Case summary¶
Missing resources
Some case-level resources (e.g. panel coverage, BAF plots, Summary of Findings) and raw sequencing files (VCFs) for the case are not yet supported in the New IB, but will be in future. In the meantime, please continue to use the IP to review these resources.
PID
Non-NHS users are only able to view minimal patient information; patient sex, patient ID and Clinical Indication. Patient name, date of birth and NHS number are only visible to NHS users.
Opening a case from the IP navigates to the case summary page by default.
This page provides the ability to:
- View patient, case and clinical information
- View any case warnings displayed across the top of the page
- Link out to the SNV, CNV, and STR pages (N.B. currently only the SNV page is populated as cases with Tiered CNVs and/or Tiered STRs are not supported)
- Check the versions of software and datasets used by the pipeline and displayed in the New IB to aid interpretation
- Check the release version of the New IB
Case warnings¶
Case warnings will appear at the top of the screen in a banner, as shown below.
Please refer to the Rare Disease Genome Analysis Guide for further information. The warnings could include the following:
Key
| Warning | Description |
|---|---|
| Case closed | This case has been added to CVA and a Summary of Findings has been created in the Interpretation Portal. You can view the details of the closed case here, but edits are not allowed. To make changes, re-open the case by changing its status back to In Progress. |
| Consent status | The patient has changed their mind about consent for this test, please discuss next steps with the referring clinician |
| Case permissions | You do not have the permissions to take actions, such as commenting, flagging, classifying and exporting. Talk to an administrator if you want to make changes to this case. |
| PID permissions | You don't have the permission to view patient identifiable information with your current permissions, if you think this is wrong, get in touch with Service Desk |
| Low coverage | <95% of the autosomal genome covered at ≥15x calculated from reads with mapping quality >10 and >85x10^9 bases with Q≥30, after removing duplicate reads and overlapping bases after adaptor and quality trimming. |
| Saliva sample | Genome sequencing performed using DNA extracted from saliva. There is a risk of poorer quality sequencing data for saliva samples. |
| Unusual sex karyotype | At least one member of the family has a sex karyotype that is not XX or XY |
| Incorrect or discordant sex karyotype | Reported karyotypic and phenotypic sex are discrepant but the karyotypic sex is supported by the sex inferred from the genomic data in at least one family member |
| Inferred genetic and reported sex discordant | Reported sex is discrepant from the inferred genetic sex and the Disorders of Sex development panel has been applied |
| Unknown phenotypic sex | Phenotypic sex is unknown for at least on member of a family |
| Poor quality CNV calls | Majority of CNV calls in the proband are expected to be of poor quality |
| Suspected poor quality CNV calls | An increased number of poor quality CNV calls is suspected |
| Uniparental disomy | ddddddddd [mat|pat]UPDnn [i|h|m][c|p] Uniparental disomy detected that segregates with disease. |
| No warnings | If there aren’t any warnings reported, there won’t be any shown on the case summary page |
Case header¶
The case header contains basic case information. Additional patient and case information can be found on the top right of the banner by clicking the respective drop down menus.
Key
| # | Section | Description |
|---|---|---|
| 1 | Interpretation Portal link-out | Opens the case in the IP in a new tab |
| 2 | Full name | Patient’s first and last name as captured from TOMS |
| 3 | Year of birth | Patient’s year of birth as captured from TOMS |
| 4 | NHS number | Patient’s NHS number as captured from TOMS |
| 5 | Genomic sex | Genomic sex for the patient |
| 6 | Case status | Interpretation status of the case within the New IB, e.g. whether the analysis is in progress or pending secondary review, etc. See the case status page for more info |
| 7 | Patient info | Click here for additional patient information |
| 8 | Case info | Click here for additional case information |
| 9 | Current user | Initials of current user. When clicked on, displays the current user's name, email and a log out button |
Patient info drop-down¶
This header drop-down displays the minimal set of information for the patient.
