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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Diseasome</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="stylesheet" href="style.css">
<!-- bootstrap CDN -->
<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet">
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js"></script>
<!-- <script src='https://cdnjs.cloudflare.com/ajax/libs/pako/2.0.3/pako.min.js'></script>-->
<!-- font awesome -->
<!-- <script src="https://kit.fontawesome.com/31149d48b0.js" crossorigin="anonymous"></script> -->
</head>
<body>
<!-- top banner -->
<nav class="navbar navbar-expand-sm bg-dark navbar-dark ">
<!-- <div id="mySidepanel" class="sidepanel">
<a href="javascript:void(0)" class="closebtn" onclick="closeNav()">×</a>
<a class="nav-link" href="#notices">Notices</a>
</div> -->
<div>
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link" href="#notices">Notices</a>
</li>
<li class="nav-item">
<a class="nav-link" target="_blank" href="https://github.com/episphere/diseasome">Github Code</a>
</li>
<li class="nav-item"><a class="nav-link" target="_blank"
href="https://observablehq.com/@lorenasandoval88/hierarchical-clustering"
target="_blank">Notebook</a>
</li>
<li class="nav-item">
<a class="nav-link" target="_blank" href="https://gitter.im/episphere/PRS">Discussion</a>
</li>
<li class="nav-item">
<a class="nav-link" target="_blank" href="">
<img style="vertical-align:top" src="youtube_img.png" width="20" height="20"></img> Tutorial</a>
</li>
</ul>
</div>
</nav>
<!-- side panel ----------------------------------------------->
<section class="bgimage" id="home">
<div class="container-fluid">
<div class="col-lg-10 col-md-10 col-sm-10 col-xs-10 hero-text">
<h4 class="hero_title">Diseasome</h3>
<p class="hero_desc">Calculation of multiple <a class="link-unstyled"
href="https://www.nature.com/articles/nrg.2016.27" target="_blank"><u>risk profiles</u></a>
for
<br><a class="link-unstyled" href='https://opensnp.org/'
target="_blank">23andme</a> reports,using the <a class="link-unstyled" href='https://www.pgscatalog.org' target="_blank">PGS Catalog</a>.</p>
<button class="glow-on-hover"
onclick="location.href='https://observablehq.com/@lorenasandoval88/polygenic_risk_scores_sdk'"
type="button">
Get Started</button>
</div>
</div>
</section>
<!-- Tab content -->
<!-- <div class="tab">
</div> -->
<div class="tab">
<button id = "prsButton" class="tablinks" onclick="openTab(event, 'PRS')">Calculate PRS</button>
<button class="tablinks" onclick="openTab(event, 'PGS catalog')">Explore the PGS catalog</button>
<button class="tablinks" onclick="openTab(event, 'OpenSNP')">Explore OpenSNP</button>
<!-- <button id = "prsButton" class="tablinks" onclick="openTab(event, 'PRS')">Calculate PRS</button> -->
</div>
<div id = "selection"></div>
<!-- PRS ------------------------------------------>
<div id="PRS" class="tabcontent">
<div id=prsDiv></div><br>
<h3>PRS</h3>
<p>A prototype personal risk score <a class="link-unstyled" href="https://episphere.github.io/prs"
target="_blank"> <u>calculator</u></a> , created for research purposes, was developed to demonstrate how
the PGS Catalog can be privately and readily applied to readily available direct-to-consumer genetic testing
services, such as 23andMe. No software download, installation, or configuration is needed. The PRS web
calculator matches individual PGS catalog entries with an individual's 23andMe genome data composed of 600k
to 1.4 M single-nucleotide polymorphisms (SNPs). Beta coefficients provide researchers with a convenient
assessment of risk associated with matched SNPs. This in-browser application was tested in a variety of
personal devices, including smartphones, establishing the feasibility of privately calculating personal risk
scores with up to a few thousand reference genetic variations and from the full 23andMe SNP data file
(compressed or not).</p>
<div id=prsButton></div>
</div>
<!-- 23 and me ------------------------------------------>
<div id="OpenSNP" class="tabcontent">
<h3>OpenSNP</h3>
<p>OpenSNP.org is a repository to which users can upload their SNP-sets (and exome-VCFs) from a variety of
direct-to-consumer genetic testing brands including 23andMe.</p>
