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Xue LL, Wang F, Xiong LL, Du RL, Zhou HL, Zou Y, Wu MX, Yang MA, Dai J, He MX, Wang TH. A single-nucleotide polymorphism induced alternative splicing in Tacr3 involves in hypoxic-ischemic brain damage. Brain Res Bull 2020; 154:106-115. [PMID: 31722250 DOI: 10.1016/j.brainresbull.2019.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/28/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023]
Abstract
Single-nucleotide polymorphism (SNP) and Alternative splicing (AS) were found to be implicated in certain diseases, nevertheless, the contributions of mRNA SNPs and AS to pathogenesis in developing rat brains with hypoxic-ischemic encephalopathy (HIE) remained largely vague. Additionally, the disease associated with Tacr3 was normosmic congenital hypogonadotropic hypogonadism, while the relationship between HIE and Tacr3 remained largely elusive. The current study was designed to investigate the differentially expressed mRNAs and related SNPs as well as AS in neonatal rats subjected to HIE to identify if the exhibition of AS was associated with SNPs under pathological condition. Firstly, we used postnatal day 7 Sprague-Dawley rats to construct neonatal HIE model, and analyzed the expression profiles of SNP mRNA in hypoxic-ischemic (HI) and sham brains by using RNA sequencing. Then four genes, including Mdfic, Lpp, Bag3 and Tacr3, connecting with HIE and exhibiting SNPs and AS were identified by bioinformatics analysis. Moreover, combined with exonic splicing enhancer (ESE) and alternative splice site predictor (ASSP) analysis, we found that Tacr3 is associated specifically with HIE through 258547789 G > A SNP in inside the Alt First Exon and 258548573 G > A SNP in outside the Alt First Exon. Taken together, our study provides new evidence to understand the role of Tacr3 in HIE and it is possibly a potential target for the treatment of HIE in future clinic trial.
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MESH Headings
- Animals
- Humans
- Male
- Rats
- Alternative Splicing/genetics
- Animals, Newborn
- Brain/metabolism
- Disease Models, Animal
- Hypoxia-Ischemia, Brain/genetics
- Hypoxia-Ischemia, Brain/metabolism
- Neurons/metabolism
- Polymorphism, Single Nucleotide/genetics
- Rats, Sprague-Dawley
- Receptors, Neurokinin-3/genetics
- Receptors, Neurokinin-3/metabolism
- Receptors, Tachykinin/genetics
- Receptors, Tachykinin/metabolism
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Affiliation(s)
- Lu-Lu Xue
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China
| | - Fang Wang
- Department of Science and Technology, Kunming Medical University, Kunming 650031, China
| | - Liu-Lin Xiong
- Department of Anesthesiology, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P. R. 563000, China
| | - Ruo-Lan Du
- Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China
| | - Hao-Li Zhou
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Zou
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Ma-Xiu Wu
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Ming-An Yang
- Division of Biostatistics and Epidemiology, School of Public Health, San Diego State University, USA
| | - Jing Dai
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Man-Xi He
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.
| | - Ting-Hua Wang
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China.
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2
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Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One 2019; 14:e0222329. [PMID: 31513639 PMCID: PMC6742455 DOI: 10.1371/journal.pone.0222329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Methylation patterns established and maintained at CpG sites may be altered by single nucleotide polymorphisms (SNPs) within these sites and may affect the regulation of nearby genes. Our aims were to: 1) identify and generate a database of SNPs potentially subject to epigenetic control by DNA methylation via their involvement in creating, removing or displacing CpG sites (meSNPs), and; 2) investigate the association of these meSNPs with CpG islands (CGIs), and with methylation profiles of DNA extracted from tissues from cattle with divergent feed efficiencies detected using MIRA-Seq. Using the variant annotation for 56,969,697 SNPs identified in Run5 of the 1000 Bull Genomes Project and the UMD3.1.1 bovine reference genome sequence assembly, we identified and classified 12,836,763 meSNPs according to the nature of variation created at CpGs. The majority of the meSNPs were located in intergenic regions (68%) or introns (26.3%). We found an enrichment (p<0.01) of meSNPs located in CGIs relative to the genome as a whole, and also in differentially methylated sequences in tissues from animals divergent for feed efficiency. Seven meSNPs, located in differentially methylated regions, were fixed for methylation site creating (MSC) or destroying (MSD) alleles in the differentially methylated genomic sequences of animals differing in feed efficiency. These meSNPs may be mechanistically responsible for creating or deleting methylation targets responsible for the differential expression of genes underlying differences in feed efficiency. Our methyl SNP database (dbmeSNP) is useful for identifying potentially functional "epigenetic polymorphisms" underlying variation in bovine phenotypes.
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Affiliation(s)
| | | | - Sheila T Nagamatsu
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Marcelo F Carazzolle
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,National Center for High Performance Computing (CENAPAD-SP), University of Campinas, Campinas, São Paulo, Brazil
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Lynsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.,Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Stephanie D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont, United States of America
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Flavia L Lopes
- São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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3
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Papanikolaou IG, Giannelou P, Anagnostou E, Mavrogianni D, Drakakis P, Loutradis D. Combined study on the single nucleotide polymorphisms in the follicle-stimulating hormone receptor (Ser680Asn) and anti-Müllerian hormone receptor type II (-482A>G) as genetic markers in assisted reproduction. Horm Mol Biol Clin Investig 2019; 38:hmbci-2018-0077. [PMID: 30904901 DOI: 10.1515/hmbci-2018-0077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/10/2019] [Indexed: 12/30/2022]
Abstract
Background Infertile women may have underlying genetic abnormalities. There is, at present, a significant number of studies on the relation between the follicle stimulating hormone receptor (FSHR) or anti-Müllerian hormone type II receptor (AMHRII) polymorphisms and response to in-vitro fertilisation (IVF) treatment. However, it is not yet clear which genotype or combination of genotypes is favourable towards a better ovarian stimulation and pregnancy outcome. Materials and methods In this study we assessed the distribution of the genotypes of FSHR Ser680Asn and of AMHRII -482A>G gene polymorphisms in a group of 126 infertile women and a control group of 100 fertile women by using real-time polymerase chain reaction (RT-PCR). Results Statistical analysis showed that the frequency of the genotypes is similar in both control and IVF/ intracytoplasmic sperm injection (ICSI) groups. Further investigation of the frequency of the nine possible combinations of these polymorphisms in the groups revealed no correlation between infertility and combination of the polymorphisms. Women with one polymorphism have on average 5.5 units higher levels of AMH compared to women carrying no polymorphism. In women with no polymorphisms, for each unit of FSH increase, the average concentration of blood AMH is expected to be 72% lower. Conclusion The distribution of the FSHR Ser680Asn and of the AMHRII -482A>G gene polymorphisms, in the Greek population is similar in fertile and infertile women. The study showed that FSH and AMH correlated levels in certain cases could be used to estimate a patient's ovarian reserve.
