the Nutrigenomics Information Portal, a web-based resource for the international nutrigenomics society. This portal aims at becoming the prime source ofinformation and interaction for nutrigenomics scientists through a collaborative effort.
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171
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Harrap SB. Blood pressure genetics: time to focus. ACTA ACUST UNITED AC 2012; 3:231-7. [PMID: 20409965 DOI: 10.1016/j.jash.2009.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 06/09/2009] [Indexed: 12/21/2022]
Abstract
This review briefly charts the recent history of the genetic study of high blood pressure (BP). After an inconsistent start it was hoped that very large genome-wide association studies (GWAS) might be able to provide some reliable answers. The two largest and most recent GWAS: CHARGE and GlobalBPgen were able to identify, despite some significant inconsistencies, genetic loci that accounted for only about 2% of the genetic factors believed to influence BP. The loci were associated with an estimated effect on BP of 1 mm Hg or less. No doubt many other loci exerting even smaller (<0.5 mm Hg) exist. This review contends that it is time to focus on the loci that can be viewed as confirmed, rather than extending the GWAS searches for less significant genetic influences. It is time to identify the precise deoxyribonucleic acid variants affecting BP, understand their mechanisms of action and think of ways in which such knowledge can be used to prevent and treat high BP in novel, effective, and possibly tailored ways.
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Affiliation(s)
- Stephen B Harrap
- Department of Physiology, University of Melbourne, Victoria, Australia
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172
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Mitjans M, Gastó C, Catalán R, Fañanás L, Arias B. Genetic variability in the endocannabinoid system and 12-week clinical response to citalopram treatment: the role of the CNR1, CNR2 and FAAH genes. J Psychopharmacol 2012; 26:1391-8. [PMID: 22826533 DOI: 10.1177/0269881112454229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
First line treatment of major depression is based on selective serotonin re-uptake inhibitors (SSRIs) that enhance serotonergic neurotransmission by blocking the serotonin transporter. However, clinical response is a complex phenomenon in which other systems such as the endocannabinoid system could be involved. Given the evidence for the role of the endocannabinoid system in the pathogenesis of depression as well as in the mediation of antidepressant drug effects, the aim of this study was to analyze genetic variability in the endocannabinoid system genes (CNR1, CNR2 and FAAH genes) and their role in clinical response (at week 4) and remission (at week 12) in SSRI (citalopram) treatment in a sample of 154 depressive outpatients, all of Spanish origin. All patients were treated with citalopram and followed over 12 weeks. Severity of depressive symptomatology was evaluated by means of the 21-item Hamilton Depression Rating Score (HDRS). No differences were found in any of the genotype distributions according to response or remission. The longitudinal study showed that (i) the CNR1 rs1049353-GG genotype conferred a better response to citalopram treatment in the subgroup of male patients and (ii) G allele carriers (CNR2 rs2501431) presented higher HDRS scores in the follow-up than AA homozygous allele carriers. Our results seem to suggest the involvement of CNR1 and CNR2 genes in clinical responses to citalopram treatment.
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Affiliation(s)
- Marina Mitjans
- Unitat d'Antropologia, Universitat de Barcelona, Barcelona, Spain
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173
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Cardoso S, Lau W, Eiras Dias J, Fevereiro P, Maniatis N. A candidate-gene association study for berry colour and anthocyanin content in Vitis vinifera L. PLoS One 2012; 7:e46021. [PMID: 23029369 PMCID: PMC3461038 DOI: 10.1371/journal.pone.0046021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 08/27/2012] [Indexed: 01/28/2023] Open
Abstract
Anthocyanin content is a trait of major interest in Vitis vinifera L. These compounds affect grape and wine quality, and have beneficial effects on human health. A candidate-gene approach was used to identify genetic variants associated with anthocyanin content in grape berries. A total of 445 polymorphisms were identified in 5 genes encoding transcription factors and 10 genes involved in either the biosynthetic pathway or transport of anthocyanins. A total of 124 SNPs were selected to examine association with a wide range of phenotypes based on RP-HPLC analysis and visual characterization. The phenotypes were total skin anthocyanin (TSA) concentration but also specific types of anthocyanins and relative abundance. The visual assessment was based on OIV (Organisation Internationale de la Vigne et du Vin) descriptors for berry and skin colour. The genes encoding the transcription factors MYB11, MYBCC and MYC(B) were significantly associated with TSA concentration. UFGT and MRP were associated with several different types of anthocyanins. Skin and pulp colour were associated with nine genes (MYB11, MYBCC, MYC(B), UFGT, MRP, DFR, LDOX, CHI and GST). Pulp colour was associated with a similar group of 11 genes (MYB11, MYBCC, MYC(B), MYC(A), UFGT, MRP, GST, DFR, LDOX, CHI and CHS(A)). Statistical interactions were observed between SNPs within the transcription factors MYB11, MYBCC and MYC(B). SNPs within LDOX interacted with MYB11 and MYC(B), while SNPs within CHI interacted with MYB11 only. Together, these findings suggest the involvement of these genes in anthocyanin content and on the regulation of anthocyanin biosynthesis. This work forms a benchmark for replication and functional studies.
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Affiliation(s)
- Silvana Cardoso
- Laboratory of Plant Cell Biotechnology, Instituto de Tecnologia Química e Biológica, Oeiras, Portugal.
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174
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Vidal RO, do Nascimento LC, Mondego JMC, Pereira GAG, Carazzolle MF. Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 2012; 35:331-4. [PMID: 22802718 PMCID: PMC3392885 DOI: 10.1590/s1415-47572012000200014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both cultivars. Our method identified more than 6,000 SNPs in tolerant and sensitive Brazilian cultivars in those drought stress related genes. Among these SNPs, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (MYB, WRKY) related to tolerance to abiotic stress.