Key
| # | Section | Description |
|---|---|---|
| 1 | Name | Patient’s name as captured from TOMS |
| 2 | Date of birth | Patient’s date of birth as captured from TOMS |
| 3 | Genomic sex | Patient’s sex as captured from TOMS |
| 4 | NHS number | Patient’s NHS number as captured from TOMS |
| 5 | Patient ID | The patient’s ID as captured from TOMS |
| 6 | Clinical indication | Patient’s clinical indication from the Test Directory, defined during the test order. |
| 7 | Present HPO terms | HPO terms for the proband. Each term has a link-out to its page on the HPO website. Where the case has 5 or less HPO terms these will be displayed in the drop-down, otherwise a link will be displayed, showing the HPO term count, which when clicked on will open a table overlay with pagination allowing all terms to be navigated through. If the proband has no HPO terms, then a '-' will be visible |
Case info drop-down¶
For information on the New IB case status, please see the case status page.
Key
| # | Section | Description |
|---|---|---|
| 1 | Referral ID | The Referral ID for the patient |
| 2 | Case status | Interpretation Status of the case in the New IB, e.g. whether the analysis is in progress. See the case status page for more info |
| 3 | Update case status | This button can be used to update the New IB case status (for more details, se the case status page) |
Patient information¶
This section contains patient-specific details.
Key
| # | Section | Description |
|---|---|---|
| 1 | Name | Patient name |
| 2 | Year of birth | Patient year of birth |
| 3 | Reported sex | Reported sex for the patient |
| 4 | Genomic sex | Genomic sex for the patient |
| 5 | NHS number | Patient NHS number |
| 6 | Patient ID | The patient’s ID as captured from TOMS |
| 7 | Consent | The patient’s consent status, e.g. Yes or No. Please visit the IP user guide for further details on patient consent. |
| 8 | Test order form | Link to the Health Test Ordering form for the patient |
Case information¶
This section contains case-specific details.
Key
| # | Section | Description |
|---|---|---|
| 1 | Test order date | The date the test was ordered |
| 2 | Analysis issue date | The date the referral has successfully arrived in the New IB |
| 3 | Referral priority | Priority for the case, e.g. Routine or Urgent |
| 4 | Referral ID | The Referral ID for the patient |
| 5 | Requester organisation | Requesting organisation defined during test ordering |
| 6 | Interpreting lab | Interpreter organisation defined during test ordering |
| 7 | Sample source | The source of the sample e.g. blood, saliva |
Clinical information¶
This section contains clinical information for the proband.
Key
| # | Section | Description |
|---|---|---|
| 1 | Clinical indication | Patient's clinical indication |
| 2 | Penetrance | Penetrance applied to the case when ordering |
| 3 | Applied GMS PanelApp panels | GMS PanelApp panels applied to the case when ordering, with linkouts to the pages in PanelApp |
Prioritisation summary¶
Here, you can see the number of unique prioritised variants by variant type, which is a summary of the Tiered variants identified by the Rare Disease Interpretation pipeline for the case (i.e. it is a count of variants, not a count of all Tiers assigned). There is also a link-out to the variant grid for each variant type, by clicking View List.
Currently, only cases with Tiered small variants (i.e. no Tiered CNVs nor Tiered STRs) are supported, thus the prioritisation summary will only show Tiered variants for small variants. Support for copy number variants and short tandem repeats will be coming soon.
Key
| # | Section | Description |
|---|---|---|
| 1 | Unique prioritised SNVs | This is a count of Tiered variants whose highest Tier corresponds to that Tier. Selecting View List will navigate to the SNV grid page which contains a list of all variants. |
| 2 | CNVs | Cases with Tiered CNVs will soon be supported. This section will then show the summary of prioritisation for those variants. |
| 3 | STRs | Cases with Tiered STRs will soon be supported. This section will then show the summary of prioritisation for those variants. |
Family information¶
This section displays information for each family member, which can navigated through by using the tabs for each family member above the table.