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MESH Headings
- Adult
- Female
- Humans
- Infertility, Female/genetics
- Infertility, Female/therapy
- Ovarian Reserve
- Polymorphism, Single Nucleotide
- Receptors, FSH/blood
- Receptors, FSH/genetics
- Receptors, Peptide/blood
- Receptors, Peptide/genetics
- Receptors, Transforming Growth Factor beta/blood
- Receptors, Transforming Growth Factor beta/genetics
- Sperm Injections, Intracytoplasmic/statistics & numerical data
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Affiliation(s)
- Ioannis G Papanikolaou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Polina Giannelou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Elli Anagnostou
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Despoina Mavrogianni
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Petros Drakakis
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Dimitrios Loutradis
- 1st Department of Obstetrics and Gynecology, Alexandra Hospital, Division of Human Reproduction, IVF Unit National and Kapodistrian University of Athens, Medical School, 62 Sirinon Street, P. Faliro, 175 61 Athens, Greece, Phone: +30 6932421747, Fax: +30 210 6454902
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4
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Xue B, Lipps D, Devineni S. Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PLoS One 2016; 11:e0168392. [PMID: 28002428 PMCID: PMC5176297 DOI: 10.1371/journal.pone.0168392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/29/2016] [Indexed: 01/08/2023] Open
Abstract
MiRNAs are short non-coding RNAs of about 22 nucleotides, which play critical roles in gene expression regulation. The biogenesis of miRNAs is largely determined by the sequence and structural features of their parental RNA molecules. Based on these features, multiple computational tools have been developed to predict if RNA transcripts contain miRNAs or not. Although being very successful, these predictors started to face multiple challenges in recent years. Many predictors were optimized using datasets of hundreds of miRNA samples. The sizes of these datasets are much smaller than the number of known miRNAs. Consequently, the prediction accuracy of these predictors in large dataset becomes unknown and needs to be re-tested. In addition, many predictors were optimized for either high sensitivity or high specificity. These optimization strategies may bring in serious limitations in applications. Moreover, to meet continuously raised expectations on these computational tools, improving the prediction accuracy becomes extremely important. In this study, a meta-predictor mirMeta was developed by integrating a set of non-linear transformations with meta-strategy. More specifically, the outputs of five individual predictors were first preprocessed using non-linear transformations, and then fed into an artificial neural network to make the meta-prediction. The prediction accuracy of meta-predictor was validated using both multi-fold cross-validation and independent dataset. The final accuracy of meta-predictor in newly-designed large dataset is improved by 7% to 93%. The meta-predictor is also proved to be less dependent on datasets, as well as has refined balance between sensitivity and specificity. This study has two folds of importance: First, it shows that the combination of non-linear transformations and artificial neural networks improves the prediction accuracy of individual predictors. Second, a new miRNA predictor with significantly improved prediction accuracy is developed for the community for identifying novel miRNAs and the complete set of miRNAs. Source code is available at:https://github.com/xueLab/mirMeta
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Affiliation(s)
- Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
- * E-mail:
| | - David Lipps
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
| | - Sree Devineni
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
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5
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Wang T, Liang Y, Li H, Li H, He Q, Xue Y, Shen C, Zhang C, Xiang J, Ding J, Qiao L, Zheng Q. Single Nucleotide Polymorphisms and Osteoarthritis: An Overview and a Meta-Analysis. Medicine (Baltimore) 2016; 95:e2811. [PMID: 26886631 PMCID: PMC4998631 DOI: 10.1097/md.0000000000002811] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/15/2016] [Accepted: 01/16/2016] [Indexed: 01/22/2023] Open
Abstract
Osteoarthritis (OA) is a complex disorder characterized by degenerative articular cartilage and is largely attributed to genetic risk factors. Single nucleotide polymorphisms (SNPs) are common DNA variants that have shown promising and efficiency, compared with positional cloning, to map candidate genes of complex diseases, including OA. In this study, we aim to provide an overview of multiple SNPs from a number of genes that have recently been linked to OA susceptibility. We also performed a comprehensive meta-analysis to evaluate the association of SNP rs7639618 of double von Willebrand factor A domains (DVWA) gene with OA susceptibility. A systematic search of studies on the association of SNPs with susceptibility to OA was conducted in PubMed and Google scholar. Studies subjected to meta-analysis include human and case-control studies that met the Hardy-Weinberg equilibrium model and provide sufficient data to calculate an odds ratio (OR). A total of 9500 OA cases and 9365 controls in 7 case-control studies relating to SNP rs7639618 were included in this study and the ORs with 95% confidence intervals (CIs) were calculated. Over 50 SNPs from different genes have been shown to be associated with either hip (23), or knee (20), or both (13) OA. The ORs of these SNPs for OA and the subtypes are not consistent. As to SNP rs7639618 of DVWA, increased knee OA risk was observed in all genetic models analyzed. Specifically, people from Asian with G-allele showed significantly increased risk of knee OA (A versus G: OR = 1.28, 95% CI 1.13-1.46; AA versus GG: OR = 1.60, 95% CI 1.25-2.05; GA versus GG: OR = 1.31, 95% CI 1.18-1.44; AA versus GA+GG: OR = 1.34, 95% CI 1.12-1.61; AA+GA versus GG: OR = 1.40, 95% CI 1.19-1.64), but not in Caucasians or with hip OA. Our results suggest that multiple SNPs play different roles in the pathogenesis of OA and its subtypes; SNP rs7639618 of DVWA gene is associated with a significantly increased risk of knee OA in Asians. Given the limited sample size, further studies are needed to evaluate this observation.
