IdeogramThe ideogram shows the whole chromosome of the selected CNV with its chromosome bands.
To change the selected region you can select a region by click-and-drag on the plot.
Gene trackIn the gene track all protein-coding genes are shown. When hovering over the genes you get more information about the gene.
Genes that are dosage-sensitive, i.e. genes that are likely to cause a phenotypic effect, are shown in orange.
There are several dosage-sensitivity scores to choose from: loeuf, pLI, pHI, pTS, %HI, HI/TS Score ClinGen.
Uploaded CNVsIn the 'Uploaded CNV' track all uploaded CNVs that intersect the selected region are shown. Deletions are visualized with red bars and duplications with
blue bars while each row represents one sample/ID.
When hovering over the start or end of the CNV a tooltip with information about the CNV is shown.
The uploaded CNVs can be filtered/ selected based on the Classification and their ID.
In case binary phenotype variables were uploaded the CNVs can also be filtered based on those.
To change the selected region you can select a region by click-and-drag on the plot or use use the move/ zoom-in/ zoom-out buttons.
ClinVar CNVsClinVar summary tab:
In the ClinVar summary track the number of interescting pathogenic/ likely pathogenic deletions and duplications from
ClinVar in 200 kb regions are shown. Numbers were calculated every 100 kb for the region 100 kb up- and downstream.
When hovering over the plot the number of deletions and duplications are shown.
To change the selected region you can select a region by click-and-drag on the plot or use use the move/ zoom-in/ zoom-out buttons.
ClinVar plot and table tab:
In the linVar plot and table tab track the individual CNVs from
ClinVar are shown in a plot and in a table.
The plot is splitted in three subpolots, one visualizes the pathogenic/likely pathogenic CNVs, one visualizes CNVs of uncertain significance
and one plot visualizes benign/likely benign CNVs. More information about the CNVs can be found in the table or by hovering over the CNVs in the plot.
The CNVs can be filtered by their clinical significance and type.
UK Biobank CNVsIn 'UK Biobank' track the combined allele frequency of interescting deletions and duplications from
the UK Biobank in 200 kb regions are shown. Numbers were calculated every 100 kb for the region 100 kb up- and downstream.
To remove small CNVs/ structural variants, all CNVs < 50kb were removed prior to the calculation.
When hovering over the plot the allele frequency of deletions and duplications are shown.
To change the selected region you can select a region by click-and-drag on the plot or use the move/ zoom-in/ zoom-out buttons.
GnomAD CNVsIn 'GnomAD' track the combined allele frequency of interescting deletions and duplications from
GnomAD in 200 kb regions are shown. Numbers were calculated every 100 kb for the region 100 kb up- and downstream.
To remove small CNVs/ structural variants, all CNVs < 50kb were removed prior to the calculation.
When hovering over the plot the allele frequency of deletions and duplications are shown.
To change the selected region you can select a region by click-and-drag on the plot or use use the move/ zoom-in/ zoom-out buttons.
Gene tableThe gene table contains all genes, their genomic coordinates, OMIM links, and gene dosage sensitivity scores.
Clingen gene disease tableThe ClinGen Gene Curation working group has developed a framework to standardize the approach to determine the clinical validity for a gene-disease pair.
The ClinGen Gene-Disease Clinical Validity curation process involves evaluating the strength of evidence supporting or refuting a claim that variation in a particular gene causes a particular disease.
Classifications derived with this framework are reviewed and confirmed or adjusted based on clinical expertise of appropriate disease experts.
Possible classifications are:
Definitive > Strong > Moderate > Limited > No known Disease Relationship > Disputed Evidence > Refuted Evidence.
More information can be found
here or
here.
Clingen regions tableThe ClinGen Dosage Sensitivity curation process collects evidence supporting/refuting the haploinsufficiency and triplosensitivity of genomic regions.
Classifications derived with this framework are reviewed and confirmed or adjusted based on clinical expertise of appropriate disease experts.
Possible scores for the Haploinsuficiency score (HI Score) and Triplosensitivity score (TS Score) are:
0 (No Evidence), 1 (Little Evidence), 2 (Emerging Evidence), 3 (Sufficient Evidence), 40 (Dosage Sensitivity Unlikely)
More information can be found
here.
CNV syndromesThe table shows expert-curated microdeletion and microduplication syndromes involved in developmental disorders from DECIPHER that intersect the selected region.
All syndromes and more information can be found at
DECIPHER.
Enrichment analysisGene set enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.
Here, all genes from the selected region are used as input to analyze whether the genes significantly overlap with an annotated gene set from the libraries.
Libraries can be changed using the dropdown menu.
More information about enrichment analyses can be found
here and descriptions of the available libraries can be found
here.