gmap.net

MARKER

MARKER has been decommissioned.

This page preserves information about MARKER and directs users to more current resources.

About MARKER

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.

How it worked

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:

Data

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.

Publications

Several publications are linked to MARKER:

Current tools

There are a number of similar tools and resources available to researchers:

Contact

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.