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Affiliation(s)
- Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, SP, Brazil
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175
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Pavey SA, Bernatchez L, Aubin-Horth N, Landry CR. What is needed for next-generation ecological and evolutionary genomics? Trends Ecol Evol 2012; 27:673-8. [PMID: 22902072 DOI: 10.1016/j.tree.2012.07.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 07/23/2012] [Accepted: 07/25/2012] [Indexed: 11/27/2022]
Abstract
Ecological and evolutionary genomics (EEG) aims to link gene functions and genomic features to phenotypes and ecological factors. Although the rapid development of technologies allows central questions to be addressed at an unprecedented level of molecular detail, they do not alleviate one of the major challenges of EEG, which is that a large fraction of genes remains without any annotation. Here, we propose two solutions to this challenge. The first solution is in the form of a database that regroups associations between genes, organismal attributes and abiotic and biotic conditions. This database would result in an ecological annotation of genes by allowing cross-referencing across studies and taxa. Our second solution is to use new functional techniques to characterize genes implicated in the response to ecological challenges.
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Affiliation(s)
- Scott A Pavey
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, QC, Canada
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176
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Wu W, Peden D, Diaz-Sanchez D. Role of GSTM1 in resistance to lung inflammation. Free Radic Biol Med 2012; 53:721-9. [PMID: 22683820 PMCID: PMC3418458 DOI: 10.1016/j.freeradbiomed.2012.05.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/18/2012] [Accepted: 05/23/2012] [Indexed: 01/04/2023]
Abstract
Lung inflammation resulting from oxidant/antioxidant imbalance is a common feature of many lung diseases. In particular, the role of enzymes regulated by the NF-E2-related factor 2 transcription factor has recently received increased attention. Among these antioxidant genes, glutathione S-transferase Mu 1 (GSTM1) has been most extensively characterized because it has a null polymorphism that is highly prevalent in the population and associated with increased risk of inflammatory lung diseases. Present evidence suggests that GSTM1 acts through interactions with other genes and environmental factors, especially air pollutants. Here, we review GSTM1 gene expression and regulation and summarize the findings from epidemiological, clinical, animal, and in vitro studies on the role played by GSTM1 in lung inflammation. We discuss limitations in the existing knowledge base and future perspectives and evaluate the potential of pharmacologic and genetic manipulation of the GSTM1 gene to modulate pulmonary inflammatory responses.
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Affiliation(s)
- Weidong Wu
- Department of Pediatrics, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, NC 7599, USA.
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177
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A distance-based cluster algorithm for genomic analysis in genetic disease. Interdiscip Sci 2012; 4:90-6. [PMID: 22843231 DOI: 10.1007/s12539-012-0124-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 11/17/2011] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
Both environmental and genetic factors play roles in the development of some diseases. Complex diseases, such as Crohn's disease or Type II diabetes, are caused by a combination of environmental factors and mutations in multiple genes. Patients who have been diagnosed with such diseases cannot easily be treated. However, many diseases can be avoided if people at high risk change their living style, one example being their diet. But how can we tell their susceptibility to diseases before symptoms are found and help them make informed decisions about their health? The susceptibility to complex diseases can be predicted through the analysis of the genetic data. With the development of DNA microarray technique, it is possible to access the human genetic information related to specific diseases. This paper used a combinatorial method to analyze the genetic casecontrol data for Crohn's disease. A distance based cluster method has been applied to publicly available genotype data on Crohn's disease for epidemiological study and achieved a highly accurate result.
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178
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Sapru A, Zaroff JG, Pawlikowska L, Liu KD, Khush KK, Baxter-Lowe LA, Hayden V, Menza RL, Convery M, Lo V, Poon A, Kim H, Young WL, Kukreja J, Matthay MA. The 4G/4G genotype of the PAI-1 (serpine-1) 4G/5G polymorphism is associated with decreased lung allograft utilization. Am J Transplant 2012; 12:1848-54. [PMID: 22390401 PMCID: PMC4018219 DOI: 10.1111/j.1600-6143.2012.03996.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Widespread thrombi are found among donor lungs rejected for transplantation. The 4G/5G polymorphism in the plasminogen activator inhibitor (PAI-1) gene impacts transcription and the 4G allele is associated with increased PAI-1 levels. We hypothesized that the 4G/4G genotype would be associated with decreased lung graft utilization, potentially because of worse oxygenation in the donor. We genotyped donors managed by the California Transplant Donor Network from 2001 to 2008 for the 4G/5G polymorphism in the PAI-1 gene. Non-Hispanic donors from 2001 to 2005 defined the discovery cohort (n = 519), whereas donors from 2006 to 2008 defined the validation cohort (n = 369). We found, that the odds of successful lung utilization among Non-Hispanic white donors were lower among donors with the 4G/4G genotype compared to those without this genotype in both the discovery (OR = 0.55, 95% CI = 0.3-0.9, p = 0.02) and validation (OR = 0.5, 95% CI = 0.3-0.9, p = 0.03) cohorts. This relationship was independent of age, gender, cause of death, drug use and history of smoking. Donors with the 4G/4G genotype also had a lower PaO2/FiO2 ratio (p = 0.03) and fewer donors with the 4G/4G genotype achieved the threshold PaO2/FiO2 ratio ≥ 300 (p = 0.05). These findings suggest a role for impaired fibrinolysis resulting in worse gas exchange and decreased donor utilization.
