The spring release of HGMD Professional now contains a total of 224,642 mutation entries. That's 4,372 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 batch search mode will now allow prioritization of variants by class (eg. DM class).
HGMD Professional is one of the most valuable resource in variant interpretation and research. Click below to download our whitepaper on how HGMD Pro helps clinical labs avoid the clinical blindspot which providing the most comprehensive resource for published, disease-causing, germline mutations.
This new version of ANNOVAR contains some minor fixes and improvements: fixed a bug in calculating upstream distance that print when -separate is specified in annotate_variation.pl, improvements to coding_change.pl to report more stopgain/stoploss and fix use-of-uninitialized-value issue, slight change to convert2annovar.pl to handle mal-formed VCF file. Per user request, we have now made hg38 version of ensGene available through ANNOVAR directly so that users do not need to build it themselves. avsnp150 is available through ANNOVAR now in hg19 and hg38 coordinate, to annotate your variants with dbSNP identifiers. Finally, the tatest clinvar (20170905) is available now through ANNOVAR in hg19 and hg38 coordinates. A long-standing problem on multi-allelic variants in ClinVar is now addressed, so that multi-allelic variants are now correctly assigned to the corresponding benign/pathogenic categories. The 20170130/20170501 versions are also updated to resolve this issue.
Learn more about how ANNOVAR can be used with HGMD for variant annotation.
Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC® release 2018.1, PROTEOME™ release 2018.1.
The winter release of HGMD Professional now contains a total of 220,270 mutation entries. That’s 6,112 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
HGVS nomenclature has been added for the non-coding micro-lesions and regulatory substitutions.
HGMD Professional is one of the most valuable resource in variant interpretation and research. Click here to download our white paper on how HGMD Pro helps clinical labs avoid the clinical blind spot which providing the most comprehensive resource for published, disease-causing, germline mutations.
There are no new updates with ANNOVAR with this release.
Learn more about how ANNOVAR can be used with HGMD for variant annotation.
Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC® release 2017.3, PROTEOME™ release 2017.3. Release notes can be found here.
The fall release of HGMD Professional now contains a total of 214,158 mutation entries. That’s 5,790 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 extended cDNA sequences were only available for a small number of genes, and have been out of date for some time. We have now added a link to a new extended cDNA sequence for each gene based on hg38 sequence and annotations. The sequence is shown split between the full exonic sequence in uppercase, and 50 bp of flanking intronic sequence in lowercase. Exon numbering is sequential. This feature is under ongoing development, and we plan to add in further CDS annotations at a later date. The old extended cDNA sequences, along with the old mutation viewer will be removed from HGMD Professional for the 2018.1 release.
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 Insights (QCI).
2017 July 16
ANNOVAR new version is available now! You can use the old link to download, or you can register again to get download email. This release contains some minor fixes and improvements: fixed a bug in calculating upstream distance that print when -separate is specified in annotate_variation.pl, improvements to coding_change.pl to report more stopgain/stoploss and fix use-of-uninitialized-value issue, slight change to convert2annovar.pl to handle mal-formed VCF file.
2017 September 12
There is now an hg38 version of ensGene available through ANNOVAR directly so that users do not need to build it themselves.
2017 September 29
2017Sep29: avsnp150 is available through ANNOVAR now in hg19 and hg38 coordinate, to annotate your variants with dbSNP identifiers.
2017 October 13
Latest clinvar (20170905) is available now through ANNOVAR in hg19 and hg38 coordinates. A long-standing problem on multi-allelic variants in ClinVar is now addressed, so that multi-allelic variants are now correctly assigned to the corresponding benign/pathogenic categories. The 20170130/20170501 versions are also updated to resolve this issue.
Learn more about how ANNOVAR can be used with HGMD for variant annotation.
Updated tracks have been released concurrent with the HGMD release for all HGMD-related tracks. Additional major tracks updated include TRANSFAC® release 2017.3, and PROTEOME™ release 2017.3. Release notes can be found here.
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).
The following new database updates have been made available in ANNOVAR since the last release announcement.
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.
We’re happy to announce that new releases of our products are now available.
These releases offer a number of new features and improvements. You can find release highlights and visit the individual product pages to view the detailed release notes.
CLC Genomics Workbench 10.0: https://digitalinsights.qiagen.com/products/clc-genomics-workbench/
Ingenuity Variant Analysis: https://digitalinsights.qiagen.com/products/ingenuity-variant-analysis/
QCI Interpret: https://digitalinsights.qiagen.com/products/qiagen-clinical-insight/
Biomedical Genomics Workbench 4.0: https://digitalinsights.qiagen.com/products/biomedical-genomics-workbench/
CLC Microbial Genomics Module 2.0: https://digitalinsights.qiagen.com/clc-microbial-genomics-module-latest-improvements/
CLC Genomics Server 9.0 and CLC Command Line Tools 4.0: https://digitalinsights.qiagen.com/products/clc-genomics-server/latest-improvements/current-line/
CLC Main Workbench 7.8: https://digitalinsights.qiagen.com/products/clc-main-workbench/latest-improvements/current-line/
CLC Sequence Viewer: https://digitalinsights.qiagen.com/products/clc-sequence-viewer-latest-improvements/
CLC Genome Finishing Module 1.7: https://digitalinsights.qiagen.com/plugins/clc-genome-finishing-module/latest-improvements/
This post is authored by Gnosis Data Analysis I.K.E.
We are proud to announce a new release for BioSignature Discoverer, the plugin specifically devised for identifying collection of biomarkers in omics data.
