Case Summary¶
Opening a case from the case list or the IP will take a user to the case summary page by default. From this page, users are able to:
- Check the release version of the DSS
- View any case warnings displayed across the top of the page
- Review the case and 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 info from the referral
Case Header¶
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 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.
Case Info¶
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 case management.
Case Information¶
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 |
Summary of Analysis¶
Tumour and Germline¶
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
This circos plot does not represent a real patient tumour sample.
Tumour First (Germline Later)¶
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. 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 should disappear soon.
Sample and Sequencing Quality Information¶
Tumour Sample¶
Key
| # | Section | Description |
|---|---|---|
| 1 | Tumour information | Information about the Tumour type; primary or metastatic; presentation and other details about the tumour. |
| 2 | Tumour sample information | Information about the tumour content of the tumour sample, both from the lab as from the whole genome sequencing data. Tumour content is shown in percentages: <40% is low tumour content. 40-60% is medium. >60% is high. |
| 3 | Tumour sequencing quality information | Information about the coverage, and other details about the quality of the sequencing from the tumour sample. |
Germline Sample¶
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. |
Case warnings¶
Cases that do not pass the quality control checks performed on the genomic data will show a warning tat the top of the case summary page. Please refer to the Analysis guide for further information. The warnings could include the following:
| # | Section | Description |
|---|---|---|
| 1 | Low level cross-patient tumour contamination | Cross-patient contamination in a tumour sample between 1% and 2.5%. Sample may have higher incidence of contaminating germline variants reported in the somatic variant calls. |
| 2 | Low tumour purity | Calculated tumour content <30% and/or >40% of somatic variants with <6% VAF. Sample may have reduced sensitivity for somatic variants, which may also impact calculation of tumour mutation burden and mutational signatures. |
| 3 | Potential low-quality sample | Tumour sample fails one or more of the sequencing quality control thresholds applied for evenness of coverage, GC dropout, AT dropout and average fragment size. As a result, there may be an increased risk of false positive or negative variants. |
| 4 | Low germline coverage | Mean germline coverage <15x OR less than 95% of the reference genome is covered with a minimum of 15x. Low germline coverage affects the efficiency of somatic variant detection such that sensitivity is reduced, potentially below 95%. This results in an increased risk of false negative results and tumour mutation burden and mutational signatures are not reliably calculated. Sensitivity and precision of germline variant detection may also be reduced. |
| 5 | Low level cross-patient germline contamination | Cross patient contamination in a germline sample between 3% and 8%. Germline variants are not reported due to the risk of false positives. Validation experiments show that somatic variant detection is not affected by germline contamination levels between 3-8% therefore somatic variants are reported. |
| 6 | Low tumour in normal (TiN) contamination | The germline sample has a low level of contamination with DNA derived from the tumour (between 1% and 5%). Consequently, the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. |
| 7 | High tumour in normal (TiN) contamination | Germline sample has a high level of contamination with DNA derived from the tumour (above 5%). Consequently, the sensitivity of somatic variant detection is likely to be reduced, resulting in an increased risk of false negative findings. |
| 8 | Results not accredited | This analysis was performed on a sample type that is not in the scope of accreditation for the Genomics England Pipeline. Any finding should be validated before use. |
| 9 | No quality warnings | If there aren’t any warnings reported, there won’t be any shown on the case summary page. |
TINC Case warnings¶
Haematological cases have additional tumour in normal (TINC) quality checks, following Tumour in Normal contamination warnings could appear for a case:
| # | Section | Description |
|---|---|---|
| 1 | TINC high | The germline sample for this patient is likely to be contaminated with DNA derived from the tumour. Consequently, the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample. |
| 2 | TINC LOW | The germline sample for this patient is likely to be contaminated with DNA derived from the tumour. Consequently, the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample. |
| 3 | TINC error | The results of the computational estimation of tumour in normal contamination (TINC) are not reliable for this patient (which may be due to low tumour content in the tumour sample, or very high tumour contamination in the germline sample). Consequently, TINC cannot be excluded, and the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. To mitigate the potential loss in sensitivity, the results of somatic variant calling with an unmatched germline sample are included in this analysis alongside subtraction with the patient’s germline sample. |
| 4 | Tumour in normal contamination estimation not available | The computational estimation of tumour in normal contamination is not reliable (likely due to low tumour content in the tumour sample). Consequently, TiN cannot be excluded and the sensitivity of somatic variant detection may be reduced, potentially resulting in an increased risk of false negative findings. |
| 5 | TINC None | If there aren’t any TINC quality flags reported, there won’t be any warnings shown on the case summary page. |
Last update:
2024-05-07