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Elevated blood pressure: Our family's fault?The genetics of essential hypertension

World Journal of Cardiology 2014年第5期6卷 327-337页

作者： Aniket Natekar Randi L Olds Meghann W Lau Kathleen Min Karra Imoto Thomas P Slavin The John A. Burns School of Medicine University of Hawaii Honolulu HI 96813 United States Hawaii Community Genetics Honolulu HI96814 United States

AIM: To provide an updated review on current genetic aspects possibly affecting essential hypertension(EH), and to further elucidate their role in EH. METHODS: We searched for genetic and epigenetic factors in major studies associated with EH between Jan 2008-Oct 2013 using PubMed. We limited our search to reviews that discussed mostly human studies, and were accessible through the university online re-source. We found 11 genome wide association studies(GWAS), as well as five methylation and three miRNA studies that fit our search criteria. A distinction was not made between genes with protective effects or nega-tive effects, as this article is only meant to be a sum-mary of genes associated with any aspect of ***: We found 130 genes from the studies that met our inclusion/exclusion criteria. Of note, genes withmultiple study references include: STK39, CYP17A1, MTHFR-NPPA, MTHFR-NPPB, ATP2B1, CSK, ZNF652, UMOD, CACNB2, PLEKHA7, SH2B3, TBX3-TBX5, ULK4, CSK-ULK3, CYP1A2, NT5C2, CYP171A, PLCD3, SH2B3, ATXN2, CACNB2, PLEKHA7, SH2B3, TBX3-TBX5, ULK4, and HFE. The following genes overlapped between the genetic studies and epigenetic studies: WNK4 and BDKRB2. Several of the identified genes were found to have functions associated with EH. Many epigenetic factors were also correlated with EH. Of the epigenetic factors, there were no articles discussing siRNA and its effects on EH that met the search criteria, thus the topic was not included in this review. Among the miRNA tar-gets found to be associated with EH, many of the genes involved were also identified in the GWAS ***: Genetic hypertension risk algorithms could be developed in the future but may be of limited benefit due to the multi-factorial nature of EH. With emerging technologies, like next-generation sequenc-ing, more direct causal relationships between genetic and epigenetic factors affecting EH will likely be discov-ered creating a tremendous potential for personalized medicine using phar

关键词： Essential hypertension Epigenomics genome-wide association study Genes MicroRNAs

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Clinical and pathobiological heterogeneity of asthma—Mechanisms of severe and glucocorticoid-resistant asthma

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Health 2013年第2期5卷 344-350页

作者： Yasuhiro Matsumura Department of Internal Medicine Akishima Hospital Tokyo Japan

It is increasingly recognized that asthma represents a syndrome, and there is clinical and pathobiological heterogeneity. Many genes are reported to be associated with asthma, and may be involved in the disease heterogeneity. Diverse cells, such as T helper 1 (Th1)-cells, Th2-cells, Th17-cells, airway epithelial cells, and innate and adaptive immunity associated cells, contribute to the pathobiology of asthma independently of each other or they can also coexist and interact. Although, generally, Th2 immunity is important in most asthma endotypes, non- Th2-driven inflammation tends to be difficult to manage. Recently, increased attention has been focused on severe asthma and glucocorticoid (GC)-resistant (GC-R) asthma, in which diverse inflammatory processes may be involved. Treatment approaches should take into account pathological differences.

关键词： Asthma Phenotype genome-wide Association Study (GWAS) Glucocorticoid (GC)-Resistant (GC-R) Asthma Severe Asthma

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Genetics of type 2 diabetes

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World Journal of Diabetes 2013年第4期4卷 114-123页

作者： Omar Ali Medical College of Wisconsin

Type 2 diabetes(T2D) is the result of interaction between environmental factors and a strong hereditary *** review the heritability of T2D as well as the history of genetic and genomic research in this *** few T2D risk genes were identified using candidate gene and linkage-based studies,but the advent of genome-wide association studies has led to the identification of multiple genes,including several that were not previously known to play any role in *** replicated genes,for example TCF7L2,KCNQ1 and KCNJ11,are discussed in greater *** together,the genetic loci discovered to date explain only a small proportion of the observed *** discuss possible explanations for this "missing heritability",including the role of rare variants,gene-environment interactions and *** clinical utility of current findings and avenues of future research are also discussed.

