SOP Section 9.4
Structured Narrative of Functional Impact is found under the Experimental Tab, in the Experimental Studies section.
In most cases, this field will display "No evidence added."
This field is not directly editable in the VCI. For more information visit: https://github.com/ClinGen/clincoded/wiki/FDP-Data-Capture-Entry
SOP Section 9.5
When working in the Add Evidence Details window, if you click outside the window before clicking Submit, the window will close and unsaved data will be lost.
The evidence source is indicated in the first line.
Details entered in the "Add [Source] Evidence" selection screen do not appear.
All ACMG criteria codes in the Case/Segregation tab have associated fields.
"#" fields accept numerical input only
For PP4, HPO terms only
Fields relevant to the specific criteria code will be noted with a green background.
There are optional free text "Comment" fields associated with each data point, as well as an "Additional Comments" field at the end.
For assistance using HPO Search, see HPO Search Help
The ACMG criteria are grouped in the VCI according to the evidence required for their evaluation. To evaluate them curators must navigate to the appropriate tab:
BA1
BS1
PM2
Missense | Loss of Function | Silent & Intron | In-frame Indel |
---|---|---|---|
PM1
BS3
PS3
BS2
PS4
BS4
PP1
PM6
PS2
BP2
PM3
BP5
PP4
Each of the VCI tabs with criteria codes also supports users in manually adding Curated Evidence.
The Basic Information and Gene-centric tabs are for reference only. They do not contain criteria requiring evaluation or fields to add curated evidence.
The pull-downs allow the following choices:
Not Evaluated: The default state of an Evaluation is “Not Evaluated”. This is the appropriate selection when there is no evidence to evaluate or the particular criterion is not applicable for the variant.
Met: If the evidence meets the specified rules for a given criterion, the curator should select “Met”. Curators should provide an explanation note for all Met criteria.
Not Met: Not met can be applied if:
No evidence is identified for the criterion, OR
There is evidence, but it is not sufficient, OR
Another mutually exclusive criterion has been met.
Curators should provide an explanation note for all Not Met criteria.
Strength: The strength of evaluation for a criterion can be adjusted by selecting a strength from the pull down menu for a specific criterion.
Examine evidence associated with criteria being evaluated
Select an evaluation for all criteria related to the evidence from the pull-down
Enter an explanation in the free text box to support your selection
Click Save
Correct the erroneous evaluation and then save to proceed.
At the bottom of each tab which includes criteria for evaluation, you will see the following checkbox:
If you have evaluated all of the evidence on a particular tab to your satisfaction, you can click the checkbox and a check will appear on the tab for your reference:
This is an optional tool available to help track your progress. It is not required and is not included in the evaluation summary.
As you save your evaluations, you will notice that the Criteria Bar will indicate which criteria have been “Met” (solid color background with white criteria code), “Not Met” (grey background with colored criteria code), or remain “Not Evaluated” (white background with colored criteria code).
Additionally, the Progress Bar will automatically calculate the pathogenicity each time you save or update an evaluation
The calculated classifications follow the ACMG/AMP 5 tiers and are as follows:
Benign
Likely benign
Uncertain significance
Pathogenic
Likely pathogenic
SOP Section 7.2
Following the evaluation of each criterion (or group of criteria), curators may include associated Curated Evidence.
The Population, Variant Type, and Experimental tabs include fields to add Curated Literature Evidence by PMID.
The Case/Segregation tab (see next section) includes Curated Evidence fields which allow for additional types of evidence (e.g. Clinical Lab).
Navigate to the criteria evaluation to which you wish to add literature evidence.
Click "Add PMID" to open the "Add new PubMed Article" selection screen.
Enter PMID and click "Retrieve PubMed Article."
Confirm the retrieved citation is correct and click "Add Article."
The citation will now appear under Curated Literature Evidence.
Select the appropriate criteria code from the pulldown menu and enter a description of relevant data in the "Evidence" text box.
Click "Add Evidence". Note, both fields must be completed to proceed.
The literature evidence is now added to the evaluation along with the curator's name (and affiliation if applicable) and date/time added.
If you wish to change the criteria code or revise the evidence text summary, click Edit.
If you would like to remove the article completely, click Delete. You will be prompted to confirm deletion and have the option to cancel if you clicked delete in error.
You may now move on to evaluate other criteria, or click Add PMID to add additional article(s) to this section.
The curated literature evidence is viewable by all curators, but the Edit and Delete options are only available to user who added it.
SOP Section 9.5
Do NOT enter protected health information (PHI) in the VCI
(See yellow box at top of VCI Case/Segregation Tab)
A. If no curated evidence has been associated with this variant, the ACMG criteria codes for evaluation immediately follow the yellow box. Curated Evidence may be associated with the following individual and pairs of criteria (from top to bottom): BS2, PS4, BS4/PP1, PM6/PS2, BP2/PM3, BP5, and PP4.
B. If curated evidence has been added (to the current interpretation or a prior one), a table summarizing all entered evidence will appear before the criteria codes. This table will auto populate with any new submitted evidence.
Scroll down or select a criterion from the Criteria Bar.
Evaluation of criteria may be completed before or after adding Curated Evidence.
Before adding evidence, you must select an evidence source.
Choose an option from the "Select Source" pulldown
Available fields vary based on the source:
The first field is required (indicated with *). Additional fields are optional.
Each record has a viewable audit trail displaying which curator performed which actions at which time.
To access the audit trail, click on the button.
The audit trail is organized in reverse chronological order (i.e., the most recent records are listed first) and is only viewable by the record owners (either an individual or all members of an affiliation). The audit trail can also be searched.
Once the evaluation has been successfully saved, the interface will display:
When 2 (or more) criteria are opposites or cannot otherwise be “Met” at the same time, the save will not be successful and the interface will display:
Click to open the Add [Source] Evidence selection screen.
After filling in field(s), click to open the Add Evidence Details selection screen.
BP1
PP2
PP3
BP4
PM5
PS1
PVS1
BP7
BP3
PM4