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Affiliation(s)
- Ting Wang
- From the Center for Reproduction and Genetics (TW, HL, HL, QH, YX, CS, CZ, JX, JD, LQ), Suzhou Hospital affiliated to Nanjing Medical University, Suzhou, Jiangsu; Department of Laboratory Medicine (YL), Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai; Department of Hematology and Hematological Laboratory Science (QZ), Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China (QZ); and Department of Anatomy and Cell Biology (QZ), Rush University Medical Center, Chicago, IL
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6
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Aggarwal NT, Shah RC, Bennett DA. Alzheimer's disease: Unique markers for diagnosis & new treatment modalities. Indian J Med Res 2015; 142:369-82. [PMID: 26609028 PMCID: PMC4683821 DOI: 10.4103/0971-5916.169193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Indexed: 11/04/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease. In humans, AD becomes symptomatic only after brain changes occur over years or decades. Three contiguous phases of AD have been proposed: (i) the AD pathophysiologic process, (ii) mild cognitive impairment due to AD, and (iii) AD dementia. Intensive research continues around the world on unique diagnostic markers and interventions associated with each phase of AD. In this review, we summarize the available evidence and new therapeutic approaches that target both amyloid and tau pathology in AD and discuss the biomarkers and pharmaceutical interventions available and in development for each AD phase.
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Affiliation(s)
- Neelum T. Aggarwal
- Department of Neurology, Rush University Medical Center, Chicago, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
| | - Raj C. Shah
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
- Department of Family Medicine, Rush University Medical Center, Chicago, USA
| | - David A. Bennett
- Department of Neurology, Rush University Medical Center, Chicago, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
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7
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Strait JB, Uda M, Lakatta EG, Najjar SS. Using new tools to define the genetic underpinnings of risky traits associated with coronary artery disease: the SardiNIA study. Trends Cardiovasc Med 2009; 19:69-75. [PMID: 19679263 DOI: 10.1016/j.tcm.2009.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genomewide association studies are increasingly being applied to search for novel genes that might underlie cardiovascular diseases. In this article, we briefly review the principles that underlie modern genetic analyses and provide several illustrations from the SardiNIA study of genomewide association studies for cardiovascular risk factor traits.
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Affiliation(s)
- James B Strait
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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8
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The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single-nucleotide polymorphisms in the bovine genome. Genetics 2008; 180:639-47. [PMID: 18716328 DOI: 10.1534/genetics.108.090860] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C <--> T and A <--> G transitions have reverse complementary neighborhood patterns and so do A <--> C and G <--> T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C <--> T/A <--> G and A <--> C/G <--> T, the true neighborhood patterns for A <--> T and C <--> G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C <--> G, but increased for C <--> T/A <--> G, further for A <--> C/G <--> T, and the most for A <--> T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A <--> G and C <--> T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for approximately 20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.
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9
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Clements DN, Carter SD, Innes JF, Ollier WER. Genetic basis of secondary osteoarthritis in dogs with joint dysplasia. Am J Vet Res 2006; 67:909-18. [PMID: 16649929 DOI: 10.2460/ajvr.67.5.909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Dylan N Clements
- Connective Tissue Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, L69 3BX, UK
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10
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Abstract
The efforts to decipher the genetic causes of schizophrenia, one of the most devastating mental illnesses, have reached a turning point. Several linkage findings in schizophrenia have been replicated and, in the last few years, have been followed by systematic fine-mapping efforts to identify positional susceptibility genes. Here, we outline the evidence supporting each of the proposed positional candidate genes and identify some general areas of caution in their interpretation. Several of these findings hold considerable promise both for understanding the neuropathology of this brain disorder, the causes of which remain a mystery, but also for development of novel, mechanism-based treatments for the patients.
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Affiliation(s)
- Maria Karayiorgou
- The Rockefeller University, Laboratory of Human Neurogenetics, New York, NY 10021, USA.
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11
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Orth AP, Batalov S, Perrone M, Chanda SK. The promise of genomics to identify novel therapeutic targets. Expert Opin Ther Targets 2005; 8:587-96. [PMID: 15584864 DOI: 10.1517/14728222.8.6.587] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The cataloguing of the human genome has provided an unprecedented prospectus for target identification and drug discovery. A current analysis indicates that slightly more than 3000 unique protein encoding loci are potentially amenable to pharmacological intervention (the 'druggable genome', which can be queried at http://function.gnf.org/druggable). However, the assessment of genome sequence data has not resulted in the anticipated acceleration of novel therapeutic developments. The basis for this shortfall lies in the significant attrition rates endemic to preclinical/clinical development, as well as the often underestimated complexity of gene function in higher order biological systems. To address the latter issue, a number of strategies have emerged to facilitate genomics-driven target identification and validation, including cellular profiling of gene function, in silico modelling of gene networks, and systematic analyses of protein complexes. The expectation is that the integration of these and other systems-based technologies may enable the conversion of potential genomic targets into functionally validated molecules, and result in practicable gene-based drug discovery pipelines.
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Affiliation(s)
- Anthony P Orth
- The Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121, USA
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12
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Zhang D, Wu J, Ye F, Feng T, Lee I, Yin B. Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clin Chim Acta 2005; 363:61-70. [PMID: 16122721 DOI: 10.1016/j.cccn.2005.05.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Accepted: 05/05/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Circularizable oligonucleotide probe (C-probe) is a unique molecule that offers significant advantages over conventional probes. METHODS Closed circular structure can be formed through ligation of the juxtaposed ends of the C-probe after hybridization with a target, and subsequently locked onto its target through the helical turns formed between the complementary sequences of the target and the C-probe (padlock probe). Under isothermal condition, C-probe can be amplified by rolling circle amplification (RCA) to generate multimeric single-stranded DNA (ssDNA). This multimeric ssDNA can be further amplified by a ramification mechanism (RAM) through primer extension and downstream DNA displacement, resulting in an exponential amplification. Usually, an unbiased product is generated by either RCA or ramification amplification method (or RAM) due to the generic primers of C-probe and its localization onto DNA targets. CONCLUSIONS These advantages make C-probe amplification very useful for research and molecular diagnosis, especially in areas where other techniques were proved to be inadequate. The development of C-probe-based technologies offers a promising prospect for molecular diagnosis. The applications of C-probe, RCA, RAM, in situ detection, microarray, immunoassay, single nucleotide polymorphism, and whole genome amplification, etc. are discussed in this review.