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Affiliation(s)
- A. Sapru
- Department of Pediatrics, University of California, San Francisco, CA,Corresponding author: Anil Sapru,
| | - J. G. Zaroff
- Department of Cardiology Kaiser Permanente, San Francisco, CA
| | - L. Pawlikowska
- Anesthesia and Perioperative Care, University of California, San Francisco, CA
| | - K. D. Liu
- Department of Medicine, University of California, San Francisco, CA
| | - K. K. Khush
- Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA
| | | | - V. Hayden
- California Transplant Donor Network, Oakland, CA
| | - R. L. Menza
- California Transplant Donor Network, Oakland, CA
| | - M. Convery
- Department of Pediatrics, University of California, San Francisco, CA
| | - V. Lo
- Department of Pediatrics, University of California, San Francisco, CA
| | - A. Poon
- Anesthesia and Perioperative Care, University of California, San Francisco, CA
| | - H. Kim
- Anesthesia and Perioperative Care, University of California, San Francisco, CA
| | - W. L. Young
- Anesthesia and Perioperative Care, University of California, San Francisco, CA
| | - J. Kukreja
- Department of Surgery, University of California, San Francisco, CA
| | - M. A. Matthay
- Department of Pediatrics, University of California, San Francisco, CA,Cardiovascular Research Institute, University of California, San Francisco, CA
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Schreiber R, Ferreira-Sae MC, Tucunduva AC, Mill JG, Costa FO, Krieger JE, Franchini KG, Pereira AC, Nadruz W. CYBA C242T polymorphism is associated with obesity and diabetes mellitus in Brazilian hypertensive patients. Diabet Med 2012; 29:e55-61. [PMID: 22268370 DOI: 10.1111/j.1464-5491.2012.03594.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The CYBA C242T polymorphism has been associated with cardiovascular phenotypes such as hypertension and atherosclerosis, but available data are conflicting. This report investigated the impact of this variant on hypertension and metabolic determinants of cardiovascular risk in a large Brazilian sample. METHODS We cross-sectionally evaluated 1856 subjects (826 normotensive subjects and 1030 hypertensive patients) by clinical history, anthropometry, laboratory analysis and genotyping of the CYBA C242T polymorphism. RESULTS Genotype frequencies in the whole population were consistent with the Hardy-Weinberg equilibrium and genotype distributions were not different between hypertensive and normotensive subjects. Hypertensive patients with the CC genotype presented lower fasting plasma glucose levels (5.9 ± 0.1 vs. 6.2 ± 0.1 mmol/l, P = 0.020) and waist circumference (94.5 ± 0.6 vs. 96.3 ± 0.6 cm, P = 0.028) than CT + TT ones. Similarly, the prevalence of diabetes mellitus and obesity was also lower in hypertensive patients carrying the CC genotype (16% vs. 21%, P = 0.041; 36% vs. 43%, P = 0.029, respectively). In addition, multiple and logistic regression analysis demonstrated that the CYBA C242T polymorphism was associated with glucose levels, waist circumference, obesity and diabetes mellitus in hypertensive patients independently of potential confounders. Conversely, in normotensive subjects, no significant difference in studied variables was detected between the genotype groups. CONCLUSIONS These data suggest that the T allele of the CYBA C242T polymorphism may be used as a marker for adverse metabolic features in Brazilian subjects with systemic hypertension.
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Affiliation(s)
- R Schreiber
- Department of Internal Medicine, University of Campinas, Campinas, Brazil
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180
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Hong EP, Park JW. Sample size and statistical power calculation in genetic association studies. Genomics Inform 2012; 10:117-22. [PMID: 23105939 PMCID: PMC3480678 DOI: 10.5808/gi.2012.10.2.117] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 05/14/2012] [Accepted: 05/17/2012] [Indexed: 12/17/2022] Open
Abstract
A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP) marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD), 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.
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Affiliation(s)
- Eun Pyo Hong
- Department of Medical Genetics, Hallym University College of Medicine, Chuncheon 200-702, Korea
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181
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Guo S, Li X, Gao M, Kong H, Li Y, Gu M, Dong X, Niu W. Synergistic association of PTGS2 and CYP2E1 genetic polymorphisms with lung cancer risk in northeastern Chinese. PLoS One 2012; 7:e39814. [PMID: 22761909 PMCID: PMC3382578 DOI: 10.1371/journal.pone.0039814] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/27/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Lung cancer is the most common cause of cancer-related deaths worldwide. The aim of this study was to investigate the association of five extensively-studied polymorphisms in PTGS2 (rs689466, rs5275, rs20417) and CYP2E1 (rs2031920, rs6413432) genes with lung cancer risk in a large northeastern Chinese population. METHODOLOGY/PRINCIPAL FINDINGS This is a hospital-based case-control study involving 684 patients with lung cancer and 604 cancer-free controls. Genotyping was performed using the PCR-LDR method. Data were analyzed using Haplo.stats and MDR programs. There were significant differences between patients and controls in allele/genotype distributions of rs5275 (P = 0.002/0.003) and rs6413432 (P = 0.037/0.044), as well as in genotype distributions of rs689466 (P = 0.02). The risk for lung cancer associated with the rs5275-C mutant allele was decreased by 60% (95% CI [confidence interval]: 0.21-0.74; P = 0.004) under the recessive model. Carriers of rs689466-G mutant allele had a 28% (95% CI: 0.57-0.92; P = 0.008) reduced risk of developing lung cancer relative to the AA genotype carriers. In haplotype analysis, haplotype G-C-C-T (in order of rs689466, rs5275, rs2031920 and rs6413432) decreased the odds of lung cancer by 28% (95% CI: 0.51-0.93; P = 0.019) after adjusting for confounding factors, whereas haplotype A-T-T-T had 1.49-fold (95% CI: 1.21-1.79; P = 0.012) increased risk for lung cancer. Using MDR method, the overall best model including rs5275, rs689466 and rs6413432 polymorphisms was identified with a maximal testing accuracy of 66.1% and a maximal cross-validation consistency of 10 out of 10 (P = 0.003). CONCLUSIONS/SIGNIFICANCE Our findings demonstrated a potentially synergistic association of PTGS2 and CYP2E1 polymorphisms with the underlying cause of lung cancer in northeastern Chinese.
