58f12b639fa769899cb22380678ead6325ed0499 steve Thu Aug 22 12:41:00 2013 -0700 Added announcement for new LOVD, HGMD, and UniProt Variants tracks diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index c490f79..f45fa18 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,43 +1,76 @@ - +
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+ 22 August 2013 + - Three New Human Variation Tracks Released +

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+ We are pleased to announce the release of three tracks that describe + human genetic variation. They are based on the + Leiden Open + Variation Database (LOVD), the + Human Gene + Mutation Database Public (HGMD), and amino acid mutations in the + UniProt database. The + majority of the data were collected from publications by curators in the three + databases. +

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+ The three databases have varying license restrictions. UniProt provides complete + information about the mutation amino acid change, the disease and a link to the + publications that mention it. LOVD provides the mutation and a link to a website + with disease and publication details. HGMD provides some coordinates and a link to + its own website which requires registration. +

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+ These tracks are intended for use primarily by physicians and other professionals + concerned with genetic disorders, by genetics researchers, and by advanced students + in science and medicine. While the Genome Browser database is open to the public, users + seeking information about a personal medical or genetic condition are urged to consult + with a qualified physician for diagnosis and for answers to personal questions. +

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+ We'd like to thank all three databases for their help in putting the data together. The + tracks were produced at UCSC by Maximilian Haeussler and Steve Heitner. +

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22 July 2013 - Variant Annotation Integrator

In order to assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed the Variant Annotation Integrator (VAI). Given a set of variants uploaded as a custom track (in either pgSnp or VCF format), the VAI will return the predicted functional effect (e.g., synonymous, missense, frameshift, intronic) for each variant. The VAI can optionally add several other types of relevant information, including: the dbSNP identifier if the variant is found in dbSNP, protein damage scores for missense variants from the

There are two ways to navigate to the VAI: (1) From the "Tools" menu, follow the "Variant Annotation Integrator" link. (2) After uploading a custom track, hit the "go to variant annotation integrator" button. The user's guide is at the bottom of the page, under "Using the Variant Annotation Integrator."

Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and Jonathan Casper for their input and work on this feature.

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- 2 July 2013 - - Assembly Data Hubs -

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- We are pleased to announce a new feature in the UCSC Genome Browser: - Assembly Data Hubs. -

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- Assembly Data Hubs extend the functionality of Track Data Hubs to - assemblies that are not hosted natively on the Browser. Assembly Data - Hubs were developed to address the increasing need for researchers to - annotate sequence for which UCSC does not provide an annotation - database. They allow researchers to include the underlying reference - sequence, as well as data tracks that annotate that sequence. Sequence - is stored in the UCSC twoBit format, and the annotation tracks are - stored in the same manner as Track Data Hubs. -

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- To read more about using Assembly Data Hubs, or about creating your - own, please see these guides: -

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- - http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html -

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- - http://genomewiki.ucsc.edu/index.php/Assembly_Hubs -

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- Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature. -

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2 July 2013 - Assembly Data Hubs: Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. Read more.

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2 July 2013 - New Gene Alleles feature on the details pages of UCSC genes: For each protein-coding gene in the UCSC Genes track, variant data from the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000 Genomes Project have been distilled into "gene haplotype alleles." Read more.

28 June 2013 - New UCSC Genes Track Released for GRCh37/hg19: We're happy to announce the release of an updated UCSC Genes track for the GRCh37/hg19 human Genome Browser. Read more.

27 June 2013 - New Official European Mirror Released: Announcing an official mirror for European users, with automatic redirection. Read more.

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- 26 June 2013 - - Suggestion Box Released: - Due to popular demand, we have created a suggestion box for track, assembly, - tool, and other feature requests. - Read more.

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