89 lines
59 KiB
HTML
89 lines
59 KiB
HTML
<!DOCTYPE html>
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<html amp lang="en-US" data-amp-auto-lightbox-disable transformed="self;v=1" i-amphtml-layout="" i-amphtml-no-boilerplate="">
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI - NCBI Insights"><meta property="og:description" content="Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded Human Pangenome Research Consortium (HPRC) has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences … Continue reading Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2023/06/15/access-data-hprc-at-ncbi/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2023-06-15T14:35:17+00:00"><meta property="article:modified_time" content="2023-06-15T17:08:51+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta 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<h1 class="amp-wp-title">Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI</h1>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px" data-hero-candidate="" layout="intrinsic" disable-inline-width="" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?fit=1024%2C535&ssl=1" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/HPRC_Blog-1-e1686783532112.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px"></amp-img> </figure>
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<p><span data-contrast="none">Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded </span><a href="https://www.genome.gov/about-genomics/new-human-pangenome-reference"><span data-contrast="none">Human Pangenome Research Consortium (HPRC)</span></a><span data-contrast="none"> has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences from the different genomes to one another. The pangenome allows researchers to compare these DNA sequences and get a more detailed view of the range of human genetic variation. This is the first step toward the HPRC’s goal of building a pangenome reference comprised of the genomes of 350 individuals from diverse genetic backgrounds.</span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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<p><span data-contrast="none">Data associated with the HPRC pangenome reference is available at NCBI. You can easily retrieve all the genomes that are included in the pangenome through </span><a href="https://www.ncbi.nlm.nih.gov/datasets/genome/?bioproject=PRJNA730822&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><span data-contrast="none">NCBI Datasets</span></a><span data-contrast="none">, downloading a data package containing all or a desired subset of assembly sequences and associated metadata. As more genomes are sequenced for the HPRC reference and deposited in GenBank, you’ll find them here as well. Gain access to the genome graphs connecting the assemblies of the first pangenome reference through the </span><a href="https://www.ebi.ac.uk/ena/browser/view/ERZ12792759"><span data-contrast="none">European Nucleotide Archive (ENA)</span></a><span data-contrast="none">, accessible via </span><a href="https://www.ncbi.nlm.nih.gov/bioproject/850430?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><span data-contrast="none">BioProject</span></a><span data-contrast="none">.</span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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<h5>Example</h5>
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<p><span data-contrast="none">Here is an example of genome data related to the HPRC project available at NCBI. </span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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<p><span data-contrast="none">HG002 was one of the first genome samples generated for the pangenome and was annotated by NCBI. Explore the gene content of its two parental haplotypes in the Genome Data Viewer (GDV) (paternal: </span><a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCA_021950905.1"><span data-contrast="none">HG002.pat.cur.20211005</span></a><span data-contrast="none">, maternal:</span> <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCA_021951015.1"><span data-contrast="none">HG002.mat.cur.20211005</span></a><span data-contrast="none">) and whole-genome alignments to GRCh38 in the </span><a href="https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCA_021951015.1/GCF_000001405.40/16575/9606?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><span data-contrast="none">Comparative Genome Viewer (CGV)</span></a><span data-contrast="none"> (Figure 1). You can also download the corresponding files from </span><a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/pilot/annotation_releases/9606/"><span data-contrast="none">FTP</span></a><span data-contrast="none">.</span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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<p><amp-img class="alignright size-full wp-image-11654 amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=1034%2C912&ssl=1" alt="" width="1034" height="912" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?w=1034&ssl=1 1034w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=300%2C265&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=1024%2C903&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=150%2C132&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=768%2C677&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=270%2C238&ssl=1 270w" sizes="auto, (max-width: 1034px) 100vw, 1034px" layout="intrinsic" disable-inline-width="" i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjkxMiIgd2lkdGg9IjEwMzQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><noscript><img loading="lazy" decoding="async" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=1034%2C912&ssl=1" alt="" width="1034" height="912" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?w=1034&ssl=1 1034w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=300%2C265&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=1024%2C903&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=150%2C132&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=768%2C677&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/06/Pan_Genome_CGV.png?resize=270%2C238&ssl=1 270w" sizes="auto, (max-width: 1034px) 100vw, 1034px"></noscript></amp-img></p>
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<p><i><span data-contrast="none">Figure 1. </span></i><a href="https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCA_021951015.1/GCF_000001405.40/16575/9606#CM039017.1:6065922-6853573/NC_000007.14:5968127-6764757/size=10000"><i><span data-contrast="none">Alignment of a 760Kb region on chromosome 7</span></i></a><i><span data-contrast="none"> between the </span></i><a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_021951015.1/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><i><span data-contrast="none">HG002.mat.cur.20211005</span></i></a><i><span data-contrast="none"> and </span></i><a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><i><span data-contrast="none">GRCh38.p14</span></i></a><i><span data-contrast="none"> showing a relative inversion and reversed gene order.</span></i><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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<p><span data-contrast="none">Did you know? NCBI contributed to the HPRC pangenome reference by evaluating the quality of early versions of the included genomes. We evaluated their completeness, correctness, and base accuracy using our </span><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2021/09/30/genome-quality-service/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=hprc-data-20230615"><span data-contrast="none">Assembly QC service</span></a><span data-contrast="auto">.</span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335559738":150,"335559739":0,"335559740":240}'> </span></p>
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