关键词： Type 2 diabetes Genetics TCF7L2 genome-wide association studies Heritability

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Expression quantitative trait analyses to identify causal genetic variants for type 2 diabetes susceptibility

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World Journal of Diabetes 2014年第2期5卷 97-114页

作者： Swapan Kumar Das Neeraj Kumar Section on Endocrinology and Metabolism Department of Internal Medicine Wake Forest School of Medicine

Type 2 diabetes(T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex heterogeneous metabolic phenotype in different ethnic and racial groups remains challenging. Despite recent success, the functional role of the T2D susceptibility variants implicated by genome-wide association studies(GWAS) remains largely unknown. Genetic dissection of transcript abundance or expression quantitative trait(eQTL) analysis unravels the genomic architecture of regulatory variants. Availability of eQTL information from tissues relevant for glucose homeostasis in humans opens a new avenue to prioritize GWASimplicated variants that may be involved in triggering a causal chain of events leading to T2D. In this article, we review the progress made in the field of eQTL research and knowledge gained from those studies in understanding transcription regulatory mechanisms in human subjects. We highlight several novel approaches that can integrate eQTL analysis with multiple layers of biological information to identify ethnic-specific causal variants and gene-environment interactions relevant to T2D pathogenesis. Finally, we discuss how the eQTL analysis mediated search for "missing heritability" may lead us to novel biological and molecular mechanisms involved in susceptibility to T2D.

关键词： Type 2 diabetes Single nucleotide polymorphisms Expression quantitative trait locus Expression regulatory SNPs Gene-environment interaction genome-wide association study

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Pharmacogenetics of type 2 diabetes mellitus: An example of success in clinical and translational medicine

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World Journal of Translational Medicine 2014年第3期3卷 141-149页

作者： Antonio Brunetti Francesco S Brunetti Eusebio Chiefari Department of Health Sciences University "Magna Gr?cia" of Catanzaro Department of Medical and Surgical Sciences University ‘‘Magna Gr?cia’’ of Catanzaro

The pharmacological interventions currently available to control type 2 diabetes mellitus(T2DM) show a wide interindividual variability in drug response, emphasizing the importance of a personalized, more effective medical treatment for each individual patient. In this context, a growing interest has emerged in recent years and has focused on pharmacogenetics, a discipline aimed at understanding the variability in patients' drug response, making it possible to predict which drug is best for each patient and at what doses. Recent pharmacological and clinical evidences indicate that genetic polymorphisms(or genetic variations) of certain genes can adversely affect drug response and therapeutic efficacy of oral hypoglycemic agents in patients with T2 DM, through pharmacokinetic- and/or pharmacodynamic-based mechanisms that may reduce the therapeutic effects or increase toxicity. For example, genetic variants in genes encoding enzymes of the cytochrome P-450 superfamily, or proteins of the ATP-sensitive potassium channel on the beta-cell of the pancreas, are responsible for the interindividual variability of drug response to sulfonylureas in patients with T2 DM. Instead, genetic variants in the genes that encode for the organic cation transporters of metformin have been related to changes in both pharmacodynamic and pharmacokinetic responses to metformin in metformin-treated patients. Thus, based on the individual's genotype, the possibility, in these subjects, of a personalized therapy constitutes the main goal of pharmacogenetics, directly leading to the development of the right medicine for the right patient. Undoubtedly, this represents an integral part of the translational medicine network.

关键词： Type 2 diabetes Anti-diabetic drugs Personalized therapy Genetic variants genome-wide association study

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Identification of Candidate Targeted Genes in Molecular Subtypes of Gastric Cancer

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Journal of Biomedical Science and Engineering 2017年第5期10卷 45-53页

作者： Wei Zeng Ni-Ni Rao Jie Zheng Yong-Li Wan Guang-Bin Wang Zheng-Wen Li Sang Li Department of Biomedical Engineering School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China Department of Biomedical Engineering School of Automation and Information Engineering Sichuan University of Science and Engineering Zigong China

Because of high heterogeneity, a further classification should be made for diagnosis and treatment in gastric cancer. Biomarkers selected in subtypes are important for precision medicine. Based on gene expression level, we constructed genome-wide co-expression networks for invasive, proliferative and metabolic subtype in gastric cancer respectively. The hierarchical clustering was used to get sub-networks, and hub gene sets of subtypes were got by analysis in sub-networks. Unique differential expression genes as candidate targeted genes in subtype were gained by a comparative analysis between subtypes. These genes may be helpful for improving diagnosis and therapy methods and developing new drug in gastric cancer.

