RD Tiering Browser¶
The Interpretation Browser allows users to:
- Review the variants, including Small Variants (i.e. SNVs & Indels), Copy Number Variants (CNVs) & Short Tandem Repeats (STRs) identified by interpretation services (Tiering and Exomiser) and their associated report events.
- Review the zygosity of each variant in all sequenced family members. A filled black circle indicates presence of the variant, with a single black circle indicating heterozygosity and two black circles indicating homozygosity for a variant. A "-" indicates the genotype is undetermined.
- See additional annotations (e.g. allele frequencies, HGVS annotations, in silico predictions) from CellBase for variants.
- Report on additional variants from the VCF files associated with the case.
- Comment on and add interpretative comments
- Download selected tiered variants in a TSV (Tab Separated Values) file.
- Review gene panel coverage.
- Review read level support for variants using IGV.js.
- Generate a Summary of Findings.
- Fill out a reporting outcomes questionnaire.
Reviewing Variants¶
The Interpretation Browser can be accessed from the Referral Overview Page and enables users to "close" GMS Rare disease referrals without using the DSS.
Reviewing Variants Key
| # | Section | Description |
|---|---|---|
| 1 | Create Summary of Findings | Create a Summary of Findings for the case with the number of selected variants in the (). |
| 2 | SNV/Indels | Tab displays the SNV and Indel variants prioritised by Interpretation Services applied to the case. |
| 3 | Short Tandem Repeats | Tab displays the short tandem repeats found in the case. |
| 4 | Copy Number Variations | Tab displays the copy number variants found in the case. |
| 5 | VCF Files | Tab lists the VCF files for each member of a family in a case, available for download. |
| 6 | Filters available in the Interpretation Browser | Filter variants by several parameters including by Tier (1,2 or 3), Panel Name, Penetrance, Disorder, Consequence type, Compound heterozygous and Exomiser score. Users can also enter specific gene names into the “Add variants from VCF” to add these to the bottom of the table. There is also an option to download variants as a TSV file and another option to select and add other variants from the vcf that are not prioritised in the variant table. |
| 7 | Variant | Coordinates and nucleotide change of a particular variant within a gene. The "copy button" allows variant details to be added to clipboard for pasting into Alamut |
| 8 | Genes | HGNC gene symbol and Ensembl gene ID in which the variant was found. |
| 9 | Zygosity & Read Depth | Zygosity of each member of a family for that particular variant, two unfilled circles indicating homozygous wild type, one filled and one unfilled circle indicating a heterozygote, two filled circles indicating alternate homozygous or a "-" indicating the genotype is undetermined. Read depth is displayed as reported by the Tiering Algorithm. Read depth information is currently not available for variants called by Exomiser only. |
| 10 | Max Allele Freq | Maximum alternate allele frequency for this position – from CellBase. |
| 11 | Interpretation Service | Interpretation service that identified this variant. |
| 12 | CVA Classifications | CVA classifications are based on variant classifications submtted in the reporting outcomes questionnaires of rare disease referrals from the 100K and GMS. |
| 13 | ClinVar Classifications | ClinVar annotations are pulled from a snapshot of ClinVar data stored in CellBase. If the variant is not found in ClinVar a (?) will be displayed |
| 14 | The ‘+’ sign on a variant | View additional information (including HGVS information) for a variant. |
Shading of variants
Green-shaded variants in the interpretation browser are variants that were either added from the VCF file or called by Exomiser but have not yet been validated.
External database links¶
From the Interpretation Browser it is possible to link out to DECIPHER, gnomAD v4, UCSC genome browser, OMIM, SpliceAI, VarSome.
CVA Classifications¶
CVA classifications shown in the portal are dynamically pulled from the CVA database when the Interpretation Browser page loads. The classifications are those submtted in the reporting outcomes questionnaires of rare disease referrals from the 100K and GMS. The CVA "lozenge" is a hyperlink that will take you to the associated variant page in CVA Portal
Variant Interpretation Log classifications
The CVA classifications shown in the Interpretation Browser do NOT include classifications from variant interpretation logs (VILs), they only include those that are added to the Summary of Findings, either via setting them as Primary Findings in Congencia or reporting them as described here and associated Outcomes Questionnaire
Known Pathogenic Variant Prioritisation (KPVP)¶
KPVP is an enhancement to the Genomics England Tiering algorithm that can "rescue" known pathogenic variants that previously may have been filtered out by the algorithm. For further information on the KPVP implementation please refer to the Rare Disease Genome Analysis Guide here.
ClinVar is the initial source of known pathogenic variants used by the pipeline, to faciliate access to ClinVar annotations a new ClinVar Classifications column has been added to the Interpretation Browser.
Warning
ClinVar data used by KPVP is loaded periodically into the Genomics England annotation database (CellBase). It possible that the ClinVar annotations you see in the Interpretation Browser are not as up-to-date as the "live" data in ClinVar. Live ClinVar data can be accessed by clicking the ClinVar link in the ClinVar classifications column
Read Depth¶
Read depth is displayed as reported by the Genomics England Tiering algorithm.
