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PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

L. Conde, J. M. Vaquerizas, H. Dopazo, L. Arbiza, J. Reumers, F. Rousseau, J. Schymkowitz, J. Dopazo
2006 Nucleic Acids Research  
We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping  ...  PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs.  ...  The Functional Genomics node (INB) is supported by Genoma España. LC is supported by fellowship from the CeGen (Genoma España).  ... 
doi:10.1093/nar/gkl071 pmid:16845085 pmcid:PMC1538854 fatcat:eczcvs2szrcubhpqizdc2md2ze

CRY2 Genetic Variants Associate with Dysthymia

Leena Kovanen, Mari Kaunisto, Kati Donner, Sirkku T. Saarikoski, Timo Partonen, Andreas Reif
2013 PLoS ONE  
Of these three genes, 48 single-nucleotide polymorphisms (SNPs) whose selection was based on the linkage disequilibrium and potential functionality were genotyped in 5910 individuals from a nationwide  ...  This finding together with earlier CRY2 associations with winter depression and with bipolar type 1 disorder supports the view that CRY2 gene has a role in mood disorders.  ...  For the genotyping quality control purposes, both positive (CEPH) and negative water controls were included in each 384-plate.  ... 
doi:10.1371/journal.pone.0071450 pmid:23951166 pmcid:PMC3738504 fatcat:gxfnagnggjbwtewl2is4t6rzjm

Investigation on the role of nsSNPs in HNPCC genes – a bioinformatics approach

C George Doss, Rao Sethumadhavan
2009 Journal of Biomedical Science  
The PupaSuite predicted the phenotypic effect of SNPs on the structure and function of the affected protein.  ...  Methods: The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols.  ...  Authors also thank the reviewers for their valuable comments and suggestions in the improvement of the manuscript.  ... 
doi:10.1186/1423-0127-16-42 pmid:19389263 pmcid:PMC2682794 fatcat:aernvyoul5f2vnfsm76ot5mstm

iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

Chun Meng Song, Boon Huat Yeo, Erwin Tantoso, Yuchen Yang, Yun Ping Lim, Kuo-Bin Li, Gunaretnam Rajagopal
2006 BMC Bioinformatics  
The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies.  ...  The iHAP resource, available at, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies  ...  This work is supported by the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR) of Singapore.  ... 
doi:10.1186/1471-2105-7-525 pmid:17137522 pmcid:PMC1698582 fatcat:ffq3uzlio5cctoxvj6oji6ss2e

Interleukin-1 Receptor–Associated Kinase 3 Gene Associates with Susceptibility to Acute Lung Injury

María Pino-Yanes, Shwu-Fan Ma, Xiaoguang Sun, Paula Tejera, Almudena Corrales, Jesús Blanco, Lina Pérez-Méndez, Elena Espinosa, Arturo Muriel, Lluis Blanch, Joe G. N. Garcia, Jesús Villar (+1 others)
2011 American Journal of Respiratory Cell and Molecular Biology  
After our discovery of polymorphism, we genotyped a subset of seven single-nucleotide polymorphisms (SNPs) in 336 population-based control subjects and 214 patients with severe sepsis, collected as part  ...  One of these (rs1732887) predicted the disruption of a putative human-mouse conserved transcription factor binding site, and demonstrated functional effects in vitro (P 5 0.017).  ...  Acknowledgments: The authors thank Dan Nicolae and Xiaoquan Wen for their advice using TUNA, Santiago Basaldú a for help with the statistical analysis, Tobías Felipe for Fortran scripting for handling  ... 
doi:10.1165/rcmb.2010-0292oc pmid:21297081 pmcid:PMC3265218 fatcat:gsret3ujprgylek4d4lnq4thjm