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Affiliation(s)
- David Zhang
- Department of Pathology, Mount Sinai School of Medicine, New York University, NY 10029, USA.
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13
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Lin HC, Su BH, Chang JS, Hsu CM, Tsai CH, Tsai FJ. Nonassociation of Interleukin 4 Intron 3 and 590 Promoter Polymorphisms with Bronchopulmonary Dysplasia for Ventilated Preterm Infants. Neonatology 2005; 87:181-6. [PMID: 15627726 DOI: 10.1159/000082937] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Accepted: 10/11/2004] [Indexed: 11/19/2022]
Abstract
Interleukin 4 (IL-4) stimulates and amplifies the inflammatory response, stimulates collagen synthesis in fibroblasts, promotes the progression to fibrosis and has been shown to inhibit the production of several inflammatory cytokines in the development of bronchopulmonary dysplasia (BPD) and airway hyperreactivity. We aimed to investigate whether IL-4 polymorphisms in ventilated preterm infants were associated with BPD. BPD was defined as infants who remained dependent on active respiratory support or oxygen supplementation at 36 weeks postconceptional age. A case-control study of 224 preterm infants (<30 weeks) who had respiratory distress syndrome and needed intermittent mandatory ventilation (IMV) were undertaken between January 1999 and December 2003. The typing of each genetic polymorphism was performed by polymerase-chain-reaction-based restriction analysis. Genotype distribution and allelic frequencies were compared between ventilated preterm infants who developed BPD and those who did not and the duration of IMV. The demography of these ventilated BPD and non-BPD preterm infants was not different. We observed no significant differences in genotype distribution or allelic frequency of the IL-4 intron 3 or IL-4 promoter polymorphisms between ventilated preterm infants who developed BPD and who did not. There was no significant association of the genotype or allelic frequency of IL-4 polymorphism with duration of IMV. We conclude that neither IL-4 intron 3 nor the 590 promoter polymorphism is a useful marker for predicting the susceptibility to BPD in ventilated Taiwanese preterm infants.
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Affiliation(s)
- Hung-Chih Lin
- Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan
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Abstract
The post-genomic era of functional genomics and target validation will allow us to narrow the bridge between clinically correlative data and causative data for complex diseases, such as arthritis, for which the etiological agent remains elusive. The availability of human and other annotated genome sequences, and parallel developments of new technologies that allow analysis of minute amounts of human and animal cells (peripheral blood cells and infiltrating cells) and tissues (synovium and cartilage) under different pathophysiological conditions, has facilitated high-throughput gene mining approaches that can generate vast amounts of clinically correlative data. Characterizing some of the correlative/causative genes will require reverting to the hypothesis-driven, low throughput method of complementary experimental biology using genomic approaches as a tool. This will include in silico gene expression arrays, genome-wide scans, comparative genomics using various animal models (such as rodents and zebrafish), bioinformatics and a team of well trained translational scientists and physicians. For the first time, the "genomic tools" will allow us to analyze small amounts of surgical samples (such as needle biopsies) and clinical samples in the context of the whole genome. Preliminary genomic analysis in osteoarthritis has already resurrected the debate on the semantic issues in the definition of inflammation. Further analyses will not only facilitate the development of unbiased hypotheses at the molecular level, but also assist us in the identification and characterization of novel targets and disease markers for pharmacological intervention, gene therapy, and diagnosis.
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Affiliation(s)
- Mukundan G Attur
- Departments of Rheumatology and Medicine, Hospital for Joint Diseases/NYU School of Medicine, 301 East 17th Street, New York, NY 10003, USA
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15
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Shastry BS. Role of SNP/haplotype map in gene discovery and drug development: An overview. Drug Dev Res 2004. [DOI: 10.1002/ddr.10377] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Rice MC, Heckman BM, Liu Y, Kmiec EB. Fluorescent detection and isolation of DNA variants using stabilized RecA-coated oligonucleotides. Genome Res 2003; 14:116-25. [PMID: 14672976 PMCID: PMC314288 DOI: 10.1101/gr.1386204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Several genome resequencing strategies have been developed to detect genetic variation in populations and correlate diversity with phenotypic consequences. Commonly used methods of detecting single nucleotide polymorphisms (SNPs) use PCR amplification and indirect analysis, which can create template biases and enable user contamination. Here we present a novel assay to detect and isolate DNA variants using stabile nanostructures formed directly on duplex DNA. The assay incorporates the well-established RecA-catalyzed strand invasion process with a novel stabilizing hybridization step. First, short RecA-coated oligonucleotide filaments invade duplex DNA to form a synaptic intermediate or "D-loop." Sequentially, chemically modified oligonucleotide probes anneal to the displaced DNA strand of the complex to form a stable "double D-loop." These joint molecules resist dissociation when both oligonucleotides are completely complementary to the target duplex; however, if the probes are mismatched, the complex is inherently instable and rapidly dissociates. SNPs are identified by detecting the fluorophore assimilated into stable complexes produced by homologous probes compared to unstable differentially labeled mismatched probes. Furthermore, this strategy can be used to isolate specific allelic variants by affinity purification from complex populations. Stabilized double D-Loop intermediates accordingly offer the promise of haplotyping and pharmacogenomic analysis directly in double-stranded DNA samples.