Where variants are homozygous reference the read depth is displayed as '-/-' as depth information is derived from gVCFs which contain reference blocks that report average, rather than specific, read depth for that position.
Read depth displayed in the Interpretation Browser may differ from the read depth shown in IGV as the parameters used by variant calling and tiering may result in some bases being filtered out.
Missing Read Depth
Where no read depth information is reported "N/A" is displayed. Please refer to IGV to assess read depth at these positions
Currently, read depth is NOT reported by Exomiser so this information is not available for variants called by Exomiser only.
In addition, when using add variants from VCF for 100K referrals read depth information is not available
Copy variant details¶
Clicking the "copy button" in the variant column adds the variant details, in Alamut format, into your clipboard so they can be easily pasted into the Alamut application for review there. This works for both SNVs / Indels and for Copy Number Variations.
Download Variants¶
It is possible to download variants shown in the Interpretation Browser in a TSV format. By default, all variants are selected for download, however, it is possible to select one or more individual variants for download.
Variants from the entire genome, in VCF format, can be downloaded for all family members using the VCF files tab of the Interpretation Browser.
Search for variants in genes outside of the applied panel¶
This feature enables users to add variants from genes that were not included in the original panel used for variant prioritisation.
This feature enables GLHs to assess variants in genes that might have only recently been identified as having an association with the clinical indication in the referral.
To add variants in a gene outside of the panel applied click the “Add variants from VCF” button. Enter the HGNC gene symbol for the gene you would like to review variants in and click the “Search” button.
The search term is case sensitive so “KCNJ11” will work whereas “kcnj11” will not.
After clicking the search button, any variants with a PASS status in the VCF files will be added to the Interpretation Browser and can be reviewed and reported in the same way.
Please note that a phenotype must be assigned before the variant can be added to the summary of findings.
Attention
Only variants with a PASS status in the VCF file can be added to the Interpretation Browser table. Currently non-PASS variants can only be viewed in the Congenica DSS
Short Tandem Repeats (STRs)¶
Results of STR tiering can be viewed and STR pile-up graphs downloaded. In addition, STRs can be selected and commented on for inclusion in the case’s Summary of Findings.
STRs are listed in priority order (Tier 1 > Tier 2 > Tier Null) and can be filtered based on the tier assigned
Grace Update to STR tiering
Referrals processed through the bioinformatics pipeline prior to the Grace release, the portal displays only Tier 1 and Tier 2 STRs with their associated pile-up plots
Referrals processed after the Grace release, in addition to Tiered STRs "Tier Null" STRs will be displayed along with their pile-up plots.
Tier Null STRs are those detected by the WGS bioinformatics pipeline but the number of STR repeats is less than the normal threshold (as curated in Panelapp).
For Further information on STR tiering please refer to the Rare Disease analysis guide here.
STRs Key
| # | Section | Description |
|---|---|---|
| 1 | Short Tandem Repeats | Tab displays the STRs in a case (if any) |
| 2 | Download STRs TSV | Download the STRs in the case |
| 3 | Tier Filter | This option allows users to delimite the results by Tiers (1, 2, Null) |
| 4 | STR box | This box contains the details of the STR, including the tier, locus, repeat motif, normal number of repeats and the pathogenic number of repeats |
| 5 | Location | The genomic coordinates for the STR |
| 6 | Panels | The panels that have been applied to the case |
| 7 | Zygosity | This table details the number of copies the patient has on both alleles |
| 8 | Pile-Up Graph | This button allows users to download the pile-up graph for this STR |
| 9 | Report Events | This table displays the details of the STRs found in the case |
| 10 | Score | Displays the tier (if any) of the STR, this can be Tier 1, Tier 2, or Tier Null |
| 11 | Genomic Entity | Displays the gene name and ENSG ID |
| 12 | Mode of Inheritance | The mode of inheritance, as listed in PanelApp, for the gene on the panel applied |
| 13 | Panel Name | The panel(s) applied to the case in relation to the gene in the “Genomic Entity” column |
| 14 | Panel Version | The version of the panel applied |
| 15 | Penetrance | The penetrance of the clinical indication |
| 16 | Clinical Indication | The clinical indication the patient has been assigned |
| 17 | Interpretation Service | The interpretation service (e.g. Tiering) that has been applied to the variant to give the score |
Copy Number Variants (CNVs)¶
Attention
Following the "Danny" release of NGIS, high quality calls between 2 kb-10Kb derived from the proband are additionally included in tiered CNVs. These are CNVs that overlap with genes or contain regions defined in the virtual gene panel(s) applied to the patient. High quality CNV calls >2 kb that neither overlap with genes nor contain regions defined in the virtual gene panel(s) will be included in tier null CNVs.
The CNV vcf for the proband, available for download in the interpretation portal, will include these cnvs. The CNV vcf extension is updated to .enhanced.cnv.vcf.gz where these CNVs are called.