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Affiliation(s)
- Shujie Guo
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobo Li
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Gao
- Department of Respiratory Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hong Kong
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuqiong Li
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingliang Gu
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqun Dong
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island, United States of America
- * E-mail: (WN); (XD)
| | - Wenquan Niu
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (WN); (XD)
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182
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Nyholt DR. Using genomic data to make indirect (and unauthorized) estimates of disease risk. Public Health Genomics 2012; 15:303-11. [PMID: 22722694 DOI: 10.1159/000336546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The number of genetic factors associated with common human traits and disease is increasing rapidly, and the general public is utilizing affordable, direct-to-consumer genetic tests. The results of these tests are often in the public domain. A combination of factors has increased the potential for the indirect estimation of an individual's risk for a particular trait. Here we explain the basic principals underlying risk estimation which allowed us to test the ability to make an indirect risk estimation from genetic data by imputing Dr. James Watson's redacted apolipoprotein E gene (APOE) information. The principles underlying risk prediction from genetic data have been well known and applied for many decades, however, the recent increase in genomic knowledge, and advances in mathematical and statistical techniques and computational power, make it relatively easy to make an accurate but indirect estimation of risk. There is a current hazard for indirect risk estimation that is relevant not only to the subject but also to individuals related to the subject; this risk will likely increase as more detailed genomic data and better computational tools become available.
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Affiliation(s)
- D R Nyholt
- Queensland Institute of Medical Research, Brisbane, Qld., Australia.
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183
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Dusse F, Frey UH, Bilalic A, Dirkmann D, Görlinger K, Siffert W, Peters J. The GNB3 C825T polymorphism influences platelet aggregation in human whole blood. Pharmacogenet Genomics 2012; 22:43-9. [PMID: 22082654 DOI: 10.1097/fpc.0b013e32834e1674] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Platelet aggregation varies among individuals; and genetic factors may alter platelet activation through G-protein-coupled receptors, thus influencing results of point-of-care platelet aggregometry in whole blood. We tested the hypothesis that the C825T polymorphism of the gene GNB3 encoding the G-protein β-3 subunit and the platelet GPIIIa Pl(A1)/(A2) polymorphism of the glycoprotein IIIa influence platelet aggregation. METHODS Evoked [thrombin receptor activating peptide (TRAP), ADP, TXA(2) agonist U46619, epinephrine, and collagen] platelet aggregation in whole blood was measured using impedance aggregometry (Multiplate) in 143 healthy individuals (age: 40.2 years ±11.7 SD). Genotypes were determined using pyrosequencing and restriction analysis. Data were analyzed by linear one-way analysis of variance and Student's t-test, linear and multiple regression, and the χ(2)-test, as appropriate. RESULTS Homozygous carriers of the GNB3 825C-allele showed significantly (P≤0.022) increased maximum aggregation for EC(75) dosages compared with CT and TT genotypes [e.g. ADP: CC 150±36 vs. TT 126±33 aggregation unit (AU); thrombin receptor activating peptide: CC 175±46 vs. TT 150±38 AU; U46619: CC 164±33 vs. 149±32 AU; epinephrine: CC 66±41 vs. TT 48±34 AU]. In contrast, genotypes of glycoprotein IIb/IIIa PI(A)-polymorphism had no effect. Regression analysis revealed the GNB3 C825T polymorphism as an independent factor for enhanced platelet aggregation, besides factors such as female sex and blood cell values. CONCLUSION In human whole blood, the GNB3 825CC genotype is associated with enhanced platelet aggregation.
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Affiliation(s)
- Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital, University of Duisburg-Essen, Essen, Germany.
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Design, conduct, and analysis of a multicenter, pharmacogenomic, biomarker study in matched patients with severe sepsis treated with or without drotrecogin Alfa (activated). Ann Intensive Care 2012; 2:15. [PMID: 22694772 PMCID: PMC3403963 DOI: 10.1186/2110-5820-2-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 06/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A genomic biomarker identifying patients likely to benefit from drotrecogin alfa (activated) (DAA) may be clinically useful as a companion diagnostic. This trial was designed to validate biomarkers (improved response polymorphisms (IRPs)). Each IRP (A and B) contains two single nucleotide polymorphisms that were associated with a differential DAA treatment effect. METHODS DAA is typically given to younger patients with greater disease severity; therefore, a well-matched control group is critical to this multicenter, retrospective, controlled, outcome-blinded, genotype-blinded trial. Within each center, DAA-treated patients will be matched to controls treated within 24 months of each other taking into account age, APACHE II, cardiovascular, respiratory, renal, and hematologic dysfunction, mechanical ventilation status, medical/surgical status, and infection site. A propensity score will estimate the probability that a patient would have received DAA given their baseline characteristics. Two-phase data transfer will ensure unbiased selection of matched controls. The first transfer will be for eligibility and matching data and the second transfer for outcomes and genotypic data. The primary analysis will compare the effect of DAA in IRP + and IRP - groups on in-hospital mortality through day 28. DISCUSSION A design-based approach matching DAA-free to DAA-treated patients in a multicenter study of patients who have severe sepsis and high risk of death will directly compare control to DAA-treated groups for mortality by genotype. Results, which should be available in 2012, may help to identify the group of patients who would benefit from DAA and may provide a model for future investigation of sepsis therapies.