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Affiliation(s)
- Michael C Rice
- Department of Biology, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
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17
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Abstract
Mice have become the mammalian model of choice for the application of genetics in biomedical research due to the evolutionary conservation of physiological systems and their attendant pathologies among all mammals as well as the exceptional power of genetic research technologies in the species. Beginning from aberrant phenotypes, a large number of mouse mutants and natural polymorphisms have been cloned, providing much information about the molecular basis of physiological processes. Additionally, the variable expression of these mutations in different inbred strain backgrounds has demonstrated the importance of modifier genes, which are also susceptible to cloning. Research efforts are keeping pace with these developments. In the area of gene discovery, large, government-funded mutagenesis programs now exist, and as a matter of great practical importance, recent evidence suggests that the same genes may be involved in the natural polymorphisms affecting disease in mice and humans. In parallel, dramatic advances are also being made in our ability to measure physiological processes in mice, and the advent of expression profiling promises revolutionary advances in understanding phenotype at the molecular level. Gene-driven approaches have relied on engineering the mouse genome, including adding, subtracting, and replacing genes and, most recently, the ability to control gene activity reversibly. Together, these multiple advances in our technical abilities have created extraordinary opportunities for future discovery.
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18
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Abstract
During the past decade, mutations affecting liability to central obesity have been discovered at a phenomenal rate, and despite few consistently replicated findings, a number of intriguing results have emerged in the literature. Association studies have been proposed to identify the genetic determinants of complex traits such as central obesity. The advantages of the association method include its relative robustness to genetic heterogeneity and the ability to detect much smaller effect sizes than is detectable using feasible sample sizes in linkage studies. However, the current literature linking central obesity to genetic variants is teeming with reports of associations that either cannot be replicated or for which corroboration by linkage has been impossible to find. Explanations for this lack of reproducibility are well rehearsed, and typically include poor study design, incorrect assumptions about the underlying genetic architecture, and simple overinterpretation of data. These limitations create concern about the validity of association studies and cause problems in establishing robust criteria for undertaking association studies. In this article, the current status of the literature of association studies for genetic dissection of central obesity is critically reviewed.
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Affiliation(s)
- R Rosmond
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Göteborg, Sweden.
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19
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Chung HW, Seo JS, Hur SE, Kim HL, Kim JY, Jung JH, Kim LH, Park BL, Shin HD. Association of interleukin-6 promoter variant with bone mineral density in pre-menopausal women. J Hum Genet 2003; 48:243-248. [PMID: 12768442 DOI: 10.1007/s10038-003-0020-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Accepted: 02/24/2003] [Indexed: 11/24/2022]
Abstract
Interleukin-6 (IL6) has many roles essential to the regulation of the immune response, hematopoiesis, and bone resorption. Three single-nucleotide polymorphisms (SNP) in the IL6 promoter region were genotyped by the single-base extension method. The frequencies of each SNP were 0.002 ( IL6-597 G--> A), 0.27 ( IL6-572 G--> C), and 0.002 ( IL6-174 G--> C) in a Korean population ( n=1,082). IL6-597 G--> A and IL6-174 G--> C were totally linked together ( d(2)=1) and showed very low allele frequencies (0.002), which are common in Caucasians. On the other hand, the frequency of the IL6-572 G--> C*C allele was much higher (0.27) than that in Caucasian populations (<0.07). One of the IL6 promoter SNPs, viz., IL6-572 G--> C, showed significant associations with bone mineral density (BMD), i.e., the C allele was associated with increased BMD ( P=0.02, co-dominant model; P=0.007, dominant model). The mean BMD was highest in homozygous C individuals (0.67+/-0.15), lowest in homozygous G individuals (0.58+/-0.19), and intermediate in heterozygotes (0.64+/-0.21). In the present study, we describe a variant in the IL6 promoter region that shows positive association with higher BMD in a gene-dose-dependent manner in pre-menopausal women.
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Affiliation(s)
- Hye Won Chung
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Woman's University, 158-710, Seoul, Korea
| | - Jeong-Sun Seo
- Department of Biochemistry and Molecular Biology, ILCHUN Molecular Medicine Institute, College of Medicine, Seoul National University, 28 Yungun-dong, Chonro-gu, 110-744, Seoul, Korea.
| | - Sung Eun Hur
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Woman's University, 158-710, Seoul, Korea
| | - Hyung Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Woman's University, 158-710, Seoul, Korea
| | - Jun Yeon Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., 11th Floor, Maehun Building, 13 Chongro 4 Ga, Chongro Gu, 110-834, Seoul, Korea
| | - Ji Hyun Jung
- Department of Genetic Epidemiology, SNP Genetics Inc., 11th Floor, Maehun Building, 13 Chongro 4 Ga, Chongro Gu, 110-834, Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., 11th Floor, Maehun Building, 13 Chongro 4 Ga, Chongro Gu, 110-834, Seoul, Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics Inc., 11th Floor, Maehun Building, 13 Chongro 4 Ga, Chongro Gu, 110-834, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics Inc., 11th Floor, Maehun Building, 13 Chongro 4 Ga, Chongro Gu, 110-834, Seoul, Korea
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20
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Affiliation(s)
- Sambasivarao Damaraju
- Polyomx Program (www.polyomx.org), Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
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21
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Abstract
The prospect for genetic testing to better delineate the risk for coronary heart disease will become a reality in the next decade. Advances in this area will follow the accelerated trajectory in our ability to dissect the genetics of complex diseases including coronary heart disease. A brief overview of the present state of knowledge will follow the discussion of present approaches in discovering these genetic predispositions. The key issues that will likely shape the field in the near future will also be presented.
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Affiliation(s)
- Ramtin Agah
- Cleveland Clinic Foundation, Dept. of Cardiovascular Medicine, 9500 Euclid Ave. F-25, Cleveland, OH 44195, USA
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22
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Norbert PW, Roses AD. Pharmacogenetics and pharmacogenomics: recent developments, their clinical relevance and some ethical, social, and legal implications. J Mol Med (Berl) 2003; 81:135-40. [PMID: 12755119 DOI: 10.1007/s00109-002-0415-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In recent debates on novel procedures of molecular medicine pharmacogenomics is attracting more and more attention as a genotype-based approach for improving safety and efficacy of the use of therapeutic substances. Promoted by basic knowledge generated in the field of medical genomics, facilitated by novel technological tools for mapping genetic variation in individuals, and supported by results of initial clinical studies linking specific genotypes to metabolic characteristics of individuals important for assessing drug response, procedures of pharmacogenetics and pharmacogenomics now are starting to impact significantly on clinical research and development and medical practice. In this situation assessing the goals, risk, and benefits of pharmacogenetics and pharmacogenomics is essential for the medically successful, ethically justifiable, and socially acceptable implementation of genotype-based diagnosis and pharmacotherapy. We discuss the current state of the art in pharmacogenetics and pharmacogenomics and introduce a model for evidence based assessment of its goals, risk, and benefits. We differentiate here between pragmatic and normative issues in the development of pharmacogenomics in order to contrast prevailing, insufficiently interest-based modes of public technology assessment with the evidence-based mode that can be established as part of clinical study design. Finally, we provide a framework for the analysis of social accountability that can be used for technology development and technology assessment with regard to pharmacogenomics in particular and molecular medicine in general.
