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Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
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class="xref-sep">,</span><a id="xref-aff-2-1" class="xref-aff" href="#aff-2">2</a><span class="xref-sep">,</span><a id="xref-aff-3-1" class="xref-aff" href="#aff-3">3</a><span class="xref-sep">,</span><a id="xref-fn-1-1" class="xref-fn" href="#fn-1">6</a>, </li> <li class="contributor" id="contrib-2" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Alex+Salazar&sortspec=date&submit=Submit">Alex Salazar</a></span><a id="xref-aff-1-2" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-fn-1-2" class="xref-fn" href="#fn-1">6</a>, </li> <li class="contributor" id="contrib-3" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Yaran+Zhang&sortspec=date&submit=Submit">Yaran Zhang</a></span><a id="xref-aff-1-3" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-4" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Sven+van+der+Lee&sortspec=date&submit=Submit">Sven van der Lee</a></span><a id="xref-aff-1-4" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-aff-2-2" class="xref-aff" href="#aff-2">2</a>, </li> <li class="contributor" id="contrib-5" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Marc+Hulsman&sortspec=date&submit=Submit">Marc Hulsman</a></span><a id="xref-aff-1-5" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-aff-2-3" class="xref-aff" href="#aff-2">2</a><span class="xref-sep">,</span><a id="xref-aff-3-2" class="xref-aff" href="#aff-3">3</a>, </li> <li class="contributor" id="contrib-6" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Lydian+Knoop&sortspec=date&submit=Submit">Lydian Knoop</a></span><a id="xref-aff-1-6" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-7" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Sanduni+Wijesekera&sortspec=date&submit=Submit">Sanduni Wijesekera</a></span><a id="xref-aff-1-7" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-8" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Jana+Krizova&sortspec=date&submit=Submit">Jana Krizova</a></span><a id="xref-aff-1-8" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-9" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Anne-Fleur+Schneider&sortspec=date&submit=Submit">Anne-Fleur Schneider</a></span><a id="xref-aff-1-9" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-10" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Maartje+Pennings&sortspec=date&submit=Submit">Maartje Pennings</a></span><a id="xref-aff-4-1" class="xref-aff" href="#aff-4">4</a>, </li> <li class="contributor" id="contrib-11" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Kristel+Sleegers&sortspec=date&submit=Submit">Kristel Sleegers</a></span><a id="xref-aff-5-1" class="xref-aff" href="#aff-5">5</a>, </li> <li class="contributor" id="contrib-12" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Erik-Jan+Kamsteeg&sortspec=date&submit=Submit">Erik-Jan Kamsteeg</a></span><a id="xref-aff-4-2" class="xref-aff" href="#aff-4">4</a>, </li> <li class="contributor" id="contrib-13" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Marcel+Reinders&sortspec=date&submit=Submit">Marcel Reinders</a></span><a id="xref-aff-3-3" class="xref-aff" href="#aff-3">3</a> and </li> <li class="last" id="contrib-14"><span class="name"><a class="name-search" href="/search?author1=Henne+Holstege&sortspec=date&submit=Submit">Henne Holstege</a></span><a id="xref-aff-1-10" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-aff-2-4" class="xref-aff" href="#aff-2">2</a><span class="xref-sep">,</span><a id="xref-aff-3-4" class="xref-aff" href="#aff-3">3</a></li> </ol> <ol class="affiliation-list"> <li class="aff"><a id="aff-1" name="aff-1"></a><address><sup>1</sup>Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081HV Amsterdam, The Netherlands; </address> </li> <li class="aff"><a id="aff-2" name="aff-2"></a><address><sup>2</sup>Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081HV Amsterdam, The Netherlands; </address> </li> <li class="aff"><a id="aff-3" name="aff-3"></a><address><sup>3</sup>Delft Bioinformatics Lab, Delft University