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186
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Palmer TM, Lawlor DA, Harbord RM, Sheehan NA, Tobias JH, Timpson NJ, Davey Smith G, Sterne JAC. Using multiple genetic variants as instrumental variables for modifiable risk factors. Stat Methods Med Res 2012; 21:223-42. [PMID: 21216802 PMCID: PMC3917707 DOI: 10.1177/0962280210394459] [Citation(s) in RCA: 618] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Mendelian randomisation analyses use genetic variants as instrumental variables (IVs) to estimate causal effects of modifiable risk factors on disease outcomes. Genetic variants typically explain a small proportion of the variability in risk factors; hence Mendelian randomisation analyses can require large sample sizes. However, an increasing number of genetic variants have been found to be robustly associated with disease-related outcomes in genome-wide association studies. Use of multiple instruments can improve the precision of IV estimates, and also permit examination of underlying IV assumptions. We discuss the use of multiple genetic variants in Mendelian randomisation analyses with continuous outcome variables where all relationships are assumed to be linear. We describe possible violations of IV assumptions, and how multiple instrument analyses can be used to identify them. We present an example using four adiposity-associated genetic variants as IVs for the causal effect of fat mass on bone density, using data on 5509 children enrolled in the ALSPAC birth cohort study. We also use simulation studies to examine the effect of different sets of IVs on precision and bias. When each instrument independently explains variability in the risk factor, use of multiple instruments increases the precision of IV estimates. However, inclusion of weak instruments could increase finite sample bias. Missing data on multiple genetic variants can diminish the available sample size, compared with single instrument analyses. In simulations with additive genotype-risk factor effects, IV estimates using a weighted allele score had similar properties to estimates using multiple instruments. Under the correct conditions, multiple instrument analyses are a promising approach for Mendelian randomisation studies. Further research is required into multiple imputation methods to address missing data issues in IV estimation.
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Affiliation(s)
- Tom M Palmer
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK.
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187
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Zoldoš V, Novokmet M, Bečeheli I, Lauc G. Genomics and epigenomics of the human glycome. Glycoconj J 2012; 30:41-50. [PMID: 22648057 DOI: 10.1007/s10719-012-9397-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/11/2012] [Accepted: 05/14/2012] [Indexed: 12/17/2022]
Abstract
The majority of all proteins are glycosylated and glycans have numerous important structural, functional and regulatory roles in various physiological processes. While structure of the polypeptide part of a glycoprotein is defined by the sequence of nucleotides in the corresponding gene, structure of a glycan part results from dynamic interactions between hundreds of genes, their protein products and environmental factors. The composition of the glycome attached to an individual protein, or to a complex mixture of proteins, like human plasma, is stable within an individual, but very variable between individuals. This variability stems from numerous common genetic polymorphisms reflecting in changes in the complex biosynthetic pathway of glycans, but also from the interaction with the environment. Environment can affect glycan biosynthesis at the level of substrate availability, regulation of enzyme activity and/or hormonal signals, but also through gene-environment interactions. Epigenetics provides a molecular basis how the environment can modify phenotype of an individual. The epigenetic information (DNA methylation pattern and histone code) is especially vulnerable to environmental effects in the early intrauterine and neo-natal development and many common late-onset diseases take root already at that time. The evidences showing the link between epigenetics and glycosylation are accumulating. Recent progress in high-throughput glycomics, genomics and epigenomics enabled first epidemiological and genome-wide association studies of the glycome, which are presented in this mini-review.
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Affiliation(s)
- Vlatka Zoldoš
- University of Zagreb, Faculty of Science, Horvatovac 102a, Zagreb, Croatia.
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188
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Associations of ACE I/D, AGT M235T gene polymorphisms with pregnancy induced hypertension in Chinese population: a meta-analysis. J Assist Reprod Genet 2012; 29:921-32. [PMID: 22644634 DOI: 10.1007/s10815-012-9800-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/14/2012] [Indexed: 10/28/2022] Open
Abstract
PURPOSE There have been many studies concerning the associations of angiotensin-converting enzyme (ACE) I/D, angiotensinogen (AGT) M235T polymorphisms with pregnancy induced hypertension (PIH) among Chinese populations. However, the results were inconsistent, prompting the necessity of meta-analysis. METHODS Studies published in English and Chinese were mainly searched in EMbase, PubMed and CBM up to January 2012. RESULTS Twenty-three studies with 3,551 subjects for ACE I/D and seven studies with 1,296 subjects for AGT M235T were included. Significant associations were found between ACE I/D and PIH under dominant, recessive and allelic models. A separate analysis confined to preeclampsia suggested that ACE I/D was associated with preeclampsia under recessive model and allelic model, but not dominant model. Stratified analyses were conducted as meta-regression analysis indicated that the sample size of case group was a significant source of heterogeneity, which suggested no significant association between ACE I/D and PIH in the subgroup of more than 100 cases. Associations were found between AGT M235T and PIH under dominant genetic model (OR = 1.59; 95 %CI: 1.04-2.42), recessive genetic model (OR = 1.60; 95 %CI: 1.07-2.40), and allelic model (OR = 1.40; 95 %CI: 1.17-1.68). No publication bias was found in either meta-analysis. CONCLUSIONS The present meta-analysis suggested significant associations between ACE I/D, AGT M235T and PIH in Chinese populations. However, no significant association was found between ACE I/D and PIH in the subgroup of more than 100 cases. Studies with larger sample sizes are necessary to investigate the associations between gene polymorphisms and PIH in Chinese populations.
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189
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Abstract
A major challenge in epilepsy research is to unravel the complex genetic mechanisms underlying both common and rare forms of epilepsy, as well as the genetic determinants of response to treatment. To accelerate progress in this area, the National Institute of Neurological Disorders and Stroke (NINDS) recently offered funding for the creation of a “Center without Walls” to focus on the genetics of human epilepsy. This article describes Epi4K, the collaborative study supported through this grant mechanism and having the aim of analyzing the genomes of a minimum 4,000 subjects with highly selected and well-characterized epilepsy.