Key
| # | Section | Description |
|---|---|---|
| 1 | Family member | The family member in the case. These can be clicked on to display information for that family member within the table |
| 2 | Patient ID | Patient ID for the family member |
| 3 | NHS No | NHS number for the family member (fetched from TOMS) |
| 4 | Full name | Full name for the family member (fetched from TOMS) |
| 5 | Reported sex | Reported sex for the family member |
| 6 | Genomic sex | Genomic sex for the family member |
| 7 | Number of ChrX | Number of X chromosomes for the family member |
| 8 | Disease status | Affected status for family member |
| 9 | Sample ID | Sample ID for the family member |
| 10 | Consent | The patient’s consent status, e.g. Yes or No. Please visit the IP user guide for further details on patient consent. |
| 11 | Present HPO terms | HPO terms for the family member. Each term has a link-out to its page on the HPO website. Where the family member has 5 or less HPO terms these will be displayed in the table, otherwise a link will be displayed, showing the HPO term count, which when clicked on will open a table overlay with pagination allowing all terms to be navigated through. If the family member has no HPO terms, then a '-' will be visible |
Software and dataset versions¶
Here, you can find the versions of datasets and software used to process the case. The Pipeline section details the versions of software and datasets used by the pipeline, whilst the Interpretation section details the versions of additional resources provided in the New IB to assist with variant interpretation.
For further details on sources of specific variant annotation metadata, please see the annotations page.
N.B. Please note, the below image is for illustration purposes only and does not contain the current software versions being used to annotate your case. You must look at your case within the New IB to find the accurate software versions for your case.
Key
| # | Section | Description |
|---|---|---|
| 1 | NGIS release | The Genomics England National Genomic Informatics System release |
| 2 | CellBase | The version of the CellBase server (i.e. the software itself). CellBase is a data warehouse and open API that stores reference genomic data from public resources such as Ensembl, Clinvar, and Uniprot |
| 3 | CellBase data release | The version of the data bundle that is stored in CellBase. This is updated less frequently than the CellBase software itself |
| 4 | Tiering | The Tiering pipeline version used to prioritise the variants into Tiers. For further details see the Tiering algorithm section of the Rare Disease Genome Analysis Guide |
| 5 | ClinVar KPVP | Version of ClinVar used by Known Pathogenic Variant Prioritisation, an enhancement to the Genomics England Tiering algorithm that can "rescue" known pathogenic variants that previously may have been filtered out by the algorithm. ClinVar is one of the sources of known variants used for this. For further details, see the KPVP section of the Rare Disease Genome Analysis Guide |
| 6 | CVA KPVP | Version of CVA used by Known Pathogenic Variant Prioritisation, an enhancement to the Genomics England Tiering algorithm that can "rescue" known pathogenic variants that previously may have been filtered out by the algorithm. CVA is one of the sources of known variants used for this. For further details, see the KPVP section of the Rare Disease Genome Analysis Guide |
| 7 | Secondary annotation service | This is the pipeline that adds additional annotations to variants after they have been processed by the Genomics England Rare Disease pipeline |
| 8 | gnomAD exomes AF | The version of gnomAD exomes population frequency data displayed in the New IB |
| 9 | gnomAD genomes AF | The version of the gnomAD genomes population frequency data displayed in the New IB |
| 10 | GEL internal aggregate AF | The version of the Genomics England internal population frequency data displayed in the New IB |
| 11 | ClinVar | The ClinVar data displayed in the New IB is a snapshot of the ClinVar database taken at this date |
| 12 | CVA | CVA data is loaded into the New IB when the page is loaded, so the version of this will always be visible in the New IB as "Data queried live" |
| 13 | OMIM | The OMIM data displayed in the New IB is a snapshot of the OMIM database taken at this date |
Abbreviations
| Abbreviation | Definition |
|---|---|
| ACGS | Association for Clinical Genomic Science |
| ACMG | American College of Medical Genetics and Genomics |
| CDS | Coding DNA Sequence |
| CNV | Copy Number Variant |
| CVA | Clinical Variant Ark |
| New IB | New Interpretation Browser |
| GEL | Genomics England |
| GMS | Genomic Medicine Service |
| GLH | Genomic Laboratory Hub |
| HGVS | Human Genome Variation Society |
| HTML | Hyper Text Markup Language |
| HSCN | Health and Social Care Network (N3) |
| IGV | Integrative Genomics Viewer |
| IP | Interpretation Portal |
| NGIS | National Genomics Informatics System |
| PID | Patient Identifiable Data |
| QC | Quality Control |
| SO | Sequence Ontology |
| SNV | Single Nucleotide Variant |
| SV | Structural Variant |
| TOMS | Test Order Management Service |
| UAT | User Acceptance Testing |
| VCF | Variant Call Format File |
| WGS | Whole Genome Sequencing |