of Technology, 2628CD Delft, The Netherlands; </address> </li> <li class="aff"><a id="aff-4" name="aff-4"></a><address><sup>4</sup>Department of Genome Diagnostics, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; </address> </li> <li class="aff"><a id="aff-5" name="aff-5"></a><address><sup>5</sup>Complex Genetics of Alzheimer's Disease Group, Antwerp Center for Molecular Neurology, VIB, Antwerp B-2650, Belgium </address> </li> </ol> <ol class="fn-track"> <li class="fn-equal" id="fn-1"> <p id="p-1"><a class="rev-xref" href="#xref-fn-1-1">↵</a><span class="fn-label">6</span> These authors contributed equally to this work. </p> </li> </ol> </div> <li class="corresp" id="corresp-1">Corresponding authors: <span class="em-link"><span class="em-addr">n.tesi{at}amsterdamumc.nl</span></span>, <span class="em-link"><span class="em-addr">a.n.salazar{at}amsterdamumc.nl</span></span>, <span class="em-link"><span class="em-addr">h.holstege{at}amsterdamumc.nl</span></span></li> <div class="section abstract" id="abstract-1" itemprop="description"> <h2>Abstract</h2> <p id="p-3">Tandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present <em>otter</em> and TREAT: <em>otter</em> is a fast targeted local assembler, cross-compatible across different sequencing platforms. It is integrated in TREAT, an end-to-end workflow for TR characterization, visualization, and analysis across multiple genomes. In a comparison with existing tools based on long-read sequencing data from both Oxford Nanopore Technology (ONT, Simplex and Duplex) and Pacific Bioscience (PacBio, Sequel II and Revio), <em>otter</em> and TREAT achieve state-of-the-art genotyping and motif characterization accuracy. Applied to clinically relevant TRs, TREAT/<em>otter</em> significantly identify individuals with pathogenic TR expansions. When applied to a case-control setting, we replicate previously reported associations of TRs with Alzheimer's disease, including those near or within <em>APOC1</em> (<em>P</em> = 2.63 × 10<sup>−9</sup>), <em>SPI1</em> (<em>P</em> = 6.5 × 10<sup>−3</sup>), and <em>ABCA7</em> (<em>P</em> = 0.04) genes. Finally, we use TREAT/<em>otter</em> to systematically evaluate potential biases when genotyping TRs using diverse ONT and PacBio long-read sequencing data sets. We show that, in rare cases (0.06%), long-read sequencing from coverage drops in TRs, including the disease-associated TRs in <em>ABCA7</em> and <em>RFC1</em> genes. Such coverage drops can lead to TR misgenotyping, hampering the accurate characterization of TR alleles. Taken together, our tools can accurately genotype TRs across different sequencing technologies and with minimal requirements, allowing end-to-end analysis and comparisons of TRs in human genomes, with broad applications in research and clinical fields. </p> </div> <div class="section fn-group" id="fn-group-1"> <h2>Footnotes</h2> <ul> <li class="fn-supplementary-material" id="fn-4"> <p id="p-62">[Supplemental material is available for this article.]</p> </li> <li class="fn" id="fn-5"> <p id="p-63">Article published online before print. Article, supplemental material, and publication date are at <a href="https://www.genome.org/cgi/doi/10.1101/gr.279351.124">https://www.genome.org/cgi/doi/10.1101/gr.279351.124</a>. </p> </li> <li class="fn" id="fn-6"> <p id="p-64">Freely available online through the <em>Genome Research</em> Open Access option. </p> </li> </ul> </div> <ul class="history-list"> <li xmlns:hwp="http://schema.highwire.org/Journal" class="received" hwp:start="2024-03-15"><span class="received-label">Received </span>March 15, 2024. </li> <li xmlns:hwp="http://schema.highwire.org/Journal" class="accepted" hwp:start="2024-10-03"><span class="accepted-label">Accepted </span>October 3, 2024. </li> </ul> <ul class="copyright-statement"> <li class="fn" id="copyright-statement-1"><a href="/site/misc/terms.xhtml">© 2024 Tesi et al.; Published by Cold Spring Harbor Laboratory Press</a></li> </ul> <div class="license" id="license-1"> <p id="p-2">This article, published in <em>Genome Research</em>, is available under a 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