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Affiliation(s)
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- Center for Human Genome Variation, Duke University, Durham, North Carolina 27708, USA
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190
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Stephens HAF. Immunogenetic surveillance of HIV/AIDS. INFECTION GENETICS AND EVOLUTION 2012; 12:1481-91. [PMID: 22575339 DOI: 10.1016/j.meegid.2012.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/05/2012] [Accepted: 04/06/2012] [Indexed: 11/28/2022]
Abstract
Evolutionary pressure by viruses is most likely responsible for the extraordinary allelic polymorphism of genes encoding class I human leukocyte antigens (HLA) and killer immunoglobulin-like receptors (KIR). Such genetic diversity has functional implications for the immune response to viruses and generates population-based variations in HLA class I allele frequencies and KIR gene profiles. The HIV-1 virus has relatively recently established itself as a major human pathogen, rapidly diversifying into a variety of phylogenetic subtypes or clades (A-G) and recombinants in different populations. HIV-1 clade C is the most common subtype in circulation accounting for 48% of all infections, followed by HIV-1 clades A and B which are responsible for 13% and 11% of infections in the current pandemic, respectively. Candidate gene studies of large cohorts of predominantly HIV-1 clade B but also clades C and A infected patients, have consistently shown significant associations between certain HLA class I alleles namely HLA-B*57, B*58, B*27, B*51 and relatively low viraemia. However, there is evidence that other associations between HLA-B*15, B*18 or B*53 and levels of HIV-1 viraemia are clade-specific. Recent genome-wide association studies of HIV-1 clade B exposed cohorts have confirmed that HLA-B, which is the most polymorphic locus in the human genome, is the major genetic locus contributing to immune control of viraemia. Moreover, the presence of natural killer cell receptors encoded by KIR-3DL1 and 3DS1 genes together with certain HLA class I alleles carrying the KIR target motif Bw4Ile80, provides an enhanced ability to control HIV-1 viraemia in some individuals. It is likely that rapid co-evolution of HIV-1 immune escape variants together with an adjustment of human immune response gene profiles has occurred in some exposed populations. Taken together, immunogenetic surveillance of HIV-1 exposed cohorts has revealed important correlates of natural immunity, which could provide a rational platform for the design and testing of future vaccines aimed at controlling the current AIDS pandemic.
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Affiliation(s)
- Henry A F Stephens
- UCL Centre for Nephrology and the Anthony Nolan Laboratories, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK.
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191
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Gao M, Wang Y, Shi Y, Liu D, Liang Y, Yu Y, Zhaobin J, Zhu L, Jin S. The relationship between three well-characterized polymorphisms of the angiotensin converting enzyme gene and lung cancer risk: a case-control study and a meta-analysis. J Renin Angiotensin Aldosterone Syst 2012; 13:455-60. [PMID: 22538550 DOI: 10.1177/1470320312443912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND AND OBJECTIVE The gene encoding angiotensin converting enzyme (ACE) is a promising candidate for lung cancer. We aimed to assess three well-characterized polymorphisms of the ACE gene (A-240T, I/D, A2350G) and lung cancer in Chinese people, and complete a meta-analysis of the association of I/D polymorphism with lung cancer. METHODS AND RESULTS In our case-control study, a total of 684 patients with lung cancer and 602 age-matched controls were recruited. Genotyping was performed using polymerase chain reaction (PCR) and ligase detection reactions (LDR) techniques. Single-locus analysis indicated that carriers of the A-240T allele had a significantly increased risk for lung cancer under additive (odds ratio (OR)=1.2; 95% confidence interval (CI): 1.02-1.42; P=0.027) and recessive (OR=1.8; 95% CI: 1.24-2.63; P=0.002) models, and that DD genotype carriers were 1.97 times more likely to develop lung cancer (95% CI: 1.25-3.11; P=0.004) compared with those with the I allele under the recessive model. However, no significance was observed in further haplotype analysis (P>0.05). In a meta-analysis of ACE gene insertion-deletion (I/D) polymorphism from six studies with 1183 lung cancer patients and 1065 controls, we failed to detect any significant association (overall OR=1.09; 95% CI: 0.84-1.41). A low probability of publication bias was observed. CONCLUSIONS Our results suggest that ACE gene A-240T polymorphism might be a genetic marker for the development of lung cancer in Chinese people.
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Affiliation(s)
- Min Gao
- Department of Respiratory Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Hayward A, Mason AS, Dalton-Morgan J, Zander M, Edwards D, Batley J. SNP discovery and applications in Brassica napus. ACTA ACUST UNITED AC 2012. [DOI: 10.5010/jpb.2012.39.1.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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193
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A genetic instrument for Mendelian randomization of fibrinogen. Eur J Epidemiol 2012; 27:267-79. [PMID: 22388766 DOI: 10.1007/s10654-012-9666-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 02/17/2012] [Indexed: 10/28/2022]
Abstract
Mendelian randomization studies on fibrinogen commonly use a single genetic variant as an instrument, but this may explain only a small proportion of the total phenotypic variance. We examined the contribution of multiple common single nucleotide polymorphisms (SNPs) and haplotypes in the entire fibrinogen gene cluster to plasma fibrinogen levels in two prospective cohorts, for use as instruments in future Mendelian randomization studies. Genotypes for 20 SNPs were determined in 2,778 middle-age (49-64 years) men from the Second-Northwick-Park-Heart Study (NPHS-II). These were replicated in 3,705 men from the Whitehall-II study (WH-II). Plasma fibrinogen levels were determined six times in NPHS-II and three times in WH-II. The minor alleles of four SNPs from the FGB gene, two from the FGA gene, and one from the FGG gene were associated with higher plasma fibrinogen levels. SNP rs1800790 (-455G>A) commonly used in Mendelian randomization studies was associated with R2=1.22% of the covariate adjusted residual variance in fibrinogen level. A variable selection procedure identified one additional SNP: rs2070011 (FGA) altogether explaining R2=1.45% of the residual variance in fibrinogen level. Using these SNPs no evidence for causality between the fibrinogen levels and coronary heart diseases was found in instrumental variables analysis. In the replication cohort, WH-II, the effects of the two SNPs on fibrinogen levels were consistent with the NPHS-II results. There is statistical evidence for several functional sites in the fibrinogen gene cluster that determine an individual's plasma fibrinogen levels. Thus, a combination of several SNPs will provide a stronger instrument for fibrinogen Mendelian randomization studies.
