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<h1>Haplotype Mapping Project Scenarios</h1>
<ul>
<li><a HREF=#ScenarioGetSNPsForGene>Find SNPs in specific locations</a> </li>
<li><a HREF=#ScenarioHaplotypes>Multifactorial disease</a></li>
<li><a HREF=#ScenarioLinkage>Linkage</a></li>
<li><a HREF=#ScenarioBlocks>Block size</a></li>
<li><a HREF=#ScenarioPanel>Panel Information</a></li>
<li><a HREF=#ScenarioIndividual>Individual Information</a></li>
<li><a HREF=#ScenarioPanelSNP>Types of SNPs in a panel</a></li>
</ul>
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<h2><A NAME= ScenarioGetSNPsForGene>Name: </a>Find SNPs in specific locations</h2>
<P><B>Scenario: </B>An investigator has a candidate region that is thought to be involved in a Mendelian disease.</P>
<P>
He knows it is between STS markers M and N but that it is most closely linked to gene X. So he wants to find out:
<ul>
<li>What are the known SNPs in gene (or exon) X?</li>
<li>What are the known SNPs between STS markers M and N?</li>
<li>Which SNPs in gene X cause a non-synonymous amino acid change?</li>
<li>Which are the SNPs in gene X that have allele frequency data?</li>
</ul>
</p>
<p>
For each SNP he wants information on:
<ul>
<li>SNP position, rs id, ss id and tsc SNP id so he can verify and cross-reference the information from different sources</li>
<li>In order to reproduce the data he wants to know what the assay was to find the SNP (primers, pcr primers, extension probes).</li>
<li>Who was the submitter and when was it submitted? (In case he has any follow up queries).</li>
<li>What are the 5' flank and 3' flank that uniquely determine the SNP?</li>
</ul>
</P>
<hr>
<h2><A NAME= ScenarioHaplotypes>Name: </a>Multifactorial disease</h2>
<P><B>Scenario: </B>
A biologist is studying a multifactorial disease. He knows that one of the factors is linked to gene x and another to SNP y. However, in order to assay for the disease he needs to investigate which are the possible haplotypes associated with each region. He wants to know:</P>
<ul>
<li>Does this SNP/gene fall into a defined haplotype block? If so, in which populations is it defined? Which are the known haplotypes in the haplotype block that include gene x and what are their frequencies?</li>
<li>Which are the known haplotypes and their frequencies for the block that includes SNP y?</li>
</ul>
</p>
<hr>
<h2><A NAME= ScenarioLinkage>Name: </a>Linkage</h2>
<P><B>Scenario: </B>
A researcher thinks he has found a gene that is closely linked to a disease. He wants to find out which other genes and SNPs are common inherited with this gene so he can target them in his search for the mutation.</P>
<P>He wants to know:</P>
<ul>
<li>What is the haplotype block structure around SNP t?</li>
<li>Which other genes are in the same haplotype block structure as gene y?</li>
<li>Which are the genes in the block between SNP t and gene y?</li>
<li>What is the linkage disequilibrium between SNPs t, v, and u?</li>
</ul>
</p>
<hr>
<h2><A NAME= ScenarioBlocks>Name: </a>Block size</h2>
<P><B>Scenario: </B>
A researcher investigating hotspots of recombination wants to analyse the haplotype block size distribution in different populations.</P>
<P>He requires the following data:</P>
<ul>
<li>A download all of the block positions and sizes for each population studied.</li>
<li>The sizes of the blocks in each population if the stringency of what constitutes a block is increased.</li>
</ul>
</p>
<hr>
<h2><A NAME= ScenarioPanel>Name: </a>Panel Information</h2>
<P><B>Scenario: </B>
An investigator wants more information on the structure of the panel he uses for his research. He has the panel ID but wants to find out:</P>
<ul>
<li>The number of individuals in the panel.</li>
<li>The IDs of each of the panel DNAs.</li>
<li>The pedigrees associated with each individual in the panel.</li>
<li>The panel description.</li>
</ul>
</p>
<hr>
<h2><A NAME= ScenarioIndividual>Name: </a>Individual Information</h2>
<P><B>Scenario: </B>
An investigator wants more information on the set of individuals used for his research. He has the individuals' IDs but wants to find out:</P>
<ul>
<li>What population does each individual belong to?</li>
<li>What panel does each individual belong to?</li>
<li>The pedigrees associated with each individual.</li>
</ul>
</p>
<hr>
<h2><A NAME= ScenarioPanelSNP>Name: </a>Types of SNPs in a panel</h2>
<P><B>Scenario: </B>
An investigator wants to access the raw data for the SNP genotyping project. He wants to get the genotypes of each of the SNPs in each of the panels.</P>
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