<h6 style="color: rgb(6, 137, 231);">Select an openSNP datatype below:</h6>
<div id=snp></div>
<div id="snpButton"></div>
<br>
<div style="position:relative;left:100px;bottom:0px;text-align:left">
<span style="font-size: 13pt;">OpenSNP phenotypes</span>
</div>
<div id=snpPheno></div>
<div id="snpPhenoButton"></div>
<div id=snpPhenoPie></div>
<div id=snpPhenoPieButton></div>
</div>
<!-- pgs scoring counts bar plot ----------------------------->
<div id="PGS catalog" class="tabcontent">
<h3>The Polygenic Score (PGS) Catalog</h3>
<p>The PGS Catalog is an open database of published polygenic scores (PGS), annotated with relevant metadata;
including scoring files (variants, effect alleles/weights).</p>
<div class="tab">
<button class="tablinks" onclick="openTab(event, 'Categories', true)">Categories</button>
<button class="tablinks" onclick="openTab(event, 'Traits', true)">Traits</button>
<button class="tablinks" onclick="openTab(event, 'EFO_ids', true)">EFO_ids</button>
</div>
<!-- --------------------->
<div id="Categories" class="tabcontent">
<h6 style="color: rgb(6, 137, 231);">Select a PGS category below:</h6>
<div id="topBarCategories"></div>
<p id="description1" style="font-size:10px;color:blue"></p>
<div id="secondBarCategories"></div>
<div id="secondBarCategoriesButton"></div>
<div id="betasBarCategoriesButton"></div>
<div id="betasBarCategories"></div>
<!-- --------------------->
<br>
<h6 id="pieHeader"></h6>
<div class="spinner-border m-5" style="display: none;" role="status" id="spinner2">
<span class="visually-hidden">Loading...</span>
</div>
<div id="pgsPie"></div>
<div id="thirdBarCategories"></div>
<div id="thirdBarCategoriesButton"></div>
<div id="betasthirdBarCategoriesButton"></div>
<div id="betasthirdBarCategories"></div>
<div class="spinner-border m-5" role="status" id="spinner">
<span class="visually-hidden">Loading...</span>
</div>
</div>
<!-- --------------------->
<div id="Traits" class="tabcontent">
<h6 style="color: rgb(6, 137, 231);">Select a PGS category below:</h6>
<div id="topBarTraits"></div>
<div class="spinner-border m-5" style="display: none;" role="status" id="spinner3">
<span class="visually-hidden">Loading...</span>
</div>
<div id="secondBarTraits"></div>
<div id="secondBarTraitsButton"></div>
<div id="betassecondBarTraitsButton"></div>
<div id="betassecondBarTraits"></div>
</div>
</div>
<!-- --------------------->
<div id="EFO_ids" class="tabcontent">
<h6 style="color: rgb(6, 137, 231);">Select an EFO id below:</h6>
<div id="topBarEFO_ids"></div>
<p id="description1" style="font-size:10px;color:blue"></p>
</div>
<!-- scripts----------------------------------------------->
<script src="tabs.js"></script>
<script type="module" src="sdk/prs.js"></script>
<script type="module" src="sdk/storage.js"></script>
<script type="module" src="sdk/get23.js"></script>
<script type="module" src="sdk/getPgs.js"></script>
<script type="module" src="sdk/ui.js"></script>
<script type="module" src="sdk/main.js"></script>
<script type="module" src="sdk/plots.js"></script>
<script type="module" src="dependencies.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/3.3.0/math.min.js"></script>
<!-- privacy section-->
<section id="notices">
<span style="font-size:large;">Privacy:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
All data and calculations take place in the browser. No data or calculations circulate by a server. This
application is, foremost, an exercise in privacy-preserving biomedical informatics for consumer genomics
data.
</span><br>
<span style="font-size:large;">Scope/Limitations:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
This calculator was devised as an implementation proof of concept. It has a number of important
limitations
for epidemiology research and it does not meet criteria for clinical use. The current tool uses
pre-imputation genotype data and thus results in a low number of SNP matches. Most important, only the
relative risk model <a href='https://www.nature.com/articles/nrg.2016.27#Sec5' target="_blank">(Box 1,
eq
2)</a> is calculated, with no effort to determine absolute risk of disease. Finally, the risk
calculation will only be attempted for PGS catalog entries reporting effects as beta values under
"effect_weight".</span>
</section>
</body>