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23
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Andersen PS, Jespersgaard C, Vuust J, Christiansen M, Larsen LA. High-throughput single strand conformation polymorphism mutation detection by automated capillary array electrophoresis: validation of the method. Hum Mutat 2003; 21:116-22. [PMID: 12552558 DOI: 10.1002/humu.10161] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Capillary array electrophoresis (CAE) is a novel technique, which allows for high throughput analysis of DNA fragments. When screening for mutations in whole populations or large patient groups it is necessary to have robust and well-characterized setups for high throughput analysis. For large-scale mutation screening, we have developed procedures for single strand conformation polymorphism (SSCP) assays using CAE (CAE-SSCP) whereby we may increase both the sensitivity and the throughput compared to conventional SSCP analysis. In this study we have validated CAE-SSCP by 1) comparing detection by slab-gel based SSCP with CAE-SSCP of mutations in the MYH7, MYL2, and MYL3 genes encoding sarcomere proteins from patients suffering from hypertrophic cardiomyopathy; and 2) by constructing a series of 185 mutants having substitution mutations, as well as insertion/deletion mutations, or some combinations of these, in different sequence contexts in four exons and different positions relative to the end of the amplicon (three from the KCNQ1 gene, encoding a cardiac potassium channel, and one from the TNNI3 gene encoding cardiac troponin I). The method identified 181 out of 185 mutations (98%), and the data suggest that the position of mutation in the fragment had no effect on the sensitivity. Analysis of the specificity of the method showed that only very few mutants could not be distinguished from each other and there were no false positives.
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Affiliation(s)
- Paal Skytt Andersen
- Department of Clinical Biochemistry, Statens Serum Institut, Copenhagen, Denmark.
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24
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Reis A. Dissecting the genetic component of complex diseases in humans. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2002:1-15. [PMID: 12060997 DOI: 10.1007/978-3-662-04747-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- A Reis
- Institute für Humangenetik, Friedrich-Alexander Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany.
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25
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Chumakov I, Blumenfeld M, Guerassimenko O, Cavarec L, Palicio M, Abderrahim H, Bougueleret L, Barry C, Tanaka H, La Rosa P, Puech A, Tahri N, Cohen-Akenine A, Delabrosse S, Lissarrague S, Picard FP, Maurice K, Essioux L, Millasseau P, Grel P, Debailleul V, Simon AM, Caterina D, Dufaure I, Malekzadeh K, Belova M, Luan JJ, Bouillot M, Sambucy JL, Primas G, Saumier M, Boubkiri N, Martin-Saumier S, Nasroune M, Peixoto H, Delaye A, Pinchot V, Bastucci M, Guillou S, Chevillon M, Sainz-Fuertes R, Meguenni S, Aurich-Costa J, Cherif D, Gimalac A, Van Duijn C, Gauvreau D, Ouellette G, Fortier I, Raelson J, Sherbatich T, Riazanskaia N, Rogaev E, Raeymaekers P, Aerssens J, Konings F, Luyten W, Macciardi F, Sham PC, Straub RE, Weinberger DR, Cohen N, Cohen D, Ouelette G, Realson J. Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia. Proc Natl Acad Sci U S A 2002; 99:13675-80. [PMID: 12364586 PMCID: PMC129739 DOI: 10.1073/pnas.182412499] [Citation(s) in RCA: 684] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A map of 191 single-nucleotide polymorphism (SNPs) was built across a 5-Mb segment from chromosome 13q34 that has been genetically linked to schizophrenia. DNA from 213 schizophrenic patients and 241 normal individuals from Canada were genotyped with this marker set. Two 1,400- and 65-kb regions contained markers associated with the disease. Two markers from the 65-kb region were also found to be associated to schizophrenia in a Russian sample. Two overlapping genes G72 and G30 transcribed in brain were experimentally annotated in this 65-kb region. Transfection experiments point to the existence of a 153-aa protein coded by the G72 gene. This protein is rapidly evolving in primates, is localized to endoplasmic reticulum/Golgi in transfected cells, is able to form multimers and specifically binds to carbohydrates. Yeast two-hybrid experiments with the G72 protein identified the enzyme d-amino acid oxidase (DAAO) as an interacting partner. DAAO is expressed in human brain where it oxidizes d-serine, a potent activator of N-methyl-D-aspartate type glutamate receptor. The interaction between G72 and DAAO was confirmed in vitro and resulted in activation of DAAO. Four SNP markers from DAAO were found to be associated with schizophrenia in the Canadian samples. Logistic regression revealed genetic interaction between associated SNPs in vicinity of two genes. The association of both DAAO and a new gene G72 from 13q34 with schizophrenia together with activation of DAAO activity by a G72 protein product points to the involvement of this N-methyl-d-aspartate receptor regulation pathway in schizophrenia.
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26
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Sheffield LJ. The hunt for new genes and polymorphisms that can control the response to drugs. Pharmacogenomics 2002; 3:679-86. [PMID: 12223052 DOI: 10.1517/14622416.3.5.679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
There has been a great increase in the knowledge of understanding the genetic basis for individual variation in response to drugs. The study of variation in gene structure (polymorphism) can now predict the likely metabolic behavior in an individual for a number of drugs. This review documents the different strategies that can be used to find new genes and polymorphisms within these genes. Candidate genes can be used in case-control studies or studies where the parents of the person having an adverse effect from the drug are used as controls. New genes are being discovered in the drug development process and the technological development in molecular biology is expected to greatly enhance knowledge of the genes that regulate drug metabolism.