Next generation tools for the annotation of human SNPs

Rachel Karchin
2009 Briefings in Bioinformatics  
Computational biology has the opportunity to play an important role in the identification of functional single nucleotide polymorphisms (SNPs) discovered in large-scale genotyping studies, ultimately yielding  ...  Affymetrix genotyping array A microarray designed to identify known single nucleotide polymorphisms, given genomic DNA from an individual.  ...  Acknowledgements The author thanks Dr Melissa Cline for valuable discussions.  ... 
doi:10.1093/bib/bbn047 pmid:19181721 pmcid:PMC2638621 fatcat:wrxufl5ayvd2nc7v5x3a4d3dr4

Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources

A. D. Johnson
2009 Circulation: Cardiovascular Genetics  
which all 4 possible nucleotides are observed within a database or population Somatic SNP: a SNP whose origin is in nongerm line cells, for example in cancer cells SNP (single nucleotide polymorphism)  ...  large-scale genetic association projects.  ... 
doi:10.1161/circgenetics.109.872010 pmid:20031630 pmcid:PMC2789466 fatcat:hpihw32xhjbapibxxvggljvnum

Genetic Predictors of Increase in Suicidal Ideation During Antidepressant Treatment in the GENDEP Project

Nader Perroud, Katherine J Aitchison, Rudolf Uher, Rebecca Smith, Patricia Huezo-Diaz, Andrej Marusic, Wolfgang Maier, Ole Mors, Anna Placentino, Neven Henigsberg, Marcella Rietschel, Joanna Hauser (+14 others)
2009 Neuropsychopharmacology  
The strongest association was observed for rs962369 in BDNF (p ¼ 0.0015).  ...  The associations observed with polymorphisms in BDNF suggest the involvement of the neurotrophic system in vulnerability to suicidality.  ...  and South London, and Maudsley NHS Foundation Trust (National Institute for Health Research, Department of Health, UK).  ... 
doi:10.1038/npp.2009.81 pmid:19641488 fatcat:dluay2v2f5d5jbo6e4xrfiu7ki

Associations between cytokine gene variations and self-reported sleep disturbance in women following breast cancer surgery

Emely Alfaro, Anand Dhruva, Dale J. Langford, Theresa Koetters, John D. Merriman, Claudia West, Laura B. Dunn, Steven M. Paul, Bruce Cooper, Janine Cataldo, Deborah Hamolsky, Charles Elboim (+3 others)
2014 European Journal of Oncology Nursing  
Conclusions-Polymorphisms in cytokine genes may partially explain inter-individual variability in sleep disturbance.  ...  Key results-Patients who were younger and who had higher comorbidity and lower functional status were more likely to be in the high sustained sleep disturbance class.  ...  Table 1 1 Summary of Single Nucleotide Polymorphisms Analyzed for Pro-and Anti-Inflammatory Cytokine Genes and Self-reported Sleep Disturbance Eur J Oncol Nurs.  ... 
doi:10.1016/j.ejon.2013.08.004 pmid:24012192 pmcid:PMC3946647 fatcat:x7puvbpblnaxjjp2eow5oipyoy

Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations

A. Moreno-Estrada, K. Tang, M. Sikora, T. Marques-Bonet, F. Casals, A. Navarro, F. Calafell, J. Bertranpetit, M. Stoneking, E. Bosch
2009 Molecular biology and evolution  
Among the significant cases, a robust set of 11 genes was then further explored for signatures of recent positive selection using single nucleotide polymorphism (SNP) data.  ...  We genotyped 223 SNPs in 39 worldwide populations from the HGDP-CEPH diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each  ...  Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12:1805-1814.  ... 
doi:10.1093/molbev/msp134 pmid:19578157 fatcat:vh76ebaxqnd3xl2dgeocj37ina

Mini Review Identifying human disease genes: advances in molecular genetics and computational approaches

S.M. Bakhtiar, A. Ali, S.M. Baig, D. Barh, A. Miyoshi, V. Azevedo
2014 Genetics and Molecular Research  
However, general purpose databases, with standardized and versatile query capability, are the backbone of most large-scale sequence databases.  ...  Similarly, a single nucleotide polymorphism (SNP), a sequence variant that occurs at more than 99% frequency in a population, can make a certain population susceptible to a particular disease or even infection  ...  especially for complex disorders such as cancer.  ... 
doi:10.4238/2014.july.4.23 pmid:25061732 fatcat:haexibltpfekjm7ldl25ixejpq

