Variant Analysis Release Notes 2013

Release 2.3.20131217

New Features/Fixes:

  • Mitochondrial variants from multiple mitochondrial reference sequences are now supported (and translated to RCRS coordinates), including genome annotations and findings, for new analyses.


  • Sample-specific Allele Fraction can be added via Edit Columns and viewed in genotype icon tooltips for new analyses which have AD and DP variant data, to see the percentage of reads with the variant allele.


  • Ingenuity Pathway Analysis users now get links in gene and drugs views to jump into IPA.
  • Father and Mother subject IDs are now shown in Analysis Overview page when pedigree information exists when analysis was run for reference.


  • New Position detail in the variant panel provides copyable position text and links to genome browsers (IGV and UCSC) to streamline review of raw read pileups or other local information.



Content versions:

Ingenuity Knowledge Base (Zosma_131203.000), COSMIC (v67), dbSNP (Build 138 (08/09/2013)), 1000 Genome Frequency (v3), TargetScan (v6.2), EVS (ESP6500 0.0.21), 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 (10/01/2013)


Release 2.3.20131107

New Features/Fixes:

  • Import in-house (INFO) annotations from VCF files as custom annotations during Analysis creation.

Screen Shot 2013-11-07 at 9.32.05 AM


  • Set your preferred default Variant table annotations to be shown for all your analyses.

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  • Create analysis sample search now returns samples with matching clinical feature annotations.
  • Confidence Filter Passed upstream pipeline filter option is enabled for CGI var files.
  • Mendelian inheritance genetics filter now also retains heterozygous variants in parents that are not transmitted to any child.

Content Versions:

Ingenuity Knowledge Base (Zildun_131104.000), COSMIC (v66), dbSNP (Build 138 (08/09/2013)), 1000 Genome Frequency (v3), TargetScan (v6.2), EVS (ESP6500 0.0.21), 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 (08/01/2013)

Release 2.2.20131017

New Features/Fixes:

  • Pathways page now provides list of drugs ordered by their ability to counteract the impact of mutations on the pathway, with links to supporting literature evidence and drug view that provides summary of the compounds’ pharmacology, clinical trials, and targets.

Screen Shot 2013-10-17 at 10.03.27 AM

  • SKAT-O algorithm (which automatically optimizes between burden test and association test) is now used by the Statistical Association filter (Case or Control option), to identify genes or pathways with an excess burden of rare variants (the p-values and optimal weights are shown in the corresponding Genes or Pathways pages).
  • Gene panel samples may now be purchased directly within the application.
  • Performance enhancements for large analyses.

Release 2.2.20130919

New Features/Fixes:

  • Variants that fall within ENCODE transcription factor binding sites can now be selected in the Predicted Deleterious filter.


  • A new “ENCODE TFBS” Regulatory Site indicates regions observed to be bound by a transcription factor (specified in the Regulators column and the Variant details view).

Screen Shot 2013-09-19 at 8.53.23 AM

  • The Variant table search box now does exact gene symbol matches when quoted and supports dbSNP rs number search.
  • COSMIC identifiers can now be added to the Variant table view via Edit Columns.
  • The Fused to annotation now indications chromosomal breakpoint location of fusion partner.

Content Versions:

Ingenuity Knowledge Base (Yildun__130911.001), COSMIC (v65), dbSNP (Build 138 (08/09/2013)), 1000 Genome Frequency (v3), TargetScan (v6.2), EVS (ESP6500 0.0.21), 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 (08/01/2013)

Release 2.1.20130815

New Features/Fixes:

  • Confidence Filter passed upstream pipeline enabled for Complete Genomics samples.
  • New analyses are shown in ‘queued’ status until they start ‘running’.
  • VCF export documentation enhanced.
  • Genetic Analysis filter now defaults to paired for tumor: normal pair with same subject ID.
  • Samples that were paid activated whose term has expired now have ‘expired’ status.
  • Sample expiration dates added to My Samples details panel and export.
  • Notification added for renewal-eligible activated samples nearing expiration.

Release 2.1.20130621

New Features/Fixes:

  • Usability improvements including legends for pathway diagrams.


Content Versions:

Ingenuity Knowledge Base (Xiphias _130613.000), COSMIC (v64), dbSNP (Build 137), 1000 Genome Frequency (v3), TargetScan (v6.2), EVS (ESP6500 0.0.19), 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 (5/14/2012), PolyPhen-2 (HumVar Training set 2011_12)

Release 2.0.20130604

New Features/Fixes:

  • Confidence Filter with Usual Suspects options for both most exonically variable genes and/or 100 base windows.

Screen Shot 2013-06-04 at 7.13.19 PM

  • High-volume upload using DataStream uploader using the link in the upload sample window.

Screen Shot 2013-06-03 at 8.41.36 PM

Screen Shot 2013-06-06 at 9.38.29 AM

  • Simplification of the sample activation method.