关键词： Gastric Cancer Molecular Subtype genome-wide Co-Expression Network Targeted Gene

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Systems psychopharmacology:A network approach to developing novel therapies

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World Journal of Psychiatry 2016年第1期6卷 66-83页

作者： Peter J Gebicke-Haerter Central Institute of Mental Health Medical Faculty MannheimHeidelberg University

The multifactorial origin of most chronic disorders of the brain, including schizophrenia, has been well accepted. Consequently, pharmacotherapy would require multitargeted strategies. This contrasts to the majority of drug therapies used until now, addressing more or less specifically only one target molecule. Nevertheless, quite some searches for multiple molecular targets specific for mental disorders have been undertaken. For example, genome-wide association studies have been conducted to discover new target genes of disease. Unfortunately, these attempts have not fulfilled the great hopes they have started with. Polypharmacology and network pharmacology approaches of drug treatment endeavor to abandon the one-drug one-target thinking. To this end, most approaches set out to investigate network topologies searching for modules, endowed with "important" nodes, such as "hubs" or "bottlenecks", encompassing features of disease networks, and being useful as tentative targets of drug therapies. This kind of research appears to be very promising. However, blocking or inhibiting "important" targets may easily result in destruction of network integrity. Therefore, it is suggested here to study functions of nodes with lower centrality for more subtle impact on network behavior. Targeting multiple nodes with low impact on network integrity by drugs with multiple activities("dirty drugs") or by several drugs, simultaneously, avoids to disrupt network integrity and may reset deviant dynamics of disease. Natural products typically display multi target functions and therefore could help to identify useful biological targets. Hence, future efforts should consider to combine drug-target networks with target-disease networks using mathematical(graph theoretical) tools, which could help to develop new therapeutic strategies in long-term psychiatric disorders.

关键词： Polypharmacology Drug-target networks Network topology Disease networks genome-wide association studies Epigenetics Schizophrenia Herbal extracts

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LOH-profiling by SNP-mapping in a case of multifocal head and neck cancer

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World Journal of Clinical Oncology 2012年第2期3卷 24-28页

作者： Jens Pfeiffer Wolfgang Maier Gerd J Ridder Karim Zaoui Ralf Birkenhger Department of Otorhinolaryngology Head and Neck Surgery University of Freiburg 79106 Freiburg Germany

AIM: To introduce an approach for the detection of putative genetic host factors that predispose patients to develop head and neck squamous cell carcinomas(HNSCC).METHODS: HNSCC most often result from the accumulation of somatic gene alterations found in tumor cells. A cancer-predisposing genetic background must be expected in individuals who develop multiple cancers, starting at an unexpectedly young age or with little carcinogen exposure. genome-wide loss of heterozygosity(LOH) profiling by single nucleotide polymorphism microarray mapping was performed in a patient with a remarkable history of multifocal ***: Regions of genomic deletions in germline DNA were identified on several chromosomes with a remarkable size between 1.6 Mb and 8.1 Mb(mega base-pair). No LOH was detected at the genomic location of the tumor suppressor gene ***: Specific patterns of germline DNA deletions may be responsible for susceptibility to HNSCC and should be further analyzed.

关键词： genome-wide analysis Head and neck cancer Loss of heterozygosity Multifocal cancer Single nucleotide polymorphism microarray Squamous cell carcinoma

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Assessing Likelihood of Having False Positives Caused by Population Stratification

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Open Journal of Genetics 2019年第1期9卷 15-29页

作者： Renfang Jiang Jianping Dong Department of Mathematical Sciences Michigan Technological University Houghton USA