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Affiliation(s)
- Leslie J Sheffield
- Genetic Health Services Victoria, Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Australia.
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27
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Pickering J, Bamford A, Godbole V, Briggs J, Scozzafava G, Roe P, Wheeler C, Ghouze F, Cuss S. Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms. Nucleic Acids Res 2002; 30:e60. [PMID: 12060698 PMCID: PMC117302 DOI: 10.1093/nar/gnf060] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Association studies using common sequence variants or single nucleotide polymorphisms (SNPs) may provide a powerful approach to dissect the genetic inheritance of common complex traits. Such studies necessitate the development of cost-effective, high throughput technologies for scoring SNPs. The method described in this paper for the co-detection of both alleles of a SNP in a single homogeneous reaction combines the specificity of a high fidelity DNA ligation step with the power of rolling circle amplification. The incorporation of Amplifluor energy transfer primers enables signal detection in a homogeneous format, making this approach highly amenable to automation. The adaptation of the genotyping method for high throughput screening using conventional liquid handling systems is described.
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Affiliation(s)
- Judith Pickering
- Amersham Biosciences UK Ltd, The Grove Centre, AL16, White Lion Road, Amersham, Buckinghamshire HP7 9LL, UK.
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28
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Turner D, Choudhury F, Reynard M, Railton D, Navarrete C. Typing of multiple single nucleotide polymorphisms in cytokine and receptor genes using SNaPshot. Hum Immunol 2002; 63:508-13. [PMID: 12039528 DOI: 10.1016/s0198-8859(02)00392-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Associations have been described between polymorphisms in cytokine genes and severity of autoimmune diseases, outcome of infectious disease, and outcome following transplantation. Many methods now exist for typing single nucleotide polymorphisms (SNPs) and these can be applied to typing cytokine gene and cytokine receptor gene variation. A system for typing multiple cytokine and receptor gene polymorphisms using a primer extension method, SNaPshot (Applied Biosystems, Foster City, CA, USA), has been assessed. The development of this methodology may enable other laboratories to type for cytokine SNPs in different populations and facilitate research into the effect of genetic polymorphism in the cytokine network in transplantation and disease.
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Affiliation(s)
- David Turner
- Department of Histocompatibility and Immunogenetics, North London Centre, National Blood Service, London, United Kingdom.
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29
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Dalma-Weiszhausz DD, Chicurel ME, Gingeras TR. Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field. Genet Epidemiol 2002; 23:4-20. [PMID: 12112245 DOI: 10.1002/gepi.216] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The advent of molecular technologies that allow the collection and analysis of large amounts of genetic data is rapidly transforming the field of genetic epidemiology. Whether monitoring infectious outbreaks or identifying genotypic variations that underlie disease susceptibility, genetic epidemiology relies heavily on the analysis of multiple, independently derived results. By allowing the simultaneous monitoring of thousands of genetic or expression data points, microarrays are emerging as particularly powerful tools. Several recent reviews have described array manufacturing and the types of scientific questions that can exploit this technology, but few have addressed how the intended use of an array can dictate its design. This review will focus on this latter issue, with particular emphasis on the genetic epidemiology of infectious disease. The design of arrays for genotyping, expression profiling, and fingerprinting are presented, and examples of recent epidemiological studies are used to illustrate the applications' strong points and limitations. In addition to discussing arrays' ability to provide global views of gene identity or function, the review will describe design options for creating arrays that detect multiple genetic variations. It will also examine the reliability of array-generated fingerprints, assay accessibility, and possibilities for sharing and comparing data across studies. Although many challenges lie ahead, microarrays' multiple abilities appear uniquely poised to accelerate the advance of genetic epidemiology's multiple fronts.
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30
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Abstract
The advent of the genomic era has brought about several new fields of study, one of them being pharmacogenomics, which seeks to link drug treatment (pharmaco-) with the individual's genetic make-up (genomics). Pharmacogenomics holds many promises for improved treatment of a large variety of medical conditions, including immunosuppression for organ transplantation and autoimmune disease. Many of these promises have, however, not yet been fulfilled. In this brief overview of the subject, we attempt to provide insights into the evolving field of pharmacogenomics and discuss some of its potential benefits and promises, technological tools used by pharmacogenomics, the reasons for delays in breakthroughs in the field, and the relevance of pharmacogenornics to immunosuppression.
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Affiliation(s)
- Yoram Yagil
- Department of Nephrology and Hypertension, Faculty of Health Sciences, Ben-Gurion University, Barzilai Medical Center, Ashkelon, Israel.
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31
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Adkins KK, Strom DA, Jacobson TE, Seemann CR, O'Brien DP, Heath EM. Utilizing genomic DNA purified from clotted blood samples for single nucleotide polymorphism genotyping. Arch Pathol Lab Med 2002; 126:266-70. [PMID: 11860298 DOI: 10.5858/2002-126-0266-ugdpfc] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Linking single nucleotide polymorphisms to disease etiology is expected to result in a substantial increase in the number of genetic tests available and performed at clinical laboratories. Whole blood serves as the most common DNA source for these tests. Because the number of blood samples rises with the number of genetic tests performed, alternative DNA sources will become important. One such alternative source is clotted blood, a by-product of serum extraction. Efficiently using an already procured blood sample would limit the overall number of samples processed by clinical laboratories. OBJECTIVE To determine if DNA purified from clotted blood can be effectively used for single nucleotide polymorphism genotyping. DESIGN DNA was purified from the clotted blood of 15 donors. Single nucleotide polymorphism genotyping for the methylenetetrahydrofolate reductase and factor V Leiden mutations was performed with each DNA sample by 2 independent methods. RESULTS High-quality DNA was obtained from each of the 15 individual clotted blood samples as demonstrated by UV spectrophotometric analysis, gel electrophoresis, and polymerase chain reaction amplification. The DNA was used successfully to obtain genotype data from both the methylenetetrahydrofolate reductase and factor V single nucleotide polymorphism assays for all samples tested. CONCLUSIONS Clotted blood is a clinically abundant sample type that can be used as a source of high-quality DNA for single nucleotide polymorphism genotyping.