Screen Shot 2013-06-03 at 9.04.30 PM

Release 2.0.20130517

New Features/Fixes:

  • Each user can now create multiple analyses at the same time, eliminating the need to wait to set up additional analyses.

Release 2.0.20130404

New Features/Fixes:

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Release 2.0.20130402

New Features/Fixes:

  • Easily re-use settings from another analysis to use the same filter cascade.
  • Include any custom annotations such as BED file(s) uploaded in the initial analysis or inheritance pattern selection.
  • Tentatively assign same case and control samples when creating a new analysis.

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  • The Legend now show the Confidence of a sample in lieu of the Call Quality.  For example in variant being present in each sample based on preceding Confidence Filter is now shown by dark (confident) versus light (not) color shading of Case and Control genotype icons

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  • Case (and Control) sample counts (and percentages) with variant now only include samples with Confident variant call in the Genes, Pathways, etc. summary tables.
  • The region into introns to consider for potential splice site mutations can now be increased from the canonical junctions (+/-2 nucleotides adjacent to exons) in the Predicted Deleterious filter. When enabled, intronic variants now are only counted as being in the gene by subsequent filters if they occur within this region to avoid counting overlapping genes.

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  • Now the HGVS Transcript Variant and Protein Variant columns include the coding and protein form qualifiers (c. and p. prefixes, respectively) to make the form explicit.

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  • A What’s New link will appears if there’s been a new product release since your last login. The Release Notes are also available from the online Help
  • The analysis Summary tab per-sample vertical stacked bar charts by value are now scaled by # variants (max across all samples) rather than % total variants within each sample. This better calls out visually if certain samples are skewed with many more variants than expected overall or for a particular value.

Release 2.0.20130314

New Features/Fixes:

  • Missense variants (majority of variants in a genome) can be selected for separately  from other types of (typically more deleterious) variants in Predicted Deleterious filter
  • PolyPhen-2 is now available to exclude variants it predicts are not functionally benign

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  • The gene details panel list for the Genes, Groups/Complexes, Pathways, Processes, and Diseases summary pages summarizes number of samples with variants in the gene for cases and controls as well as the inferred impact of the variants on the gene activities (loss, normal/carrier status, or gain of function).

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  • The click on a gene in the gene details panel jumps to Variants table with the gene in the search box to quickly see the corresponding variants
  • Summary tab now enables per-sample bar chart view of the values to quickly identify any outliers

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  • Exome server project data is distinguished between zero (no exomes with variant gets 0%) and no data, including in Common Variants filter.
  • Cytoband in Variant Details panel  is hyperlinked now to UCSC genome browser which enables quick access to multiple sequence alignments and chromosome and position details.

Release 2.0.20130228

New Features/Fixes:

  • Enabled any user to share a preview (or inactive analyses) with anyone (except him/herself)
  • Enabled VCF export of variant (single and multi-sample)
  • Now display ratio of transition vs. transversion frequencies in sample details view and in analysis overview for sample quality metrics
  • Tooltip added to compound-het
  • Canonical pathway view: display pathway summary and legend  ( Click on “I” icon to display)
  • Added quality-awareness for “mendelian/transient/de novo” filter in GA – a variant that fails to meet Confidence filter for a sample behaves as if it was not called in the sample
  • Multiple high-confidence junction files are supported for gene fusion

Release 2.0.20130214

New features / Fixes:

  • New Confidence filter enables multiple means of selecting variants based on quality considerations, including call confidence, PASS status from upstream variant calling pipeline, and read depth.
  • Call quality is migrated from Genetic Filter to a preceding Confidence Filter for existing analyses
  • Genetic Analysis and Statistical Association filters only count samples as having a variant which satisfy the Confidence filter selection criteria
  • Compound heterozygous specification is viewable and configurable for analyses
  • Variants that contribute to compound heterozygous status for a variant in any sample are shown in a table at the bottom of the Sample Details window
  • Variants that impact drug binding can now be selected with Pharmacogenetics filter
  • Pathway viewer enables Drug Targets to be highlighted
  • Symmetric gene and pathway burden test (C-Alpha)

Content Versions:

Ingenuity Knowledge Base (Wasat 130128.000), COSMIC (v62), dbSNP (Build 137), 1000 Genome Frequency (v3), TargetScan (v6.2), EVS (ESP6500 0.0.18), 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 (5/14/2012), PolyPhen-2 (HumVar Training set 2011_12Z

Release 1.3.20130124

New features / Fixes:

  • Sample search including over clinical features now can be done at Case/Control sample selection stage of analysis creation
  • Filter widgets updated to improve performance and provide vertical scroll bar for low resolution monitors
  • Genetic Analysis filter with gene-level exclude setting now excludes variants not kept in other group; default Genetic Analysis filter is now same-stringency gene-level keep and variant-level exclude