CNV tiering results are displayed in two tables, the “CNV Call Level Table” and the “CNV Gene Level Table”.
CNV Call Level Table¶
The Call Level Table lists all the CNVs identified in the proband and allows users to select and comment on CNV calls they may want to include in Summary of Findings.
CNV Call Level Table Key
| # | Section | Description |
|---|---|---|
| 1 | Copy Number Variations | This tab displays the CNVs in the case (if any) |
| 2 | Download CNVs | This button allows users to download all, or a selection of CNVs in a TSV file. Users can select particular CNVs to download by clicking on the “+” next to the genomic coordinates of the particular CNV and checking the box next to it |
| 3 | Genomic Coordinates | The genomic coordinates of the CNV (which link out to IGV) and the link to DGV |
| 4 | Cytobands | The cytobands relating to the genomic coordinates of the CNV |
| 5 | CNV Type | Whether the CNV is a ’LOSS’ or a ‘GAIN’ |
| 6 | Copy Number | The number of copies of the region present in the sample |
| 7 | Size bp | The size in base pairs of the CNV |
| 8 | Allele Frequency by reciprocal overlap (LOSS only) | The allele frequency of the CNV by the computational overlap between structural variants |
| 9 | Allele frequency by frequency track (LOSS only) | The allele frequency from the frequency track applied |
| 10 | Proportion of patients with CNV by reciprocal overlap (GAIN only) | The proportion (percentage) of patients with this CNV by overlap |
| 11 | Proportion of patients with CNV by frequency track (GAIN only) | The proportion (percentage) of patients with this CNV by the frequency track applied |
| 12 | Number of protein coding genes | The number of protein coding genes affected by the CNV |
| 13 | ISCA id of the pathogenic region in the panel applied | The ISCA ID of the pathogenic region in the applied panel |
| 14 | Link to ISCA ID in PanelApp | The link out to the ISCA ID with pathogenicity |
CNV Gene Level Table¶
The Gene Level Table lists all of the genes that overlap CNV calls in the proband.
CNV Gene Level Table Key
| # | Section | Description |
|---|---|---|
| 1 | Gene | The gene name and gene ENSG ids affected by a CNV |
| 2 | Genomic Coordinates of the CNV | The genomic coordinates of the CNV |
| 3 | CNV Type | The CNV type (’LOSS’ or ‘GAIN’) |
| 4 | Copy Number | The number of copies in the patient sample |
| 5 | Size, bp | The size of the CNV |
| 6 | All panels containing this gene | Genes which link to PanelApp, displaying the panels which include this gene |
| 7 | Tiered | The tier of the CNV (TIERA or null) |
| 8 | DGV | A link out to DGV for this CNV |
Report Events¶
Variants (SNVs, Indels, CNVs and STRs) in the Interpretation Browser have one or more report events. Report events indicate how the variant is scored and weighed against the clinical indications depending on the panel and interpretation service applied.
Report Events Key
| # | Section | Description |
|---|---|---|
| 1 | Report Events | Report events table. This can be viewed by clicking the ‘+’ sign to the left of the variant. |
| 2 | Selection box | The check box to the left of every report event enables the user to select it for reporting. |
| 3 | Score | Priority assigned to the variant by an interpretation service against the clinical indication. This can change depending on the panel applied. NOTE: The exomiser score displayed is the "combined" phenotype and variant score |
| 4 | Genomic entity | Gene and the Ensembl gene id linking out to the ensemble gene page. |
| 5 | Mode of Inheritance | Known mode of inheritance for the gene with respect to the clinical indication. |
| 6 | Panel Name | Each panel applied to the case is listed and used to prioritise. |
| 7 | Panel Version | Panel version when the panel was applied to a particular case. |
| 8 | Penetrance | Known penetrance data of a gene with respect to the clinical indication. |
| 9 | Clinical Indication | Clinical indication of the patient being assessed. |
| 10 | Interpretation Service | The interpretation service that assigned a priority to a report event. |
| 11 | Show/Hide Variant Details | This button helps the user to view/hide further information about a variant. See: Figure 9 |
Additional Annotations¶
Further information about a variant such as allele frequencies, HGVS annotations, in silico predictions and disease associations are retrieved from external databases held in CellBase.
Additional Annotations Key
| # | Section | Description |
|---|---|---|
| 1 | Positional and allelic details | Variant coordinates, alleles and HGVS notation. |
| 2 | Most severe consequence type | Most severe consequence of the variant with respect to a transcript. |
| 3 | Consequence Types | Other known or predicted consequences of the variant with respect to other transcripts of the gene and protein consequences when applicable. |
| 4 | Population Frequencies | Reported frequency of the variant in a number of populations is retrieved when available. |
| 5 | Variant Trait Association | Known association of the variant with respect to disease. |
| 6 | Gene Trait Association | Known associations of the gene where the variant is located with respect to disease. |