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32
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Brazell C, Freeman A, Mosteller M. Maximizing the value of medicines by including pharmacogenetic research in drug development and surveillance. Br J Clin Pharmacol 2002; 53:224-31. [PMID: 11874384 PMCID: PMC1874316 DOI: 10.1046/j.0306-5251.2001.01556.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2000] [Accepted: 11/06/2001] [Indexed: 11/20/2022] Open
Abstract
Genetics provides significant opportunities to maximize the safety and efficacy of medicines. Over the next 3--5 years, it may be possible to develop tools that use selective information from patients' DNA to enable healthcare professionals to predict more accurately those patients at risk of serious adverse events to some medicines currently available. This is likely to be followed, over the next 5--10 years, by the application of the technology to predict more accurately if individual patients will obtain a therapeutic benefit from a particular medicine. The ability to accurately predict patient response will inevitably change the way medicines are developed, evaluated, and prescribed. Advances in single nucleotide polymorphism (SNP) map technology are likely to drive this innovation. Abbreviated SNP profiles will provide the means to define medicine response tests, thereby allowing clinicians to select the medicine to which the patient is likely to gain the greatest benefit and least risk. This will help to maximize efficacy and reduce the incidence of drug-related adverse events. It may be possible to identify SNP profiles during larger Phase II clinical trials which predict efficacy, and use these to form the basis of Phase III entry criteria. As a result, Phase III trials may be streamlined for many medicines making them smaller, more efficient, and more focused. In addition it may be possible to incorporate pharmacogenetics into postmarketing surveillance strategies to provide a means to identify SNPs which predict uncommon serious adverse drug reactions, and so refine the initial medicine response test. The ability to develop drugs with a predictable response will allow clinicians to provide targeted treatment for patients, with greater confidence of safety and efficacy. Patients therefore will receive more efficacious, timely, and well-tolerated medicines. The challenge for those involved in drug development is to model and evaluate the application of pharmacogenetics so that steps can be taken to realize this potential.
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Affiliation(s)
- C Brazell
- Genetics Research, GlaxoSmithKline, Greenford Road, Greenford, Middlesex UB6 0HE.
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33
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Hewett D, Samuelsson L, Polding J, Enlund F, Smart D, Cantone K, See CG, Chadha S, Inerot A, Enerback C, Montgomery D, Christodolou C, Robinson P, Matthews P, Plumpton M, Wahlstrom J, Swanbeck G, Martinsson T, Roses A, Riley J, Purvis I. Identification of a psoriasis susceptibility candidate gene by linkage disequilibrium mapping with a localized single nucleotide polymorphism map. Genomics 2002; 79:305-14. [PMID: 11863360 DOI: 10.1006/geno.2002.6720] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Psoriasis is a chronic inflammatory disease of the skin with both genetic and environmental risk factors. Here we describe the creation of a single-nucleotide polymorphism (SNP) map spanning 900-1200 kb of chromosome 3q21, which had been previously recognized as containing a psoriasis susceptibility locus, PSORS5. We genotyped 644 individuals, from 195 Swedish psoriatic families, for 19 polymorphisms. Linkage disequilibrium (LD) between marker and disease was assessed using the transmission/disequilibrium test (TDT). In the TDT analysis, alleles of three of these SNPs showed significant association with disease (P<0.05). A 160-kb interval encompassing these three SNPs was sequenced, and a coding sequence consisting of 13 exons was identified. The predicted protein shares 30-40% homology with the family of cation/chloride cotransporters. A five-marker haplotype spanning the 3' half of this gene is associated with psoriasis to a P value of 3.8<10(-5). We have called this gene SLC12A8, coding for a member of the solute carrier family 12 proteins. It belongs to a class of genes that were previously unrecognized as playing a role in psoriasis pathogenesis.
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Affiliation(s)
- Duncan Hewett
- UK Discovery Genetics, GlaxoSmithKline Research and Development, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
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34
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Abstract
The elucidation of the assumed genetic contribution to the predisposition towards schizophrenia is a scientifically challenging enterprise with considerable impact on therapeutic possibilities. A pharmacogenetic approach, targeted to the clinical response to medication, provides a promising alternative as a means of investigation, with the prospect of gaining knowledge about the disease and of developing an individually tailored medical treatment. This review will focus on dopamine receptor genes which have, due to the dopamine hypothesis of schizophrenia, been a prime target in pharmacogenetic studies of schizophrenia. The current status of the studies results will be displayed and future prospects will be discussed.
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Affiliation(s)
- J Scharfetter
- Universitätsklinik für Psychiatrie, Abteilung für Allgemeine Psychiatrie, Währinger Gürtel 18-20, A-1090 Wien, Austria.
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35
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Abstract
Alzheimer's disease (AD) is the most common cause of dementia in the elderly population. Three genes have been identified that cause the less common early-onset, familial cases of the disease: the amyloid precursor (APP) protein gene on chromosome 21, the presenilin 1 (PSEN1) gene on chromosome 14 and the presenilin 2 (PSEN2) gene on chromosome 1. Mutations in these genes account for << 2% of the total number of AD cases. More than 50% of the cases are late-onset and related to the apolipoprotein E (APOE) gene on chromosome 19. The apolipoprotein E locus is a susceptibility gene, with polymorphisms affecting both risk and age-of-onset of the disease. Intense efforts are underway to identify additional susceptibility genes and promising regions on chromosomes 6, 9, 10 and 12 have been identified through whole genome scans. In addition, the genetic basis of several other non-AD inherited dementias has been unravelled. Discovery of the genetically relevant genes will aid in the elucidation of the pathogenesis of AD. The high-throughput tools of pharmacogenomics for gene-to-function-to-target studies can provide a quicker means of monitoring how mutations and polymorphisms affect model systems' adaptations to the altered genes, possibly identifying signal transduction or biochemical pathways. This relevant information can then be used for drug target selection and pharmacogenetics.
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Affiliation(s)
- A M Saunders
- Box 2900, Department of Medicine (Neurology), Duke University Medical Center, Durham, NC 27710, USA.
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