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SNPselector: a web tool for selecting SNPs for genetic association studies

H. Xu, S. G. Gregory, E. R. Hauser, J. E. Stenger, M. A. Pericak-Vance, J. M. Vance, S. Zuchner, M. A. Hauser
2005 Bioinformatics  
Single nucleotide polymorphisms (SNPs) are commonly used for association studies to find genes responsible for complex genetic diseases.  ...  SNPselector takes a list of gene names or a list of genomic regions as input and searches the Ensembl genes or genomic regions for available SNPs.  ...  ACKNOWLEDGEMENTS We would like to thank Carrie Browning, Liyong Wang, Jason Rose and others for their helpful suggestions.  ... 
doi:10.1093/bioinformatics/bti682 pmid:16179360 pmcid:PMC1361283 fatcat:dlksubfrpnec7adwpbdo47unla

An integrative scoring system for ranking SNPs by their potential deleterious effects

P. H. Lee, H. Shatkay
2009 Bioinformatics  
As of yet, little has been done to quantitatively assess the possible deleterious effects of SNPs for effective association studies.  ...  We also demonstrate, through a comparative study, that our system improves upon other function-assessment systems for SNPs, by assigning significantly higher FS scores to already known disease-related  ...  By combining the two most representative selection approaches for SNPs, we expect to provide a comprehensive SNP prioritization system for facilitating effective association studies on common and complex  ... 
doi:10.1093/bioinformatics/btp103 pmid:19228803 fatcat:jyochomi7bfztgh6f74hne67iu

Next generation tools for the annotation of human SNPs

Rachel Karchin
2009 Briefings in Bioinformatics  
The medical genetics and molecular biology communities are increasingly turning to computational biology methods to prioritize interesting SNPs found in linkage and association studies.  ...  A 'conserved SNP' is a SNP that is at a conserved sequence position. dbSNP reference identifiers These are identifiers given to SNPs by the dbSNP database at NCBI.  ...  Acknowledgements The author thanks Dr Melissa Cline for valuable discussions.  ... 
doi:10.1093/bib/bbn047 pmid:19181721 pmcid:PMC2638621 fatcat:wrxufl5ayvd2nc7v5x3a4d3dr4

Candidate Single Nucleotide Polymorphism Selection using Publicly Available Tools: A Guide for Epidemiologists

Parveen Bhatti, Deanna M. Church, Joni L. Rutter, Jeffery P. Struewing, Alice J. Sigurdson
2006 American Journal of Epidemiology  
The authors show a "real world" application of some existing bioinformatics tools for use in large epidemiologic studies and genetic analyses.  ...  Because only 1% might be expected to confer more than modest individual effects in association studies, the selection of predictive candidate variants for complex disease analyses is formidable.  ...  ACKNOWLEDGMENTS This research was supported in part by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and the Center for Cancer Research, National Cancer Institute,  ... 
doi:10.1093/aje/kwj269 pmid:16923772 fatcat:32oy7p6o7bg3fc77d2kzlkwwxy

SNPit: A federated data integration system for the purpose of functional SNP annotation

Terry H. Shen, Christopher S. Carlson, Peter Tarczy-Hornoch
2009 Computer Methods and Programs in Biomedicine  
A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies.  ...  Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases.  ...  The authors would like to extend thanks to the BioDIAG and UII group for their contributions to the SNPit project.  ... 
doi:10.1016/j.cmpb.2009.02.010 pmid:19327864 pmcid:PMC2680224 fatcat:i4af257bjncetgcytzsnahlggq

SNP locator: a candidate SNP selection tool

José A. Seoane, Vanessa Aguiar Pulido, Alba Cabarcos, Sonsoles Quintela, Juan Ramon Rabuñal, Julián Dorado
2013 International Journal of Data Mining Modelling and Management  
As an example of usage of this architecture, a web tool for candidate SNP selection has been developed. Thus, several BioMOBY services have been created as the model layer of the web application.  ...  During her studies, she performed two final year projects, both in the field of biomedicine.  ...  QuickSNP (Grover et al., 2007) is a web server that allows the user to select SNPs for association studies.  ... 
doi:10.1504/ijdmmm.2013.055863 fatcat:kvywvhzkw5aolddgsthgpquyea

Genetic variations in regulatory pathways of fatty acid and glucose metabolism are associated with obesity phenotypes: a population-based cohort study

S W van den Berg, M E T Dollé, S Imholz, D L van der A, R van 't Slot, C Wijmenga, W M M Verschuren, C Strien, C L E Siezen, B Hoebee, E J M Feskens, J M A Boer
2009 International Journal of Obesity  
In addition, two SNPs (in SIRT1 and SCAP in women only) were associated with BMI alone. A functional SNP, in IL6, was strongly associated with waist.  ...  Conclusion: In this explorative study among participants of a large population-based cohort, five SNPs, mainly located in transcription mediator genes, were strongly associated with obesity phenotypes.  ...  Acknowledgements The authors thank the epidemiologists and fieldworkers of the Municipal Health Service in Doetinchem for their contribution to the data collection for this study.  ... 
doi:10.1038/ijo.2009.152 pmid:19652658 fatcat:exqni3lkdzb55bxydlwudnxmqa

A consolidated catalogue and graphical annotation of dbSNP polymorphisms in the human tissue kallikrein (KLK ) locus

