Clinical
Discovery
Tuesday, July 4, 2017

HGMD, ANNOVAR and Genome Trax releases

HGMD Professional

The summer release of HGMD Professional now contains a total of 208,368 mutation entries. That’s 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.

View the complete HGMD statistics

 

New HGMD feature

The original mutation viewer no longer reliably functions in many web browsers due to support for NPAPI being 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.

 

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 QIAGEN Clinical Insight for Hereditary Cancer, which includes HGMD. The following is a table summarizing key features between HGMD Public, Pro, and QIAGEN Clinical Insight (QCI).

 

ANNOVAR

The following new database updates have been made available in ANNOVAR since the last release announcement.

  • 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.
  • gx operation is added in table_annovar so that xref information for genes (such as gene-disease relationships) can be included (see quick start-up for 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 -polish argument, upstream variants now show distance to transcriptional start, splice variants at UTR now shows details, etc.
  • -xreffile with multiple annotation columns has been implemented. Please re-download the code to get this feature.
  • Updated refGene, knownGene, ensGene definition and FASTA file on hg18/hg19/hg38 coordinates are available to download with -webfrom annovar argument. However, users can always build the latest version yourself.
  • Updated instructions on how to handle noncoding variants in COSMIC version 81 here.

 

Genome Trax

Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC® release 2017.2, and PROTEOME™ release 2017.2. Release notes can be found here.

 

 

Note: This release will be available from July 7, 2017.

 


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