What’s new in the
Summer 2017 Release

New gnomAD database for filtering Common Variants

We’re very excited to announce the availability of the gnomAD dataset in Ingenuity Variant Analysis. Within the Common Variants filter there is now a new population to filter common variants:

gnomAD is the second iteration of the popular ExAC content with the addtion of population genomes and exomes. The dataset contained in gnomAD consists of 123,136 exomes and 15,496 genomes. More information on gnomAD can be found at the gnomAD website.

 

New Centogene Variant Annotations

Centogene’s CentoMD database is the world’s largest rare disease mutation database which combines clinical genetic information with actual clinical patient case data. This database is rich with information including genotype-phenotype data on not-yet-published variants leading to even more evidence-driven insights. If a variant has CentoMD annotations, it will display a CentoMD link in the properties window. Clicking on the link will link out to the CentoMD website to display additional Centogene annotations. To view the additional Centogene annotations a subscription to CentoMD is required.

 

 

 

 

 

 

Ashkenazi Jewish subpopulation is now available

Given that gnomAD contains 5000+ Ashkenazi Jewish individuals, this release provides a subpopulation frequency for Ashkenazi Jewish if filtering with gnomAD within the Common Variants filter.

 

My Filters

Introducing My Filters. You can now save your cascade filtering settings under my filters that you can access via the new My Filters tab:

 

Within the My Filters tab you will see your collection of saved filters that you can apply to existing and future IVA analysis. Also, if you have access to QIAGEN Clinical Insights (QCI) you can make these filters available to QCI for pre-filtering (by IVA) then exporting the filtered variants to QCI for reporting. Saved filters can be shared with other IVA users.

 

To create a filter simply click the floppy disk icon at the top of the filter cascade:

 

To save the filter cascade settings. You’ll need to name your filter setting and optionally a brief description:

 

To see all your saved filters, click on the My Filters tab:

 

To apply you saved filter to a new analysis on the pre-configurator window:

 

Streamlined Export of Filters to QIAGEN Clinical Insight

After optimizing filter settings in Variant Analysis, such filters can be saved in My Filters which are also available as Pre-filter Settings within QIAGEN Clinical Insights (QCI). Now QCI users can upload large VCF files directly within QCI (exome/genomes) and select a list of pre-filters from the user’s Variant Analysis’ My Filters library. This saves the QCI user from having to first upload via Variant Analysis, pre-filter, then export to QCI.

 

Support for HPO Terms in the Biological Context Filter

You can now directly enter HPO terms in the Biological Context filter rather than adding biological terms. Simply upload a text file containing a list of HPO terms using the Upload file(s) link within the Biological Context filter.

 

Improved Error Messaging for VCF File Upload Failures

When customers experience a failed VCF upload, having useful error message will help users troubleshoot the upload problems with the VCF file. Additionally, users in this release of the Variant Analysis API will experience richer error messages in the event of an empty or invalid sample and have the ability to request further details and counters regarding the sample.

 

Improved Indel Handling in Allele Frequency Community (AFC)

Normalize and left-align all indels in user opted-in datasets in AFC while incorporating gnomAD into AFC.

 

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