DistiLD Database: diseases and traits in linkage disequilibrium blocks

Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. 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? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not in LD are in different blocks. By projecting SNPs and genes onto LD blocks, the DistiLD database aims to increase usage of existing GWAS results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database is available at http://distild.jensenlab.org/.

[1]  E. Marcotte,et al.  Prioritizing candidate disease genes by network-based boosting of genome-wide association data. , 2011, Genome research.

[2]  Andrew D. Johnson,et al.  Bmc Medical Genetics an Open Access Database of Genome-wide Association Results , 2009 .

[3]  David C. Wilson,et al.  Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease. , 2009, American journal of human genetics.

[4]  Debasis Dash,et al.  HGVbaseG2P: a central genetic association database , 2008, Nucleic Acids Res..

[5]  K. Frazer,et al.  Human genetic variation and its contribution to complex traits , 2009, Nature Reviews Genetics.

[6]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[7]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[8]  K. Sirotkin,et al.  The NCBI dbGaP database of genotypes and phenotypes , 2007, Nature Genetics.

[9]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

[10]  M. Olivier.  A haplotype map of the human genome. , 2003, Nature.

[11]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[12]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[13]  P. Matthews,et al.  Pathway and network-based analysis of genome-wide association studies in multiple sclerosis , 2009, Human molecular genetics.

[14]  H. Hakonarson,et al.  Analysing biological pathways in genome-wide association studies , 2010, Nature Reviews Genetics.

[15]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[16]  Manuel A. R. Ferreira,et al.  Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. , 2009, American journal of human genetics.

[17]  Muin J Khoury,et al.  GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies , 2011, European Journal of Human Genetics.

[18]  Marit Holden,et al.  GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies , 2008, Bioinform..

[19]  M. Daly,et al.  Genetic Mapping in Human Disease , 2008, Science.

[20]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[21]  Michael Kuhn,et al.  Reflect: augmented browsing for the life scientist , 2009, Nature Biotechnology.

[22]  Montgomery Slatkin,et al.  Linkage disequilibrium — understanding the evolutionary past and mapping the medical future , 2008, Nature Reviews Genetics.

[23]  C Zapata,et al.  THE D' MEASURE OF OVERALL GAMETIC DISEQUILIBRIUM BETWEEN PAIRS OF MULTIALLELIC LOCI , 2000, Evolution; international journal of organic evolution.

[24]  Pardis C Sabeti,et al.  Linkage disequilibrium in the human genome , 2001, Nature.