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Add an Association in Knowledge Network

When you have determined that an association exists between a gene or variant and a particular disease, record the association in Knowledge Network.

Association data and evidence citations appear in reports. For information about including associations in a case report, see Reports.

1. From the Knowledge Network, select Add Association.
2. Specify the following association data:
• Biomarker type
• Transcript type
• VEP version
• Genome build
• Curation level
• Curation details
3. If curation details include position data, select Verify.
• If there are errors, correct the data and select Verify.
• If there are no errors, select a transcript from the Transcript drop-down menu.
4. Select Next.
5. Select Mendelian from the Association Type drop-down menu.

NOTE

Knowledge Network supports only Mendelian associations for BaseSpace Variant Interpreter.

6. Select Next.
7. Complete the Association Details fields. Details vary by association type.
8. For SNV nucleotide associations, add evidence as follows. Evidence criteria are used in the association details calculated classification.
  1. Select Add New Criteria and then select the ACMG criteria level.
  2. [Optional] Select a different evidence strength. The default strength is determined by the selected criteria.
  3. To exclude criteria from the calculated classification, select Do not apply to calculation.
  4. In the Rationale field, add your rationale for the criteria.
  5. Select an evidence type and complete the evidence fields. Criteria require at least one evidence.
  6. To add more evidence to a criteria level, select Add Evidence.
9. For all other associations, add evidence as follows.
  1. Select Add New Evidence and then select the evidence type.
  2. Complete the evidence fields.
10. Select Save.
ClosedEdit an Association
1. Open the association and select Create Draft.
2. Select Edit.
3. Modify association details, criteria, and evidence as needed.

NOTE

Changing the phenotype creates a new association with the selected phenotype and disables the original association.

4. Select Approve.