{"id":15737,"date":"2017-07-04T06:25:18","date_gmt":"2017-07-04T06:25:18","guid":{"rendered":"https:\/\/staging.digitalinsights.supremeclients.com\/?p=15737"},"modified":"2020-04-28T07:18:20","modified_gmt":"2020-04-28T07:18:20","slug":"hgmd-annovar-genome-trax-release","status":"publish","type":"post","link":"https:\/\/staging.digitalinsights.supremeclients.com\/news\/blog\/clinical\/hgmd-annovar-genome-trax-release\/","title":{"rendered":"HGMD, ANNOVAR and Genome Trax releases"},"content":{"rendered":"<h4>HGMD Professional<\/h4>\n<p>The summer release of HGMD Professional now contains a total of 208,368 mutation entries. That\u2019s 4,483 more mutation entries than the previous release. Unlike other mutation databases, HGMD mutations are all backed by peer-reviewed publications where there is evidence of clinical impact.<\/p>\n<p><a href=\"https:\/\/staging.digitalinsights.supremeclients.com\/products-overview\/clinical-insights-portfolio\/human-gene-mutation-database\/\">View the complete HGMD statistics<\/a><\/p>\n<p><strong>New HGMD feature <\/strong><\/p>\n<p>The original mutation viewer no longer reliably functions in many web browsers due to support for\u00a0<a href=\"https:\/\/en.wikipedia.org\/wiki\/NPAPI\" target=\"_blank\" rel=\"noopener noreferrer\">NPAPI<\/a>\u00a0being dropped by several vendors. There is a replacement now available (link via the HGMD gene home pages) which maps coding region mutations on to the HGMD cDNA sequence, via the cDNA page. This feature is under ongoing development.<\/p>\n<p><img fetchpriority=\"high\" decoding=\"async\" class=\"alignnone size-medium_large wp-image-15738\" src=\"https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-768x126.png\" alt=\"\" width=\"768\" height=\"126\" srcset=\"https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-768x126.png 768w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-600x98.png 600w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-150x25.png 150w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-300x49.png 300w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02-900x148.png 900w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/HGMD_Prof_ss_2017_02.png 975w\" sizes=\"(max-width: 768px) 100vw, 768px\" \/><\/p>\n<p>If you are interested into a clinical-grade pathogenicity assessment for a given variant implementing the ACMG guidelines and including additional supporting data such as case counts in a hereditary cancer context, we recommend you take a look at <a href=\"https:\/\/staging.digitalinsights.supremeclients.com\/products-overview\/clinical-insights-portfolio\/qiagen-clinical-insight\/qci-interpret-for-hereditary-cancer\/\">QIAGEN Clinical Insight for Hereditary Cancer<\/a>, which includes HGMD. The following is a table summarizing key features between HGMD Public, Pro, and QIAGEN Clinical Insight (QCI).<\/p>\n<p><img decoding=\"async\" class=\"alignnone wp-image-15739 size-medium\" src=\"https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-501x600.jpg\" width=\"501\" height=\"600\" srcset=\"https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-501x600.jpg 501w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-768x919.jpg 768w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-952x1140.jpg 952w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-150x180.jpg 150w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-300x359.jpg 300w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-600x718.jpg 600w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL-900x1077.jpg 900w, https:\/\/staging.digitalinsights.supremeclients.com\/wp-content\/uploads\/2017\/07\/BB_table_2017_02_FINAL.jpg 1000w\" sizes=\"(max-width: 501px) 100vw, 501px\" \/><\/p>\n<h4>ANNOVAR<\/h4>\n<p>The following new database updates have been made available in ANNOVAR since the last release announcement.<\/p>\n<ul>\n<li>Some users complained about format change in 2017jun01 version of table_annovar, where semicolon was used instead of comma for gene-based annotation, we have now reverted this change.<\/li>\n<li>gx\u00a0operation is added in table_annovar so that xref information for genes (such as gene-disease relationships) can be included (see\u00a0<a href=\"http:\/\/annovar.openbioinformatics.org\/en\/latest\/user-guide\/startup\/\" target=\"_blank\" rel=\"noopener noreferrer\">quick start-up<\/a>\u00a0for examples), show complete amino acid change (such as c.35delG:p.G12Vfs*2) in gene annotaion in table_annovar.pl and coding_change.pl with\u00a0-polish\u00a0argument, upstream variants now show distance to transcriptional start, splice variants at UTR now shows details, etc.<\/li>\n<li>-xreffile with multiple annotation columns has been implemented. Please re-download the code to get this feature.<\/li>\n<li>Updated refGene, knownGene, ensGene definition and FASTA file on hg18\/hg19\/hg38 coordinates are available to download with\u00a0-webfrom annovar\u00a0argument. However, users can always build the latest version yourself.<\/li>\n<li>Updated instructions on how to handle noncoding variants in COSMIC version 81\u00a0<a href=\"http:\/\/annovar.openbioinformatics.org\/en\/latest\/user-guide\/filter\/#cosmic-annotations\" target=\"_blank\" rel=\"noopener noreferrer\">here<\/a>.<\/li>\n<\/ul>\n<h4>Genome Trax<\/h4>\n<p>Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC\u00ae release 2017.2, and PROTEOME\u2122 release 2017.2. Release notes can be found <a href=\"https:\/\/portal.genexplain.com\/archive\/documents\/news_20172.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">here<\/a>.<\/p>\n<p><strong>Note: This release will be available from July 7, 2017.<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"HGMD Professional The summer release of HGMD Professional now contains a total of 208,368 mutation entries. That\u2019s 4,483 more mutation&#8230;","protected":false},"author":18,"featured_media":15740,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[4,2],"tags":[433,434,42,107,75,435,44],"class_list":["post-15737","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-clinical","category-discovery","tag-annovar","tag-genome-trax","tag-hgmd","tag-human-gene-mutation-database","tag-mutations","tag-npapi","tag-release"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.9 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>HGMD, ANNOVAR and Genome Trax releases - Bioinformatics Software | QIAGEN Digital Insights<\/title>\n<meta name=\"robots\" content=\"noindex, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"HGMD, ANNOVAR and Genome Trax releases - Bioinformatics Software | QIAGEN Digital Insights\" \/>\n<meta property=\"og:description\" content=\"HGMD Professional The summer release of HGMD Professional now contains a total of 208,368 mutation entries. 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