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HGVbaseG2P: a central genetic association database

G. A. Thorisson, O. Lancaster, R. C. Free, R. K. Hastings, P. Sarmah, D. Dash, S. K. Brahmachari, A. J. Brookes
2009 Nucleic Acids Research  
The Human Genome Variation database of Genotype to Phenotype information (HGVbaseG2P) is a new central database for summary-level findings produced by human genetic association studies, both large and  ...  Such a database is needed so that researchers have an easy way to access all the available association study data relevant to their genes, genome regions or diseases of interest.  ...  HGVbaseG2P represents the world's first central database for summary-level (i.e. not person-specific) genetic association data concerning any and all traits.  ... 
doi:10.1093/nar/gkn748 pmid:18948288 pmcid:PMC2686551 fatcat:ncjtsksy5necza3hfvkchkg2nq

GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies

Tim Beck, Robert K Hastings, Sirisha Gollapudi, Robert C Free, Anthony J Brookes
2013 European Journal of Human Genetics  
ACKNOWLEDGEMENTS We thank all GWAS data generators and submitters, several previous GWAS Central data curators, Charalambos Chrysostomou and James Eales for providing technical assistance, and Gudmundur  ...  To this end, we herein describe GWAS Central, a comprehensive genetic association database, designed to enable multiple study integration via graphical displays and extensive textual content.  ...  GWAS Central: a comprehensive GWAS resource T Beck et al. European Journal of Human Genetics  ... 
doi:10.1038/ejhg.2013.274 pmid:24301061 pmcid:PMC4060122 fatcat:4htpblrgw5esxdqyncppitbz2a

IGVBrowser-a genomic variation resource from diverse Indian populations

A. Narang, R. D. Roy, A. Chaurasia, A. Mukhopadhyay, M. Mukerji, D. Dash
2010 Database: The Journal of Biological Databases and Curation  
A possible integration of IGVBrowser with HGVbaseG2P (20) can enable researchers for cross study comparison among different populations of the world for disease-gene association study. ..............  ...  Thus, the IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology.  ... 
doi:10.1093/database/baq022 pmid:20843867 pmcid:PMC2942067 fatcat:keuqx6cjdjhwhnnkm2g64wr63y

The Sri Lankan Genome Variation Database

Pubudu S. Samarakoon, Rohan W. Jayasekara, Vajira H.W. Dissanayake
2011 Sri Lanka Journal of Bio-Medical Informatics  
There is therefore a need for a central repository of this data. The SLGVD was created to fulfill this void. The SLGVD offers web based access to genetic variation information of Sri Lankan people.  ...  The Sri Lankan Genome Variation Database (SLGVD) is a database of single nucleotide polymorphisms found in Sinhalese, Sri Lankan Tamils and Moors -the three major ethnic groups in Sri Lanka.  ...  Acknowledgement The SLGVD was funded by funds from the Human Genetics Unit Development Fund, Faculty of Medicine, University of Colombo, Sri Lanka.  ... 
doi:10.4038/sljbmi.v2i1.2861 fatcat:sfkvy4vpjfchjlgofmy5a5huja

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde, Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes (+3 others)
2010 BMC Bioinformatics  
We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.  ...  At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable  ...  MAS, MD, KJV, TER, AK, JL, DA, GB, GAT, JM, and TA participated in the development of the MOLGENIS toolkit and/or have been developing applications using MOLGENIS as a platform.  ... 
doi:10.1186/1471-2105-11-s12-s12 pmid:21210979 pmcid:PMC3040526 fatcat:rpq4s7uf25fzzexdnarka22x7a

Semantically enabling a genome-wide association study database

Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes
2012 Journal of Biomedical Semantics  
This impacts on the work of GWAS Centrala free and open access resource for the advanced querying and comparison of summary-level genetic association data.  ...  Conclusions: We present a methodology for applying phenotype annotations to a comprehensive genome-wide association dataset and for ensuring compatibility with the Semantic Web.  ...  Acknowledgements We thank the curation team of Robert Hastings, Sirisha Gollapudi and Raheleh Rahbari for providing the high-quality phenotype annotations within GWAS Central.  ... 
doi:10.1186/2041-1480-3-9 pmid:23244533 pmcid:PMC3579732 fatcat:nepqhbjc5rblpd3ckwriiaw7ge

SNPs Meet CNVs in Genome-Wide Association Studies: HGV2007 Meeting Report

Xavier Estivill, Nancy J. Cox, Stephen J. Chanock, Pui-Yan Kwok, Stephen W. Scherer, Anthony J. Brookes, Greg Gibson
2008 PLoS Genetics  
a comprehensive view of the world's genetic association study findings.  ...  Anthony Brookes (University of Leicester, Leicester, United Kingdom) presented progress toward developing HGVbaseG2P, a database of genotype-to-phenotype (G2P) relationships, which aims to pull together  ... 
doi:10.1371/journal.pgen.1000068 pmid:18437244 pmcid:PMC2330071 fatcat:3iw7vfzl7fcxdinb3pzpc3xarq