The new version of the plug-in comes with several important improvements, including:
The new release immediately follows the first scientific publication demonstrating the applicability of BioSignature Discoverer in practice:
Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.
This work employs BioSignature Discoverer for identifying biomarkers characterizing leaf senescence in sunflower plants. The biomarkers allow a net separation across the senescence stages of the plants, and were identified by integratively analyzing transcriptomics and metabolomics information.
Gnosis Data Analysis I.K.E. is a university spin-off of the University of Crete whose mission is empowering companies and research institutions with powerful data analysis solutions and services.
For more details about the BioSignature Discoverer plug-in, please visit the dedicated plug-in page.
For more information about Gnosis Data Analysis, please visit their website.
We're happy to announce that new releases of our products are now available. The releases offer a number of new features and improvements. You can see a few of the highlights below and visit the individual product pages to view the detailed release notes.
Determine which isoforms have interesting biological properties or enhance your multi-omics research approaches - here are the highlights of the latest IPA release:
See the more detailed release notes:
IPA Fall Release 2016
With our fall release of Ingenuity Variant Analysis comes a number of improvements. The headlines are:
Get more details:
Ingenuity Variant Analysis Fall Release 2016
Take a look at these highlights of features and benefits you get from the QIAGEN Clinical Insight (QCI) Interpret September 2016 release:
See more feature improvements and details on the benefits:
QCI Interpret September 2016 Release
It's a pleasure to present the new releases of both workbenches and servers in our CLC product line. Here are a few highlights:
Read more about these and other new features and improvements:
Biomedical Genomics Workbench 3.5
Biomedical Genomics Server Solution 8.5
CLC Genomics Workbench 9.5
CLC Genomics Server 8.5
It's a pleasure to announce that new releases of a range of our products are now available. The new releases offer a number of new features and improvements specific for each of the products.
For more details on the updates, please visit the latest improvements/statistics pages for the products of your interest:
Biomedical Genomics Workbench 3.0
CLC Genomics Workbench 9.0
CLC Main Workbench 7.7
CLC Drug Discovery Workbench 3.0
CLC Sequence Viewer 7.7
CLC Genomics Server 8.0
CLC Server Command Line Tools 3.0
CLC Bioinformatics Database 4.7
CLC Developer Kit 9.0
CLC Genomics Developer Kit 9.0
CLC Developer Kit Server 9.0
We're pleased to deliver several new features to Ingenuity® Pathway Analysis™, to increase your insight and improve your workflow. Here’s a quick overview of what’s new.
Customizable pathway and network overlays
The 2015 IPA Winter release improves your ability to see and understand your 'omics data in the context of networks and pathways. You can customize which measurements are overlaid from your datasets and increase the intensity of the colors for more streamlined analysis. Switching overlays allows you to visualize expression data versus variant gain/loss values for example. You can also manually customize the range of colors to visually emphasize genes of interest from your dataset.
Seamless upload of Cuffdiff data files
Cuffdiff, part of the Cufflinks package, is a popular software tool that quantifies differentially expressed genes or isoforms in RNA-seq data. We’ve improved your RNA-Seq workflow by enabling direct upload of native Cuffdiff data files.
Updates to simplify your process
Open analyses, lists… there are several windows you might find open simultaneously in IPA, and it can get confusing to identify their parent project folder. The latest IPA release makes it much easier to identify the location for these open windows. We’ve also improved the traceability of IPA entities by adding a new "path" field to the Details window for items in the project manager. Finally, if you search for analyses and datasets in IPA, you can now simply right-click on a result to highlight the item in the project manager.
Please feel free to contact us with questions or comments.
You can also sign up for our upcoming webinars if you'd like to know more about IPA.
The Fall release of Ingenuity® Variant Analysis™ enriches the analysis functionality, adding speed and power, and offers new tools for the organization and management of sample analysis. We are committed to providing the most comprehensive solutions to our customers, and we’re delighted to share the highlights with you.
Analyze More Data with Greater Efficiency
Performance is important to our customers. When they pre-filter their whole genome data to exonic-only regions, they have previously been limited to data from 200 whole genome samples. We have increased that limit by 50%, so now customers can analyze up to 300 whole genome samples before the pre-filtering feature becomes mandatory. Users who are analyzing more than 300 whole genomes can either pre-filter, or bypass the pre-filter function altogether by contacting Customer Support for assistance with creating a work-around.
Better Sample Analysis and Management with New Private Control Libraries
The introduction of Private Control Libraries (PCL) delivers powerful new computation capabilities. PCLs enable users to compute and filter variant frequency from a select sample set, then compare case samples with all samples housed within the PCL. In addition, the PCL can accommodate larger volumes - up to 2000 whole genomes - when analyzing control samples, and can compare cases v. control samples using the Genetic Analysis and Statistical Analysis filters.
We have added two new tabs to PCL, which features a drag-and-drop interface to make management a snap. The first is called “My Control Libraries,” enabling you to store and easily access your PCLs. With the second tab, you can build a new library by clicking on the “New Library” tab in the “My Samples” view.
Additional Improvements
When considering other improvements that could really benefit our users, we recognized the intrinsic value of the Allele Frequency Community (AFC). We took this release as an opportunity to update the build of the AFC, which is now comprised of more than 120,000 consented exomes and genomes (about 12,000 of which are whole genomes). We have also improved integration between Ingenuity Variant Analysis and Ingenuity Pathway Analysis (the integration is in beta, with limited support), which enables Variant Analysis to export the list of gene IDs, the ACMG assessments, and the gain/loss of function information when you click on the “Export to IPA” button.
Learn more about Ingenuity Variant Analysis
