945 lines
79 KiB
Text
945 lines
79 KiB
Text
<!DOCTYPE html>
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<html lang="en" dir="ltr" prefix="content: http://purl.org/rss/1.0/modules/content/ dc: http://purl.org/dc/terms/ foaf: http://xmlns.com/foaf/0.1/ og: http://ogp.me/ns# rdfs: http://www.w3.org/2000/01/rdf-schema# schema: http://schema.org/ sioc: http://rdfs.org/sioc/ns# sioct: http://rdfs.org/sioc/types# skos: http://www.w3.org/2004/02/skos/core# xsd: http://www.w3.org/2001/XMLSchema# ">
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<head>
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<h1 class="nist-page__title">Variant calling and benchmarking in an era of complete human genome sequences</h1>
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<div class="nist-field__label">Published</div>
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<div class="nist-field__item"><time datetime="2023-04-14T12:00:00Z">April 14, 2023</time>
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<h3 class="nist-field__label">Author(s)</h3>
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<div class="nist-field__item"><span class="nist-author">Nathanael David Olson</span>, <span class="nist-author">Justin Wagner</span>, <span class="nist-author">Nathan Dwarshuis</span>, Karen Miga, <span class="nist-author">Marc L. Salit</span>, <span class="nist-author">Justin Zook</span></div>
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<h3>Abstract</h3>
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Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of the human genome. We describe how advances in long reads, deep learning, de novo assembly and pangenomes have expanded access to variant calls in increasingly challenging, repetitive genomic regions, including medically relevant regions, and how new benchmark sets and benchmarking methods illuminate their strengths and limitations. Finally, we explore the possible future of more complete characterization of human genome variation in light of the recent completion of a telomere-to-telomere human genome reference assembly and human pangenomes, and we consider the innovations needed to benchmark their newly accessible repetitive regions and complex variants.
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<div class="nist-field__item">Nature Reviews Genetics</div>
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<div class="nist-field__item"><a href="https://doi.org/10.1038/s41576-023-00590-0" target="_blank">https://doi.org/10.1038/s41576-023-00590-0</a></div>
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<div class="nist-field__item">genomics, variant calling, benchmarking</div>
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Olson, N.
|
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, Wagner, J.
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, Dwarshuis, N.
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, Miga, K.
|
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, Salit, M.
|
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and Zook, J.
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(2023),
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Variant calling and benchmarking in an era of complete human genome sequences, Nature Reviews Genetics, [online], https://doi.org/10.1038/s41576-023-00590-0, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=935532
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Created April 14, 2023, Updated November 28, 2023
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