DistiLD Database: diseases and traits in linkage disequilibrium blocks

A. Palleja, H. Horn, S. Eliasson, L. J. Jensen
2011 Nucleic Acids Research  
However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated with diseases are in linkage disequilibrium (LD) with a gene of interest  ...  Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region?  ...  use of the associations reported by GWAS, by incorporating prior functional knowledge to the genetic variants associated to a disease.  ... 
doi:10.1093/nar/gkr899 pmid:22058129 pmcid:PMC3245128 fatcat:4hvynrofjjcbzl7tadgawqwemm

Bioinformatics and statistical genomics

2008 Genomic Medicine  
Intein data obtained from InBase Intein database.  ...  Protein Post-translational Modification (PTM) is a common phenomenon in biology which regulates the function of proteins.  ...  : a central genetic association study database 1 G.  ... 
doi:10.1007/s11568-009-9081-x pmid:19488836 pmcid:PMC2694866 fatcat:kmyq6l3qefdhpaz5zsi6eyc37m

UASIS: Universal Automatic SNP Identification System

Danny C C Poo, Shaojiang Cai, James T L Mah
2011 BMC Genomics  
SNP (Single Nucleotide Polymorphism), the most common genetic variations between human beings, is believed to be a promising way towards personalized medicine.  ...  UASIS maps SNPs from different databases, including dbSNP, GWAS, HapMap and JSNP etc., into an uniform view efficiently using a proposed universal nomenclature and state-of-art alignment algorithms.  ...  Table 1 1 Alternative names of a SNP Database SNP names dbSNP rs3737965 ss4923964, ss69366921 HGVBaseG2P HGVM2256489 HGVS NM_001286.2:c.87+45G>A, NM_021735.2:c.87+45G>A NM_021736.2:c.87+45G  ... 
doi:10.1186/1471-2164-12-s3-s9 pmid:22369494 pmcid:PMC3333510 fatcat:m7uyklykuff3pgq7p7n4mbem2u

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

Xosé M. Fernández-Suárez, Michael Y. Galperin
2012 Nucleic Acids Research  
The NAR online Molecular Biology Database Collection, available at http://www. oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases.  ...  Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein-ligand binding.  ...  GWAS Central, established in 2007 as HGVbaseG2P ( 44) , has been revamped and now includes data from over 1000 studies.  ... 
doi:10.1093/nar/gks1297 pmid:23203983 pmcid:PMC3531151 fatcat:rmfh245otzh3hp3l446rfsqivy

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.  ...  We have developed GWASdb that contains 20 times more data than the GWAS Catalog and includes less significant GVs (P < 1.0 Â 10 À3 ) manually curated from the literature.  ...  GWAS Central (previously named HGVbaseG2P) is another manually curated database that provides a centralized compilation of high level summary data from genetic association studies (5) .  ... 
doi:10.1093/nar/gkr1182 pmid:22139925 pmcid:PMC3245026 fatcat:dtu4apnazfaevcdfrnyxpqprjm

Informatics and clinical genome sequencing: opening the black box

Sowmiya Moorthie, Alison Hall, Caroline F. Wright
2012 Genetics in Medicine  
Genet Med 2013:15(3):165-171  ...  Adoption of whole-genome sequencing as a routine biomedical tool is dependent not only on the availability of new high-throughput sequencing technologies, but also on the concomitant development of methods  ...  Databases of pharmacogenetic associations PharmKB (Pharmacogenomics Knowledge Base) Databases of existing clinical genetic tests EuroGenTest GTR (NIH Genetic Test Registry) UKGTN (UK Genetic Testing  ... 
doi:10.1038/gim.2012.116 pmid:22975759 fatcat:xzl7zjr7nrdvjifvvml5s475am

Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources

A. D. Johnson
2009 Circulation: Cardiovascular Genetics  
SNP Databases There are Ͼ800 databases of human genetic variation but only a few central databases that are most widely used.  ...  A handful of databases are referred to as Central or General Mutation Databases (CMDBs,GMDBs) and have a major focus on rare variation but also include common variant and association literature findings  ... 
doi:10.1161/circgenetics.109.872010 pmid:20031630 pmcid:PMC2789466 fatcat:hpihw32xhjbapibxxvggljvnum

An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research

Adam J. Webb, Gudmundur A. Thorisson, Anthony J. Brookes
2011 Human Mutation  
number is a substantial underestimate of the true frequency at which genetic association findings are being produced.  ...  Integration of genetic and medical information for health applications. http://www.diseasecard.org GWAS Central.  ... 
doi:10.1002/humu.21469 pmid:21438073 fatcat:ktr4z662qbbcri2etel6ooz73i
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