This page preserves information about MARKER and directs users to more current resources.
MARKER was a web application designed to help investigators identify variations in the human genome that affected susceptibility to disease by allowing users to explore genetic markers in their genomic context. MARKER was developed by a team based at the Wellcome Trust Centre for Human Genetics, including Dominic Kwiatkowski, Kirk Rockett, Martin Kimber, Julian Forton, Neil Hanchard and Clare Trafford. Additional acknowledgments should be made to:
Beta versions were released in 2003 and 2004. As technology advanced, other web-based tools and resources became available to researchers and MARKER usage began to drop. As a result, MARKER was decommissioned and removed from public availability in 2013.
MARKER produced interactive graphics, known as maps, that showed particular genetic markers – positions on the human genome where the DNA sequence varies between people – alongside patterns of colour that illustrated linkage disequilibrium (LD), a statistical measure of the combinations of DNA variations observed in a population. If a user clicked on the label for a genetic marker, e.g. rs6103899, MARKER would then display information about that specific marker and the surrounding region of the genome. By clicking on different markers, the user was able to navigate around a genomic region, finding out which markers have been studied in detail and which genes are nearby.
Figure 1: The typical appearance of a MARKER map.
The MARKER software allowed its users to:
Most of the data in MARKER was downloaded from the International HapMap Project, processed and used to infer linkage disequilibrium, before being loaded into a dedicated database. Some of the data were uploaded by users using their own data. The latter data were either kept private for their own use or shared publicly, depending on user preference. The gene definitions used to annotate the graphs in MARKER came from the Ensemble Genome Browser and from the NCBI Entrez Gene Database.
Several publications are linked to MARKER:
There are a number of similar tools and resources available to researchers:
The International HapMap Project describes itself as a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States that are working to develop a public resource to help researchers find genes associated with human disease and response to pharmaceuticals (HapMap Project's homepage, accessed March 2013). Most of the data served by MARKER originated from the International HapMap Project, where it can still be freely downloaded.
Reference: International HapMap Consortium. The International HapMap Project. Nature 2003 Dec 18; 426(6968): 789-96. PMID: 14685227.
The Wellcome Trust Sanger Institute provide an open access web-based tool called GLIDERS (Genome-wide LInkage DisEquilibrium Repository and Search engine), which allows researchers to see if single nucleotide polymorphisms (SNPs) have long-range linkage disequilibrium (i.e. less than 200kb) with other SNPs genotyped during Phase 2 and 3 of the International HapMap Consortium. Using this tool, associations between any pair-wise HapMap SNPs over any distance can be retrieved.
Reference: Lawrence R, Day-Williams AG, Mott R, Broxholme J, Cardon LR, Zeggini E. GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs. BMC Bioinformatics, 2009 Oct 31;10:367. doi: 10.1186/1471-2105-10-367. PMID: 19878600
The Broad Institute of Harvard and MIT provide a freely available web application called SNAP (SNP Annotation and Proxy Search). According to the SNAP website, "SNAP finds proxy SNPs based on linkage disequilibrium, physical distance and/or membership in selected commercial genotyping arrays. SNAP can also generate plots showing regional linkage disequilibrium or regional assocation."
Reference: Johnson AD, Handsaker RE, Pulit S, Nizzari MM, O'Donnell CJ, de Bakker PIW. SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap Bioinformatics, 2008 24(24):2938-2939. PMID: 18974171
Reference: Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps Bioinformatics, 2005 21(2):263-5. PMID: 15297300
If you wish to know more about the decommissioned MARKER software, please contact Kirk Rockett or the Systems Administrator at the Centre for Genomics and Global Health, which is based at the Wellcome Trust Centre for Human Genetics, in Oxford, UK.