Carolyn A. Goard, Irvin L. Bromberg, Marc B. Elliott, Eleftherios P. Diamandis
2007 Molecular Oncology  
Shaw and Carla A. Borgono for helpful discussions and advice. This work was supported in part by an Undergraduate Student Research Award to C.A.G. from the Natural Sciences and Engineering Research  ...  These programs are thus more appropriate for selecting a few specific polymorphisms of interest for functional studies or association studies on a smaller scale.  ...  SNPHunter and SNPselector are resources that focus on appropriate selection of polymorphisms specifically for association studies, and as such their main features are centred on selecting polymorphisms  ... 
doi:10.1016/j.molonc.2007.09.001 pmid:19383304 pmcid:PMC5543866 fatcat:3vvac63hdvg2rfob6p5wnvbzsu

Evaluating the accuracy of a functional SNP annotation system

Terry H Shen, Christopher S Carlson, Peter Tarczy-Hornoch
2009 BMC Bioinformatics  
The SNP Integration Tool (SNPit) is a comprehensive tool that integrates diverse, existing predictors of SNP functionality, providing the user with information for improved association study analysis.  ...  A key element in assessing role of a given SNP is determining if the variation is likely to result in change in function.  ...  Particularly to Todd Detwiler, Shannon Byler, Janos Barbero, Ron Shaker, and Eithon Cadag for their expertise and assistance.  ... 
doi:10.1186/1471-2105-10-s9-s11 pmid:19761565 pmcid:PMC2745682 fatcat:pa66piekcnbixpv4jqk2iop5n4

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS

Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca, Luciano Milanesi
2013 BMC Bioinformatics  
Possible scenarios are GWAS data re-scoring, SNPs selection for custom genotyping arrays and SNPs/diseases association studies.  ...  New tools for genetic variants interpretation and for Single Nucleotide Polymorphisms (SNPs) prioritization are actually needed.  ...  The first version of SNPranker [11] was also a web tool for SNP prioritization.  ... 
doi:10.1186/1471-2105-14-s1-s9 pmid:23369106 pmcid:PMC3548692 fatcat:kfxzfdreeffupehj6b4otwaalq

GWASdb: a database for human genetic variants identified by genome-wide association studies

Mulin Jun Li, Panwen Wang, Xiaorong Liu, Ee Lyn Lim, Zhangyong Wang, Meredith Yeager, Maria P. Wong, Pak Chung Sham, Stephen J. Chanock, Junwen Wang
2011 Nucleic Acids Research  
Recent advances in genome-wide association studies (GWAS) have enabled us to identify thousands of genetic variants (GVs) that are associated with human diseases.  ...  It can conduct pathway enrichment and PPI network association analysis for these diseases.  ...  ACKNOWLEDGEMENTS We thank Kevin Mao and Tina Yuen of The Royal College of Surgeons in Ireland for their assistance in data curation.  ... 
doi:10.1093/nar/gkr1182 pmid:22139925 pmcid:PMC3245026 fatcat:dtu4apnazfaevcdfrnyxpqprjm

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

H.-Y. Yuan, J.-J. Chiou, W.-H. Tseng, C.-H. Liu, C.-K. Liu, Y.-J. Lin, H.-H. Wang, A. Yao, Y.-T. Chen, C.-N. Hsu
2006 Nucleic Acids Research  
Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies.  ...  FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic  ...  Yuarn and Dr Pei-Ing Hwang for their valuable suggestions.  ... 
doi:10.1093/nar/gkl236 pmid:16845089 pmcid:PMC1538865 fatcat:nnmyct2co5fijlfu5evdhwiuei

Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations

Yingchang Lu, Martijn E. T. Dollé, Sandra Imholz, Ruben van 't Slot, W. M. Monique Verschuren, Cisca Wijmenga, Edith J. M. Feskens, Jolanda M. A. Boer
2008 Journal of Lipid Research  
A. Boer. Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations.  ...  Three hundred eighty-four single nucleotide polymorphisms (SNPs) across 251 genes based on pathways potentially relevant to HDL-C metabolism were selected and genotyped in 3,575 subjects from the Doetinchem  ...  Strien for DNA preparation, K. Siezen for her assistance in SNP selection, H.M. Hodemakers for genotyping assistance, and S.W. van den Berg and A.G. Heidema for their statistical advice.  ... 
doi:10.1194/jlr.m800232-jlr200 pmid:18660489 fatcat:xu6ll4aplzahdjrwuskjpiwdjm

Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping [chapter]

Rajeev K Varshney
2009 Molecular Techniques in Crop Improvement  
The availability of inexpensive high-density SNP-genotyping arrays is encouraging the plant genetics and breeding community to undertake genome-wide marker genotyping for a variety of applications.  ...  based association mapping approaches in addition to facilitate physical mapping, comparative mapping, phylogenetic studies and understanding genome organization in crop plant species.  ...  / A programme for visualization of mutations/SNPs in genes and discovery of recombination points Shah et al. (2005) SNPselector http://primer.duhs.duke.edu/ A web tool for selecting SNPs for genetic  ... 
doi:10.1007/978-90-481-2967-6_5 fatcat:haumrsfub5erlagnk3jczz362q

Candidate Gene Identification Approach: Progress and Challenges

Mengjin Zhu, Shuhong Zhao
2007 International Journal of Biological Sciences  
While the identification of candidate genes involved in genetic traits of specific interest remains a challenge, significant progress in this subject has been achieved in the last few years.  ...  Recently, being a new developing method of candidate gene approach, digital candidate gene approach (DigiCGA) has emerged and been primarily applied to identify potential candidate genes in some studies  ...  In addition, a series of software or online tools such as TAMAL, SNPsfinder, SNPselector, QuickSNP, SNPHunter, SNP-VISTA, CLUSTAG, WCLUSTAG, CASCAD, LS-SNP, QualitySNP, SNP-PHAGE and MAVIANT could been  ... 
doi:10.7150/ijbs.3.420 pmid:17998950 pmcid:PMC2043166 fatcat:du3nopokybbepfrhb4wa67fvkm
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