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Somatic Variant/ Germline Variant tabs

With the Omics Summary toggled OFF, the Somatic and Germline Variants have their own tabs and data tables. This view allows you to filter and sort the data.

  • Variants Types
    • Short (single changes in the DNA i.e., 1 base change)
    • Structural (rearrangement of the DNA i.e., translocation and inversion)
    • Copy Number (duplications or deletions of a large region)
    • Expression (RNA sequencing)

Filters

Filters are only available in the Somatic Variant/Germline Variant view (Omics Summary is toggled off). Filters on the left of the screen correspond to the table columns. Filters will only apply to the sequence type and the variant type (i.e., filtering on the Somatic Short Variants). If no filters are selected, the Omics Explorer Table will show all variants within the specific test (germline vs somatic) and variant type (short, structural, copy number, expression). When you search using filters, it searches across all transcripts, not just the canonical

List of Filters:

Filter selections within a category are “ORed”. In other words, under Coding Effect, selecting Frameshift and Splice region will return results that match Frameshift OR Splice Region. Filter selections across categories are “ANDed”. For example, if you select Gene Sets/FH and Coding Effect/Frameshift, the filtered results will match the FH Gene Set filter AND the Frameshift Coding Effect filter.

Once you add a filter, a chip with the filter name gets added above the Omics Explorer Table. You can remove the filter by deselecting it in the filter list on the left or clicking the “x” on the filter chip. You can also clear all the filters selected with the Clear All button at the top of the filters panel. - Gene Sets - ACMG 59 - DNA Repair - FH - FoundationOne CDx - FoundationOne Heme - FoundationOne Liquid - PharmGKB PGx VIP - Sanger Cancer Genes Tier1 v86 - Sanger Cancer Germline v86 - Sanger Oncogenes v86 - Sanger Tumor Suppressors v86

  • Gene search box (can search for separate genes using a comma)
  • Cancer Knowledge Base (CKB) checkbox
  • Coding Effect
    • Frameshift
    • Splice region
    • Splice site
    • Stop lost
    • Start lost
    • Nonsense
    • Inframe
    • Missense
    • UTR3
    • UTR5
    • Synonymous
  • Protein Changes (add – separate with comma)
  • Chromosome

    • Chromosome 1
    • Chromosome 2
    • Chromosome 3
    • Chromosome 4
    • Chromosome 5
    • Chromosome 6
    • Chromosome 7
    • Chromosome 8
    • Chromosome 9
    • Chromosome 10
    • Chromosome 11
    • Chromosome 12
    • Chromosome 13
    • Chromosome 14
    • Chromosome 15
    • Chromosome 16
    • Chromosome 17
    • Chromosome 18
    • Chromosome 19
    • Chromosome 20
    • Chromosome 21
    • Chromosome 22
    • Chromosome M
    • Chromosome X
    • Chromosome Y
  • Position – enter value

  • COSMIC Minimum Count – enter value
  • COSMIC IDS – enter value (separated by a comma)
  • dbSNP rs IDs – enter value (separated by a comma)
  • ClinVar Significance checkboxes
    • Pathogenic
    • Pathogenic/Likely pathogenic
    • Likely pathogenic
    • Uncertain significance
    • Likely benign
    • Benign/Likely benign
    • Benign
    • Conflicting interpretations
    • Association
    • Risk factor
    • Drug Response
    • Not provided
  • ClinVar Review Status checkboxes (can select multiple)
    • Practice Guideline
    • Reviewed By Expert Panel
    • Criteria Provided, Multiple Submitters, No Conflicts
    • Criteria Provided, Single Submitter
    • Criteria Provided, Conflicting Interpretations
    • No Assertion Criteria Provided
    • No Assertion Provided
    • No Interpretation for the Single Variant
  • Pop Freq (gnomAD) - value boxes
    • =Allele Frequency

    • <=Allele Frequency
  • Maximum Across Populations - value boxes
    • =Allele Frequency

    • <=Allele Frequency
  • Gene Class
    • Protein Coding
    • Pseudogene
    • Micro RNA
    • Short ncRNA
    • Long ncRNA
    • Immunoglobulin
    • T Cell Receptor
  • Zygosity
    • Heterozygous
    • Homozygous
    • Reference
  • Variant Allele Freq - value boxes
    • =Allele Frequency

    • <=Allele Frequency
  • Combined in Silico Prediction
    • Select % Damaging or Damaging Rank Score
    • =

    • <=
  • Individual In Silico Predictors
    • Predictor – Select between FATHMM, SIFT, MUT Taster
    • Deleterious
    • Tolerated
  • Variant Count – tells how many meet the selected filters. Anything over 999 is annotated as 999+. However, all that meet the filters will be displayed as infinite scrolling is enabled

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Last update: 2020-09-03