Population stratification is always a concern in association analysis. There is a debate on the extent of the problem in less extreme situations (Thomas and Witte [1], Wacholder et al. [2]). Wacholder et al. [3] and Ardlie et al. [4] showed that hidden population structure is not a serious threat to case-control designs. We propose a method of assessing the seriousness of the population stratification before designing association studies. If population stratification is not a serious problem, one may consider using case-control study instead of family-based design to get more power. In a case-control design, we compare chi-square statistics from a structured population (a union of two subpopulations) and a homogeneous population with the same prevalence and allele frequencies. We provide an explicit formula to calculate the chi-square statistics from 17 parameters, such as proportions of subpopulation, allele frequencies in subpopulations, etc. We choose these factors because they have potential to cause false associations. Each parameter takes a random value in a chosen range. We then calculate the likelihood of getting opposite conclusions in the structured and the homogeneous populations. This is the likelihood of having false positives caused by population stratification. The advantage of this method is to provide a cost effective way to choose between using case-control data and using family data before actually collecting those data. We conclude that sample sizes have a significant effect on the likelihood of false positive caused by population stratification. The larger the sample size is, the more likely to have false positive if the population structure is ignored. If the sample size will be smaller than 200 by budget constraints, then case-control study may be a better choice because of its power.

关键词： Population Stratification Case-Control Studies Linkage Disequilibrium genome-wide Association Studies

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Localisation of Loci Involved in Resistance to Diaporthe toxicaand Pleiochaeta setosain White Lupin (Lupinus albusL.)

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Open Journal of Genetics 2014年第3期4卷 210-226页

作者： Rosy Raman Cina Vipin David J. Luckett Raymond B. Cowley Gavin J. Ash John D. I. Harper Andrzej Kilian Harsh Raman DArT Pty Ltd. (ACT) University of Canberra Canberra Australia Graham Centre for Agricultural Innovation (An Alliance between Charles Sturt University and NSW Department of Primary Industries) Pugsley Place Wagga Wagga Agricultural Institute Wagga Wagga Australia NSW Department of Primary Industries Agricultural Institute Wagga Wagga Australia Graham Centre for Agricultural Innovation (An Alliance between Charles Sturt University and NSW Department of Primary Industries) Pugsley Place Wagga Wagga Agricultural Institute Wagga Wagga Australia School of Agricultural & Wine Sciences Charles Sturt University Wagga Wagga Australia Graham Centre for Agricultural Innovation (An Alliance between Charles Sturt University and NSW Department of Primary Industries) Pugsley Place Wagga Wagga Agricultural Institute Wagga Wagga Australia School of Agricultural & Wine Sciences Charles Sturt University Wagga Wagga Australia Graham Centre for Agricultural Innovation (An Alliance between Charles Sturt University and NSW Department of Primary Industries) Pugsley Place Wagga Wagga Agricultural Institute WaggaWagga Australia NSW Department of Primary Industries Agricultural Institute Wagga Wagga Australia NSW Department of Primary Industries Agricultural Institute Wagga Wagga Australia

L. albus is an annual grain-legume crop mainly grown for high-protein fodder worldwide but also to produce large seeds for human consumption as a snack-food. In order to make genetic gains in grain yield, assessment of the genetic variation in the germplasm and identification of loci associated with agronomic traits are essential. Phomopsis blight (PB) and Pleiochaeta root rot (PRR), caused by the fungal pathogens Diaporthe toxica and, Pleiochaeta setosa respectively, are two major yield-limiting diseases of the L. albus crop. The extent of genetic diversity in 94 accessions of L. albus comprising: Australian and exotic cultivars, advanced breeding lines, and landraces originating from 26 different countries was determined utilizing PCR-based genic, and microarray-based Diversity Arrays Technology (DArT™), markers. All accessions were evaluated for resistance to PB in two plant tissues (leaves and stems) using either sprayed or injected spore inoculum. A subset of 58 accessions was further evaluated for resistance to PRR by growing seedlings in spore-infested potting mix. The combined data of 724 (50 genic- and 674 DArT) markers were used for cluster analysis. A subset of 324 markers with call rate ≥95% and predicted disease scores of different genotypes were used to identify marker loci accounting for phenotypic variation in PB and PRR resistance using linear regression analysis. Several markers showed significant association with PB or PRR resistance at P < 0.05. Our results showed that favourable alleles for PB and PRR resistance are present in the diverse accessions investigated and they will provide valuable materials for lupin breeding.

关键词： L. albus Genetic Diversity Phomopsis Blight Pleiochaeta Root Rot DArT Linear Regression Analysis genome-wide Association Analysis

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