Variant Analysis Release Notes
2015 Release Fall
Whole Genome Prefilter Limit Increased from 199 to 299 Samples
To improve performance, users have the option to pre-filter their whole genome data to only exonic regions. When an analysis exceeds a certain volume of whole genome samples, pre-filtering is mandatory. With the Fall release, the upper limit that imposes mandatory prefiltering has been lifted from 199 to 299 whole genome samples. Now users performing analysis up to 299 whole genomes are not required to pre-filter. Users creating analysis with 300 or greater whole genomes must use pre-filter or contact Customer Support to create analysis without pre-filtering.
Private Control Libraries
Private Control Libraries (PCL) will allow users to compute variant frequency from a select set of samples and allow users to filter on those frequencies as well as compare case sample(s) vs all the samples in the PCL. The PCL will allow analysis with large volume of control samples to compute faster and enable much larger analysis sizes (up to 2000 whole genomes). One can also compare case(s) vs control samples within the
PCL using the Genetic Analysis and Statistical Analysis filters
The IVA application will feature a new tab “My Control Libraries” where you can see your collection of Private Control Libraries. Additionally there will be a new “New Library” button in the My Samples view to build new libraries.
When creating a new private control library, users can build a library by selecting and dragging the samples from the left pane to the right pane of the Create Control Library window.
After clicking the “Create” button, the library is processed offline and the user will be notified by email when the PCL is built. When the library is built, users can access and review the library using the My Control Libraries tab which will list all existing PCLs. From here one can edit the library’s meta data or delete the library.
ExAC Content As Separate Population Within Common Variants Filter
The ExAC data set has been a valuable resource when comparing variants against a healthy population. The Fall 2015 release will feature the option to select the ExAC data set for filtering common variants. The version of ExAC for the Fall 2015 release is ExAC Release 0.3 – 17th December, 2014.
The new build of the Allele Frequency Community (AFC) is based off a collection of 120,000 consented exomes and genomes. Of the 120,000 consented samples, roughly 12,000 are whole genomes and the rest are exomes.
Improved Integration with IPA™
With the Fall release, we have improved the integration between IVA and IPA. Now when you click on the Export to IPA button, IVA will export the list of gene IDs, the ACMG assessments, and the gain or loss of function information. This features is in beta and would have limited support for the Fall release. Export of data from IVA to IPA requires that any open IPA sessions be saved and closed otherwise open IPA sessions will be automatically terminated by the Export. Additionally the new Export feature will no longer automatically launch IPA but will require the user to manually login into IPA and select the data under the IVA projects folder.
2015 Release Spring
Improvements to Allele Frequency Community
Allele Frequency Community members will now be able to download all the frequencies associated with the variants contained in their donated samples. This is done via the AFC Export button in the Details panel. This feature is available to all Ingenuity Variant Analysis users even unpaid users. The only requirement is that the user must opt-into the Allele Frequency Community.
Download of Raw VCF file
With the new Spring release, Ingenuity Variant Analysis users will now be able to download the raw VCF file that was uploaded to Variant Analysis. This is a great way to back up your valuable VCF files while interpreting them. Additionally core labs and commercial service providers and now use Ingenuity Variant Analysis as a way to offer their customers a delivery method for VCF files as well as NGS analysis serivces. To download the raw VCF file, simply click on the blue file name next to ‘Files’ in the details panel.
Updates to IAT
The Ingenuity Admin Tool will now feature:
The ability to see the Ingenuity Variant Analysis subscription capacity including how much free space is available
List of Group members and each members unique samples List of samples within the subscription and which group members have access to those samples. Also when adding other IVA users to the Group, the IAT will now let you know how many unique samples the new member will be bringing into the account.
PMGD Content in IVA
Ingenuity Variant Analysis users will now have access to PGMD content included with their subscription. When PGMD annotations are available for the selected variant, PGMD details may be view through the phamacogenetics link in the Details panel.
Search for actionable variants in your NGS data with confidence.
This new release features access to the most extensive community database of allele frequencies, facilitated sharing, and instant access to HGMD content.
Allele Frequency Community
The Allele Frequency Community is a freely accessible “opt-in” community resource designed to facilitate sharing of anonymized, pooled allele frequency statistics among laboratories for the benefit of patients and biomedical research. Joining the community is free. Once you join, your NGS samples can be richly annotated with allele frequency information from the entire Community. Non-personally identifiable statistics from community members’ samples are used to expand the diversity of the database over time. More information about the Allele Frequency Community is available at www.allelefrequencycommunity.org
How to join the Allele Frequency Community
Ingenuity Variant Analysis users can opt their samples into the Allele Frequency Community by opting-in upon account signup,
or clicking the new “Settings” link within Variant Analysis,
then checking the “Contribute data …” checkbox.
Community Allele frequencies will be available as part of the Common Variants filter, and as a column in the variants table for users who have opted-in.
Instant Access to HGMD Content
Gain instant, direct access to HGMD content. New in this release, users are no longer required to obtain an HGMD license from BIOBASE for access to up-to-date HGMD content. Access HGMD content directly within Variant Analysis by clicking on a variants’ accession ID.
Ingenuity Admin Tool (IAT) and Group Access to Variant Analysis
The IAT tool enables account administrators to easily manage group membership without contacting QIAGEN Bioinformatics Customer Support. Users may be added or removed from your group through the Ingenuity Admin Tool (IAT) portal. To add a group (or become a group administrator) for your subscription license, please contact Customer Support and request the addition of group access to your Variant Analysis account.
Variant Analysis – New Purchasing Plans
Pay-by-sample plans have been eliminated in favor of a flexible tiered-based subscription model that simplifies budgeting and planning.
In October 2014, QIAGEN Bioinformatics introduced the Ingenuity Variant Analysis subscription plan. Customers can now purchase 12-month subscriptions of Variant Analysis with the ability to select subscription tiers that correspond to their anticipated sample throughput. Subscription tiers start at 50 samples (permitting an analysis of up to 50 samples). For more information on the new subscription tiers please refer to the “How Variant Analysis Subscriptions Work” on the Ingenuity Variant Analysis Resources page.
Please note: Activation codes and coupons for sample activation are no longer used in subscription plans.
Ingenuity Variant Analysis version 3.1.20150207 Content versions: Ingenuity Knowledge Base (Dagobah 141227.000), HGMD(2014.4), COSMIC (v71), dbSNP (Build 141 (05/21/2014)), 1000 Genome Frequency (v5), TargetScan (v6.2), EVS (ESP6500 0.0.30), JASPAR (10/12/2009), PhyloP hg18 (11/2009), PhyloP hg19 (01/2009), Vista Enhancer hg18 (10/27/2007), Vista Enhancer hg19 (12/26/2010), CGI Genomes (11/2011), SIFT (01/2013), BSIFT (01/2013), TCGA (09/05/2013), PolyPhen-2 (HumVar Training set 2011_12), Clinvar (08/07/2014)