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194
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Ancestry informative marker set for han chinese population. G3-GENES GENOMES GENETICS 2012; 2:339-41. [PMID: 22413087 PMCID: PMC3291503 DOI: 10.1534/g3.112.001941] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/08/2012] [Indexed: 12/02/2022]
Abstract
The population of Han Chinese is ∼1.226 billion people. Genetic heterogeneity between northern Han Chinese (N-Han) and southern Han Chinese (S-Han) has been demonstrated by recent genome-wide studies. As an initial step toward health disparities and personalized medicine in Chinese population, this study developed a set of ancestry informative markers (AIM) for Han Chinese population.
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195
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Michelakakis H, Xiromerisiou G, Dardiotis E, Bozi M, Vassilatis D, Kountra PM, Patramani G, Moraitou M, Papadimitriou D, Stamboulis E, Stefanis L, Zintzaras E, Hadjigeorgiou GM. Evidence of an association between the scavenger receptor class B member 2 gene and Parkinson's disease. Mov Disord 2012; 27:400-5. [PMID: 22223122 DOI: 10.1002/mds.24886] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 12/21/2022] Open
Abstract
Lysosomal protein 2 (LIMP2), the product of the scavenger receptor class B member 2 (SCARB2) gene, is a ubiquitously expressed transmembrane protein that is the mannose-6-phosphate-independent receptor for glucocerebrosidase (β-GCase); a deficiency in this protein causes Gaucher disease. Several studies have shown a link between mutations in the β-GCase gene and diseases characterized clinically by Parkinsonism and by the presence of Lewy body-related pathology. We hypothesized that genetic variants in the SCARB2 gene could be risk factors for Parkinson's disease (PD). A candidate-gene study of 347 Greek patients with sporadic PD and 329 healthy controls was conducted to investigate the association between 5 polymorphisms in the SCARB2 gene (rs6824953, rs6825004, rs4241591, rs9991821, and rs17234715) and the development of PD. The single-locus analysis for the 5 polymorphisms revealed an association only for the rs6825004 polymorphism: the generalized odds ratio (OR(G) ) was 0.68 (95% confidence interval [CI], 0.51-0.90), and the OR for the allelic test was OR = 0.71 (95% CI, 0.56-0.90). Haplotype analysis showed an association for the GCGGT haplotype (P < .01). Our study supports a genetic contribution of the SCARB2 locus to PD; future studies in larger cohorts are necessary to verify this finding.
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Affiliation(s)
- Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Aghia Sophidara Children's Hospital, Athens, Greece
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196
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Fridley BL, Jenkins GD, Tsai YY, Song H, Bolton KL, Fenstermacher D, Tyrer J, Ramus SJ, Cunningham JM, Vierkant RA, Chen Z, Chen YA, Iversen E, Menon U, Gentry-Maharaj A, Schildkraut J, Sutphen R, Gayther SA, Hartmann LC, Pharoah PDP, Sellers TA, Goode EL. Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes. Cancer Epidemiol Biomarkers Prev 2012; 21:529-36. [PMID: 22302016 PMCID: PMC3297690 DOI: 10.1158/1055-9965.epi-11-0741] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) for epithelial ovarian cancer (EOC), the most lethal gynecologic malignancy, have identified novel susceptibility loci. GWAS for survival after EOC have had more limited success. The association of each single-nucleotide polymorphism (SNP) individually may not be well suited to detect small effects of multiple SNPs, such as those operating within the same biologic pathway. Gene set analysis (GSA) overcomes this limitation by assessing overall evidence for association of a phenotype with all measured variation in a set of genes. METHODS To determine gene sets associated with EOC overall survival, we conducted GSA using data from two large GWAS (N cases = 2,813, N deaths = 1,116), with a novel Principal Component-Gamma GSA method. Analysis was completed for all cases and then separately for high-grade serous histologic subtype. RESULTS Analysis of the high-grade serous subjects resulted in 43 gene sets with P < 0.005 (1.7%); of these, 21 gene sets had P < 0.10 in both GWAS, including intracellular signaling pathway (P = 7.3 × 10(-5)) and macrolide binding (P = 6.2 × 10(-4)) gene sets. The top gene sets in analysis of all cases were meiotic mismatch repair (P = 6.3 × 10(-4)) and macrolide binding (P = 1.0 × 10(-3)). Of 18 gene sets with P < 0.005 (0.7%), eight had P < 0.10 in both GWAS. CONCLUSION This research detected novel gene sets associated with EOC survival. IMPACT Novel gene sets associated with EOC survival might lead to new insights and avenues for development of novel therapies for EOC and pharmacogenomic studies.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/mortality
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Mucinous/genetics
- Adenocarcinoma, Mucinous/mortality
- Adenocarcinoma, Mucinous/pathology
- Biomarkers, Tumor/genetics
- Case-Control Studies
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/mortality
- Cystadenocarcinoma, Serous/pathology
- Disease Susceptibility
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/mortality
- Endometrial Neoplasms/pathology
- Female
- Follow-Up Studies
- Gene Expression Profiling
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Humans
- Middle Aged
- Neoplasm Grading
- Neoplasm Invasiveness
- Oligonucleotide Array Sequence Analysis
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/mortality
- Ovarian Neoplasms/pathology
- Principal Component Analysis
- Prognosis
- Risk Factors
- Signal Transduction
- Survival Rate
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Affiliation(s)
- Brooke L Fridley
- Departments of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.