Cis-regulation of IRF5 expression is unable to fully account for systemic lupus erythematosus association: analysis of multiple experiments with lymphoblastoid cell lines

Elisa Alonso-Perez, Marian Suarez-Gestal, Manuel Calaza, Tony Kwan, Jacek Majewski, Juan J Gomez-Reino, Antonio Gonzalez
2011 Arthritis Research & Therapy  
Genotypes of 109 IRF5 polymorphisms, including four known functional polymorphisms, were considered.  ...  Results: A large fraction of variability in IRF5 expression was accounted for by linear regression models with IRF5 polymorphisms, but at a different level in each expression data set.  ...  Acknowledgements We thank Liming Liang of the Harvard School of Public Health (Boston, MA, USA) and William Cookson of Imperial College London (London, UK) for providing us with expression data and complementary  ... 
doi:10.1186/ar3343 pmid:21627826 pmcid:PMC3218890 fatcat:opo3dnlrx5a2lgfkohtku4soly

Associations Between Pro- and Anti-Inflammatory Cytokine Genes and Breast Pain in Women Prior to Breast Cancer Surgery

Birha McCann, Christine Miaskowski, Theresa Koetters, Christina Baggott, Claudia West, Jon D. Levine, Charles Elboim, Gary Abrams, Deborah Hamolsky, Laura Dunn, Hope Rugo, Marylin Dodd (+7 others)
2012 Journal of Pain  
nucleotide polymorphism, TNFA = tumor necrosis factor alpha Single nucleotide polymorphisms (SNPs) that violated Hardy-Weinberg expectations are denoted in italics in the MAF column.  ...  Table 1 1 Genes and Single Nucleotide Polymorphisms Analyzed for Pain versus No Pain in Women Prior to Breast Cancer Surgery Pain. Author manuscript; available in PMC 2013 May 01.  ... 
doi:10.1016/j.jpain.2011.02.358 pmid:22515947 pmcid:PMC3348353 fatcat:ugb36b3rajdlpiuc2tvcod3rli

A Field Synopsis on Low-Penetrance Variants in DNA Repair Genes and Cancer Susceptibility

Paolo Vineis, Maurizio Manuguerra, Fotini K. Kavvoura, Simonetta Guarrera, Alessandra Allione, Fabio Rosa, Alessandra Di Gregorio, Silvia Polidoro, Federica Saletta, John P. A. Ioannidis, Giuseppe Matullo
2009 Journal of the National Cancer Institute  
A computer analysis predicted that the Ϫ 77 T>C single nucleotide polymorphism (SNP) was in the core of Sp1-binding motif, which suggested its functional signifi cance ( 48 ) .  ...  Contradictory results have been published on the functional implications of these polymorphisms, but computer analyses (PupaSuite: ) have predicted for all of them an  ...  The authors take full responsibility for the study design, data collection, analysis and interpretation of the data, the decision to submit the manuscript for publication, and the writing of the manuscript  ... 
doi:10.1093/jnci/djn437 pmid:19116388 fatcat:tozkkk6kmnaphgmahy6o6xnawm

Genomic and geographic distribution of private SNPs and pathways in human populations

Tesfaye M Baye, Russell A Wilke, Michael Olivier
2009 Personalized Medicine  
They may also influence treatment outcome for a variety of drugs -an emerging and important area of study.  ...  and reconstructing the physiological functions of genes at these loci, we report a list of pathways affected by natural selection during human evolution.  ...  On a worldwide scale, human populations show large phenotypic variability, particularly for skin color, face and body shape, susceptibility to pathogens and prevalence of disease [10] .  ... 
doi:10.2217/pme.09.54 pmid:20352079 pmcid:PMC2843937 fatcat:wbdwnv4qsvanhgwr7ysm2eiqai
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