103 lines
60 KiB
HTML
103 lines
60 KiB
HTML
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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="dbSNP Enhances Scalability, Data Diversity, and Accessibility - NCBI Insights"><meta property="og:description" content="As part of the Human Genome Project, NCBI, part of the National Library of Medicine, and the National Human Genome Research Institute (NHGRI) established the Single Nucleotide Polymorphism database (dbSNP) in 1998. Over the last 25 years, dbSNP has evolved into a reliable central public repository for genetic variation data. dbSNP is a community-accepted reference … Continue reading dbSNP Enhances Scalability, Data Diversity, and Accessibility →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2023/03/30/dbsnp-scalability-diversity-accessibility/"><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="2023-03-30T16:39:19+00:00"><meta property="article:modified_time" content="2023-03-30T18:32:15+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.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" 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<h1 class="amp-wp-title">dbSNP Enhances Scalability, Data Diversity, and Accessibility</h1>
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<time datetime="2023-03-30T16:39:19+00:00">
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2 years ago </time>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.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/2023/03/dbSNP-3-e1680192089876.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.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/2023/03/dbSNP-3-e1680192089876.png?fit=1024%2C535&ssl=1" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=300%2C157&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=1024%2C535&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=150%2C78&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=768%2C401&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/03/dbSNP-3-e1680192089876.png?resize=270%2C141&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px"></amp-img> </figure>
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<div class="amp-wp-article-content">
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<p><span data-contrast="none">As part of the </span><a href="https://en.wikipedia.org/wiki/Human_Genome_Project"><span data-contrast="none">Human Genome Project</span></a><span data-contrast="none">, NCBI, part of the National Library of Medicine, and the National Human Genome Research Institute (NHGRI) </span><a href="https://pubmed.ncbi.nlm.nih.gov/10447503/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbsnp-enhancements-20230330"><span data-contrast="none">established the Single Nucleotide Polymorphism database</span></a> (<span data-contrast="none">dbSNP) in 1998. Over the last 25 years, dbSNP has evolved into a reliable central public repository for genetic variation data. dbSNP is a community-accepted reference data set for genetic research, analysis pipelines, and for both open-source and commercial tools. It is also an essential part of genetic research and discovery. For example, dbSNP data are used in nearly all human genetic variation research workflows and it serves as the foundation for commercially available ancestry testing products. </span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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<h5>Current dbSNP statistics include:</h5>
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<ul>
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<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-contrast="none">3,800 submitters from all over the world</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'>3.3 billion submitted SNP records </span></li>
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<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="none">1.1 billion Reference SNP records</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="none">1.0 billion Reference SNP records with population frequency</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="none">dbSNP accessions are cited in over 65K publications</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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</ul>
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<p></p>
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<h5>What’s new?</h5>
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<p><span data-contrast="auto">We have made numerous improvements to make molecular variation more accessible for physical mapping, population genetics, investigations into evolutionary relationships, genome wide association, and quickly quantifying the amount of variation at a given site of interest. </span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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<p><span data-contrast="auto">We have fundamentally improved our infrastructure </span><span data-contrast="auto">and </span><span data-contrast="auto">the underlying technology </span><span data-contrast="auto">and </span><span data-contrast="auto">data release processes. This makes dbSNP more reliable </span><span data-contrast="auto">and </span><span data-contrast="auto">efficient to cope with the large amounts of data </span><span data-contrast="auto">and </span><span data-contrast="auto">exponential growth over the last few years. </span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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<p><span data-contrast="auto">We created Allele Frequency Aggregator (</span><a href="https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbsnp-enhancements-20230330"><span data-contrast="none">ALFA</span></a><span data-contrast="auto">) to provide more granular allele frequencies for populations derived from 198K subjects, with the goal of 1M subjects, from dbGaP controlled-access studies. ALFA will improve the discovery of common and uncommon variations that have biological effects or contribute to disease. These data included chip array, exome, and genomic sequencing data from 12 distinct populations, including European, African, Asian, and Latin American subjects. We put these data into regular dbSNP build releases and ALFA data into RefSeq. ALFA can be accessed via the </span><a href="https://www.ncbi.nlm.nih.gov/snp/docs/entrez_help/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbsnp-enhancements-20230330"><span data-contrast="none">browser</span></a><span data-contrast="auto">, </span><a href="https://ftp.ncbi.nih.gov/snp/population_frequency/"><span data-contrast="none">FTP</span></a><span data-contrast="auto">, </span><a href="https://api.ncbi.nlm.nih.gov/variation/v0/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=dbsnp-enhancements-20230330#/ALFA%20Frequency"><span data-contrast="none">API</span></a><span data-contrast="auto">, and </span><a href="https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/"><span data-contrast="none">TrackHub</span></a><span data-contrast="auto">. On </span><a href="https://github.com/ncbi/dbsnp/tree/master/tutorials"><span data-contrast="none">GitHub</span></a><span data-contrast="auto">, we have tutorials and code examples to help with programming.</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></p>
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<p><amp-youtube layout="responsive" width="1108" height="623" data-videoid="Dzirw1Fxa3w" title="NCBI ALFA" class="i-amphtml-layout-responsive i-amphtml-layout-size-defined" i-amphtml-layout="responsive"><i-amphtml-sizer slot="i-amphtml-svc" style="display:block;padding-top:56.2274%"></i-amphtml-sizer><a placeholder href="https://youtu.be/Dzirw1Fxa3w"><amp-img src="https://i0.wp.com/i.ytimg.com/vi/Dzirw1Fxa3w/hqdefault.jpg?w=1108&ssl=1" layout="fill" object-fit="cover" alt="NCBI ALFA" class="amp-wp-enforced-sizes i-amphtml-layout-fill i-amphtml-layout-size-defined" i-amphtml-layout="fill"><noscript><img decoding="async" src="https://i0.wp.com/i.ytimg.com/vi/Dzirw1Fxa3w/hqdefault.jpg?w=1108&ssl=1" alt="NCBI ALFA"></noscript></amp-img></a></amp-youtube></p>
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<h5>Next steps</h5>
|
||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="2" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-contrast="none">The data will continue to grow by leaps and bounds over the next 25 years.</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="2" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="none">We intend to diversify the data by including genotype frequencies.</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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<li data-leveltext="" data-font="Symbol" data-listid="2" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="none">We will make the data more useful to you by making it easier to find and packaging it in consumable formats.</span><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></li>
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