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197
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Arias B, Aguilera M, Moya J, Sáiz PA, Villa H, Ibáñez MI, García-Portillo MP, Bobes J, Ortet G, Fañanás L. The role of genetic variability in the SLC6A4, BDNF and GABRA6 genes in anxiety-related traits. Acta Psychiatr Scand 2012; 125:194-202. [PMID: 21902679 DOI: 10.1111/j.1600-0447.2011.01764.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE The aims of this study were to test the individual association of the serotonin transporter gene (SLC6A4), the brain-derived neurotrophic factor gene (BDNF) and the GABA(A) α(6) receptor subunit gene (GABRA6) with anxiety-related traits and to explore putative gene-gene interactions in a Spanish healthy sample. METHOD A sample of 937 individuals from the general population completed the Temperament and Character Inventory questionnaire to explore Harm Avoidance (HA) dimension; a subsample of 553 individuals also filled in the Big Five Questionnaire to explore the Neuroticism dimension. The whole sample was genotyped for the 5-HTTLPR polymorphism (SLC6A4 gene), the Val66Met polymorphism (BDNF gene) and the T1521C polymorphism (GABRA6 gene). RESULTS Homozygous individuals for the T allele of the T1512C polymorphism presented slightly higher scores for HA than C allele carriers (F = 2.96, P = 0.019). In addition, there was a significant gene-gene interaction on HA between the 5-HTTLPR and Val66Met polymorphisms (F = 3.4, P = 0.009). CONCLUSION GABRA6 emerges as a candidate gene involved in the variability of HA. The effect of a significant gene-gene interaction between the SLC6A4 and BDNF genes on HA could explain part of the genetic basis underlying anxiety-related traits.
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Affiliation(s)
- B Arias
- Department of Animal Biology, Anthropology Section, Faculty of Biology, University of Barcelona, Spain
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198
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Lee HC, Chang TY, Yeung CY, Chan WT, Jiang CB, Chen WF, Chan HW, Yang HW, Lin M, Lee YJ. Genetic variability of interleukin 4 gene in Taiwanese children with biliary atresia. Cytokine 2012; 57:402-5. [PMID: 22227092 DOI: 10.1016/j.cyto.2011.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 12/05/2011] [Accepted: 12/14/2011] [Indexed: 01/28/2023]
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199
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Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity (Edinb) 2012; 109:34-40. [PMID: 22378357 DOI: 10.1038/hdy.2012.8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Association mapping of important traits of crop plants relies on first understanding the extent and patterns of linkage disequilibrium (LD) in the particular germplasm being investigated. We characterize here the genetic diversity, population structure and genome wide LD patterns in a set of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm from China. A diverse collection of 99 asparagus bean and normal cowpea accessions were genotyped with 1127 expressed sequence tag-derived single nucleotide polymorphism markers (SNPs). The proportion of polymorphic SNPs across the collection was relatively low (39%), with an average number of SNPs per locus of 1.33. Bayesian population structure analysis indicated two subdivisions within the collection sampled that generally represented the 'standard vegetable' type (subgroup SV) and the 'non-standard vegetable' type (subgroup NSV), respectively. Level of LD (r(2)) was higher and extent of LD persisted longer in subgroup SV than in subgroup NSV, whereas LD decayed rapidly (0-2 cM) in both subgroups. LD decay distance varied among chromosomes, with the longest (≈ 5 cM) five times longer than the shortest (≈ 1 cM). Partitioning of LD variance into within- and between-subgroup components coupled with comparative LD decay analysis suggested that linkage group 5, 7 and 10 may have undergone the most intensive epistatic selection toward traits favorable for vegetable use. This work provides a first population genetic insight into domestication history of asparagus bean and demonstrates the feasibility of mapping complex traits by genome wide association study in asparagus bean using a currently available cowpea SNPs marker platform.
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200
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Liu Y, Niu W, Wu Z, Su X, Chen Q, Lu L, Jin W. Variants in exon 11 of MEF2A gene and coronary artery disease: evidence from a case-control study, systematic review, and meta-analysis. PLoS One 2012; 7:e31406. [PMID: 22363637 PMCID: PMC3283621 DOI: 10.1371/journal.pone.0031406] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 01/10/2012] [Indexed: 12/13/2022] Open
Abstract
Background Coronary artery disease (CAD) is the most common heart disease worldwide. Association of CAD with variants in the myocyte enhancer factor 2A (MEF2A) gene, the first identified CAD-causing gene, has attracted special attention but the results are controversial. We aimed to evaluate this genetic association via a case-control study and meta-analysis. Methodology/Principal Findings We performed a case-control association study to investigate the relationship between variations in exon 11 of MEF2A gene and CAD in 1045 sporadic patients and 1008 controls enrolled angiographically among southern Chinese population, and then the data from this study were compared and discussed in a systematic review and meta-analysis with all available published studies on MEF2A gene and CAD. In total, eight variants were identified (21-bp deletion, CAG repeats, CCG repeats, a CCA deletion and four SNPs). No significant link was observed between the common (CAG)n polymorphism and CAD, whereas the rare 21-bp deletion was detected only in five affected individuals. The meta-analysis of (CAG)n polymorphism and CAD risk, including nine studies with 3801 CAD patients and 4020 controls, also provided no convincing evidence for the genetic association, even upon stratification by race (mainly Whites and Chinese). However, the 21-bp deletion was regarded as a potentially logical, albeit undetermined, candidate for CAD in the following systematic review. Conclusions/Significance Our findings failed to demonstrate a correlation between (CAG)n polymorphism with CAD, however, we concluded that the rare 21-bp deletion might have a more compelling effect on CAD than the common (CAG)n polymorphism, and MEF2A genetic variant might be a rare but specific cause of CAD/MI.
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Affiliation(s)
- Yan Liu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenquan Niu
- State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijun Wu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuxiu Su
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiujin Chen
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Jin
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail:
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