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GPSC_lineages.html
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GPSC_lineages.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>GPS :: Global Pneumococcal Sequencing Project</title>
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height: 720px;
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<h1><i class=""></i><a href="index.html"><span class="color">GPS</span></a></h1>
<div class="hmeta">Global Pneumococcal Sequencing Project</div>
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<li class=""><a id="resources_overview" href="resources_overview.html">Overview</a></li>
<li class=""><a id="sampling_map" href="sampling_map.html">Countries</a></li>
<li class=""><a id="GPSC_lineages" href="GPSC_lineages.html">Strains</a></li>
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<h2>GPSC Strains</h2>
<p>
Global Pneumococcal Sequence Cluster (GPSC) is <strong>an international genomic definition of pneumococcal lineage</strong> (<a href="https://www.thelancet.com/article/S2352-3964(19)30259-2/fulltext" target="_blank">Gladstone & Lo et al 2019 Ebiomedicine</a>) defined using a clustering software named <a href="https://genome.cshlp.org/content/early/2019/01/16/gr.241455.118" target="_blank">PopPUNK</a>. This typing scheme captures all variations across the entire genome and gives us the best chance of monitoring and understanding the processes of vaccine evasion (<a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30297-X/fulltext" target="_blank">Lo & Gladstone et al 2019 Lancet Infectious Diseases</a>).
<ul style="list-style: initial; margin: initial; padding: 0 0 0 40px;">
<li>You can assign GPSC using Pathogenwatch (<a href="https://www.youtube.com/watch?v=Q8bDuZZ3hXg" target="_blank">tutorial video</a>) or command line (<a href="training_command_line.html">step-by-step instruction</a>).</li>
<li>You can explore the common GPSCs’ phylogenies in Microreact and recombination pattern in Phandango by hovering over the cluster (each cluster represents a GPSC).</li>
</ul>
</p>
<br>
<p>
The search feature below enables search by GPSC, serotype or ST.
</p>
<p><em>
For example:
<ol>
<li>Select the category 'GPSC' in the first box and type 'GPSC32' in the second box to display GPSC32.</li>
<li>Select the category 'Serotype' in the first box and choose a serotype from the dropdown to search for all of the GPSC that contain that particular serotype.</li>
<li>Select the category 'ST' in the first box to search for corresponding GPSC</li>
</ol>
</em></p>
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