Additional help resources¶
Congenica’s full user guide is available from the footer in Congenica application or via this link
This opens an HTML5 version of the guide in a new browser tab.
Users can search, browse or use the table of contents to find the information they need.
Details of additional features to aid variant review are described in depth in this full user guide.
Genomics England Service Desk¶
- Email: ge-servicedesk@genomicsengland.co.uk
- Phone: 0808 281 9535
For urgent queries, please contact us on the above phone number (available between 0900-1700, Monday – Friday, excluding bank holidays).
For help with a technical issue (e.g. a problem with the Congenica interface), please put "Technical Result Query" in the email header, alternatively for help with a clinical issue (e.g. a questions about tiered variants) then please put "Clinical Result Query" in the email header.
Using the correct terminology in the email header will allow us to ensure that the email is directed to the most appropriate person. Please include the request ID (e.g. SAP- 123-1) and or referral ID in the subject of the email where possible.
Abbreviations & Definitions¶
| Abbreviation | Description |
|---|---|
| ACMG guidelines | The American College for Medical Genetics and Genomics “Standards and Guidelines for the interpretation of sequence variants” Genetics in Medicine (2015) 17, 405–423 doi:10.1038/gim.2015.30 |
| Additional Findings | The variants that have been looked for in addition to Main Findings and consented to by the patient. Referred to as ‘Secondary Findings’ within Genomics England developed systems. |
| API | Application Programming Interface. Enable computer applications to communicate with each other, e.g. the GeL Dispatch API enables the GeL Tiering Application to communicate with the CIP applications. |
| BAM | Binary Alignment Map of an individual’s genome. |
| CIP | Clinical Interpretation Partnership |
| ClinVar | Online database that archives and aggregates information about relationships among variation and human health. |
| CVA | Clinical Variant Ark |
| ExAC | The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. http://exac.broadinstitute.org/ |
| Family ID | Links individual family members in the QC portal. Family ID in other LabKey databases may differ. |
| GeL ID | Patient identification number of the family member assigned by Genomics England. |
| Genomic Sex | Sex based on the number of observed Y chromosomes. Male if at least one Y chromosome, otherwise Female |
| GLH | Genomics Laboratory Hub |
| GMS | Genomics Medicine Service |
| JSON | JSON (JavaScript Object Notation) is a lightweight data-interchange format used to encapsulate Genomics England’s interpreted genome and interpretation request through the CIP-API. |
| LabKey | Data Server hosting patient clinical and demographic information, excluding VCFs and BAMs. |
| Log-in | Username and password |
| Main Findings | The variants that have been found and associated with the disease/disorder for which the patient has been referred. Called ‘Primary Findings’ within Genomics England developed systems. |
| Number of X Chromosomes used for interpretation | Count of observed X chromosomes in the patient used by interpretation services |
| HSCN | Secure network with firewalls used for NHS-based systems |
| PanelApp | PanelApp (Open Source) was created to enable virtual gene panels to be viewed and commented on by experts - https://panelapp.genomicsengland.co.uk/ (Best viewed in Firefox or Safari browsers) |
| Primary Findings | The variants that have been found and associated with the disease/disorder for which the patient has been referred. |
| QC Check | Quality Control checks to assess accuracy and quality of data. |
| Request ID | Unique ID that includes pedigree, gene panels and versions, HPO terms, disease penetrance and variant classification and is used by CIPs and Genomics England to transfer information between their systems. |
| Reported Sex | Sex as identified by the patient . Can be Male, Female or Unknown |
| Interpretation Request ID | Unique ID that includes pedigree, gene panels and versions, HPO terms, disease penetrance and variant classification and is used by CIPs and Genomics England to transfer information between their systems. |
| SAP ID | ID for a case in the Congenica system. |
| Secondary Findings | The variants that have been looked for in addition to Primary Findings. Users should not use this option in the Congenica system, as the variant will appear in the Summary of Findings as a Primary Finding. |
| SNV | Single Nucleotide Variant |
| STR | Short Tandem Repeat variants |
| SV | Structural Variant, including Copy Number Variants (CNVs) |
| Tier | Flag used by Genomics England to signify variants of potential relevance to the patient’s condition - will be automatically categorised into 3 tiers to aid evaluation. |
| VCF | Variant Call Format file of an individual’s genome. |