<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>MOBY Use Case Linkage Disequilibrium</title>
<meta http-equiv="content-type"
content="text/html; charset=ISO-8859-1">
<meta name="author" content="Fiona Cunningham">
</head>
<body>
<br>
<h1>Haplotype Mapping Project Use Cases </h1>
<h2><A NAME= LinkageDisequilibrium> Name:</a> Linkage Disequilibrium</h2>
<P><B>Scenario Reference: </B><A HREF='fc_hapmap_scenarios.html'>
Linkage</a></P>
<P><B>Problem: </B>Determine the linkage between two positions (e.g. genes and SNPs). </P>
<hr width="10%" align="left">
<h2> Background Knowledge: </h2>
<p> Linkage disequilibrium is a measure of how often two genes or SNPs are inherited together. Finding a marker that is highly linked to a disease gene is a useful tool in genetics.</p>
<hr width="10%" align="left">
<h2> Primary Actors: </h2>
<ol>
<li>A biologist</li>
<li>A known haplotype linkage data provider such as The SNP Consortium IN THE FUTURE!! e.g.<a HREF='http://snp.cshl.org/'>(http://snp.cshl.org/)</a>
</li>
</ol>
<hr width="10%" align="left">
<h2>Other Actors: </h2>
<an exhaustive list of other entities which must participate in
the flow of events to achieve this result>
<hr width="10%" align="left">
<h2>Initial State and Preconditions: </h2>
<p> The biologist has the name of two SNPs or SNP positions. He wishes to know how tightly linked these positions are on the genome.</p>
<p> The service provider must have linkage data for the SNPs blocks. This information should be integrated with the current SNP data.</p>
<hr width="10%" align="left">
<h2> End Result: </h2>
<p>Biologist gets data on the linkage disequilibrium between two SNPs. </p>
<hr width="10%" align="left">
<h2> Hypothetical Mobyless Workflow: </h2>
<P><B>PLEASE NOTE: THIS PROJECT IS NOT YET COMPLETE SO THIS QUERY IS NOT POSSIBLE AT THE CURRENT TIME</B></P>
<ol>
<li>The biologist browses to a known haplotype database with linkage information.</li>
<li>Biologist finds the link to the relevant search page.</li>
<li>Biologist reads literature on the search page to determine whether he can do the query he wants.</li>
<li>Biologist works out how to fill in the query form to search using two SNP names or positions. He indicates on the form that he wants linkage disequilibrium values.</li>
<li> For each pair of SNPs, the linkage disequilibrium (D') will be displayed.</li>
<li>Maybe the biologist will be able to browse the information graphically to see the pattern of distribution of SNPs, genes and markers observed in the block. It might be possible to do a dump of the information.</li>
</ol>
<br>
<hr width="10%" align="left">
<h2> Existing Workflow Limitations: </h2>
<p> The biologist must know the names of the haplotype linkage databases and where they reside, or do a Google, PubMed or similar search, to find them. It is possible he finds an existing haplotype database but that it does not provide the facility to do his query.</p>
<p>As the format required for submitting the SNPs is not known in advance, the data cannot be prepared until the website query form is examined. For example, does the user have to submit the SNP position, rs id, TSC id, ss id, or does the database accept all 4 formats?</p>
<p> The other limitations will have to be assessed once the project is nearer completion. </p>
<hr width="10%" align="left"><br>
<h2>Existing Workflow Exemplars: </h2>
<P>The web-based nature of the data means that the information is kept up to date and the biologist does not need to maintain the UI.</p>
<br>
<hr width="10%" align="left">
<h2> MOBY Workflow: </h2>
<ol>
<li>The biologist asks MOBY which haplotype databases have linkage disequilibrium values.</li>
<li>Biologist asks MOBY which of the databases can perform a query given his input data.</li>
<li>MOBY directs the biologist straight to the search page and informs the biologist which format the input data must have</li>
<li>The rest of the query proceeds as before.</li>
</ol>
<hr width="10%" align="left">
<h2>MOBY Workflow Limitations: </h2>
<p>MOBY must keep up to date with changes in the UI and data presented by the haplotype database. This is likely to change relatively quickly as this is a developing project. </p>
<hr width="10%" align="left">
<h2> MOBY Workflow Exemplars: </h2>
<P>The advantage of having MOBY here is it that the user would no longer have to search for the haplotype databases, hunt and digest the search pages, work out if there is away to formulate his query. All this could be done at the MOBY level.</P>
<hr width="10%" align="left">
<h2> Discussion: </h2>
<hr width="10%" align="left">
<h2> Priority:</h2>
<p>Mandatory. Moby should have an index and a description of each possible database site and be able to direct the biologist straight to the search page that best fits his/her needs.</P>
<hr width="10%" align="left">
<h2> Key References: </h2>
<p>
The SNP Consortium: <a HREF='http://snp.cshl.org/'>(http://snp.cshl.org/) </A></p>
<p>The National Human Genome Research Institute: <a HREF=' http://www.genome.gov/page.cfm?pageID=10005336'> (http://www.genome.gov/page.cfm?pageID=10005336)</a></p>
<hr>
</body>
</html>