Case Summary

Opening a case from the case list or the IP will take a user to the case summary page by default.

Features

• View any case warnings
• Review patient information
• View the summary of analysis
• Link out to the variant list pages
• Link out to the global analysis plots
• View the sample and sequencing information from the referral
• Check the Cellbase and Tiering software versions

Case WarningsCase HeaderCase InformationSummary of AnalysisSample and Sequencing Quality InformationAdditional information

Case warnings (sample or pipeline alerts) will appear at the top of the screen in a dropdown, as shown below.

Please refer to the Analysis guide for further information on case warnings.

The case header contains the patient name, year of birth and NHS number. Additional patient and case information can be found on the top right of the banner by clicking the respective drop down menus.

Patient InfoCase Info

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	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.

Info

Non-NHS users will be unable to see certain patient information, including the patient's name, date of birth and NHS number. Only the patient sex, patient ID and Clinical Indication will be visible.

Key

#	Section	Description
1	Referral ID	The Referral ID for the patient.
2	Case type	The samples included in the analysis e.g. Tumour and Germline or Tumour First, Germline Later.
3	Case status	Interpretation Status of the case, e.g. whether the analysis is in progress or the case is awaiting authorisation. See case management for more info

For information on the case status, please see the Getting Started guide.

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 DSS.
3	Referral Priority:	Priority for the case, e.g. “Routine” or “Urgent”.
4	Referral ID	The Referral ID for the patient.
5	Ordering hopsital	Requesting organisation defined during test ordering.
6	Interpreting lab	Interpreter organisation defined during test ordering.
7	Patient choice	The patient’s consent status, e.g. Yes or No.
8	Patient ID	The patient’s ID as captured from TOMS.

Tumour and GermlineTumour First (Germline Later)

Key

#	Section	Description
1	Summary of analysis	Summary of the domained somatic and tiered germline variants identified by the Cancer interpretation pipeline.
2	Circos plot	Plot that illustrates the distribution of somatic variants across the genome.

Info

Tumour first analysis (i.e. performed without an accompanying matched germline sample) is not yet in the scope of accreditation for the Genomics England Pipeline. Therefore, any finding should be validated before use.

Key

#	Section	Description
1	Summary of analysis	Summary of the domained somatic variants identified by the Cancer interpretation pipeline.
2	Circos plot	Plot that illustrates the distribution of somatic variants across the genome. This plot cannot be generated in the absence of a paired germline sample.

Info

Variant filtering for reported variants in tumour first cases in the cDSS may differ from that in HTMLs: in these cases, we apply both somatic and germline prioritisation algorithms to all variants with GEL internal population germline allele frequency under 2%, so all such variants will appear on the cDSS. In the HTMLs and CSV tables, all variants with either GEL internal or gnomAD population germline allele frequency over 1% and no potential effect on cancer predisposition genes (nothing in the "Interpretation as germline" field) are filtered out. We are currently working on fully harmonising the variant lists between cDSS and HTML, and this discrepancy will disappear soon.

Tumour Sample Germline Sample

Key

#	Section	Description
1	Tumour information	Information about the tumour provided by the referral.
2	Tumour sample information	Information about the tumour sample, provided by the referral and generated from the whole genome sequencing data.
3	Tumour sequencing quality information	Information about the coverage, and other details about the quality of the sequencing from the tumour sample.

Info

Calculated tumour content will not be available if a sample has a 'Low tumour purity' sample alert displayed at the top of the case summary. Tumour content cannot be reliably estimated from the data in these samples.

Key

#	Section	Description
1	Germline sample information	Information about the source; storage medium; type; primary or metastatic; and other details about the germline sample.
2	Germline sequencing quality information	Information about the coverage, and other details about the quality of the sequencing from the germline sample.

Here, you can find additional information on the case. For example, the Cellbase version it was annotated with.

Key

#	Section	Description
1	CellBase version	The version of Cellbase and the data release (if applicable) that the sample was annotated with.
2	Tiering software version	The version of the tiering pipeline used to prioritise the variants into domains/tiers.