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Add an Association in TruSight Software

Record variant associations from the Variant Details tab.

For information about including associations in a case report, see Reports.

ClosedAdd a Variant Association

Add an association for a specific variant. The association is recorded in your knowledge network as a Mendelian association at the nucleotide level.

For information about the association options, see Association Details.

1. Select a variant in the grid and then select the Variant Details tab.
2. In the Variant Details tab, select Add New Association.
3. To copy data from a gene association, select Import from Gene Associations, and then select the gene association.

Phenotype and Mode of Inheritance values are copied to the association.

4. Add one or more diseases or phenotypes as follows.
  1. In the Disease/Phenotype field, enter a disease or phenotype.
    As you type, a list of possible matches appears to assist your search. The name of the ontology is displayed in parentheses after the phenotype name.
  2. Select an entry from the list or press Enter to accept the first match.
  3. To add a custom disease or phenotype, select Add Term.
  4. To remove an entry, select ×.
5. Enter the following information:
• Classification
• Mode of Inheritance

NOTE

Mode of Inheritance is automatically selected when importing data from a gene association.

6. For SNV associations, add evidence as follows. Evidence criteria are used in the association details calculated classification.
  1. Select ACMG Calculation and then select one or more ACMG criteria levels. The calculated classification is updated to include the selected levels.
  2. For custom criteria, select the Evidence Support.
  3. [Optional] Select a different evidence strength. The default strength is determined by the selected criteria.
  4. To exclude criteria from the calculated classification, select Exclude from calculation.
  5. In the Rationale field, add your rationale for the criteria.
  6. Select an evidence type and complete the evidence fields. Criteria require at least one evidence.
  7. To add more evidence to a criteria level, select Add Evidence.
7. For all other variant types, add evidence as follows.
  1. Select Add Evidences.
  2. In the Add Evidence dialog, select Add Evidence.
  3. Select an evidence type and complete the evidence fields.
  4. To add more evidence to a criteria level, select Add Evidence.
  5. [Optional] Enter a brief description in the Curator Notes field. Curator notes do not appear on the report.
  6. Select Save.
8. [Optional] Enter a brief description in the Curator Summary field.
9. Select Save.

The association is saved and the status is listed as Enabled.

ClosedAdd a Gene Disease Association

Add an association for a specific gene in the case. The association is recorded in your knowledge network as a Mendelian association at the gene level. The gene may be associated with either a small variant or a structural variant type, but not both.

For information about the association options, see Association Details.

1. Select a variant in the grid and then select the Gene Details tab.
2. In the Gene Details tab, select Add New Association.
3. Add one or more diseases or phenotypes as follows.
  1. In the Disease/Phenotype field, enter a disease or phenotype.
    As you type, a list of possible matches appears to assist your search. The name of the ontology is displayed in parentheses after the phenotype name.
  2. Select an entry from the list or press Enter to accept the first match.
  3. To add a custom disease or phenotype, select Add Term.
  4. To remove an entry, select ×.
4. Enter the following information:
• Classification
• Mode of Inheritance
• Mechanism
• Penetrance ratio
5. [Optional] Add evidence as follows.
  1. Select Add Evidences.
  2. In the Add Evidence dialog, select Add Evidence.
  3. Select an evidence type and complete the evidence fields.
  4. To add more evidence to a criteria level, select Add Evidence.
  5. [Optional] Enter a brief description in the Curator Notes field. Curator notes do not appear on the report.
  6. Select Save.
6. [Optional] Enter a brief description in the Curator Summary field.
7. Select Save.
ClosedAdd a Gene Information Association

Gene information associations record general information about the gene to your knowledge base. The gene may be associated with either a small variant or a structural variant type, but not both.

1. Select a variant in the grid and then select the Gene Details tab.
2. In the Gene Details tab, select Gene Information Association.
3. Enter a description in the Gene Information field.
4. Select Save.

The association is saved and the status is listed as Enabled.