ClinGen / gene-and-variant-curation-tools

ClinGen's gene and variant curation interfaces (GCI & VCI). Developed by Stanford ClinGen team.
https://curation.clinicalgenome.org/
MIT License
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Update the logic and language for the GCI classification point cutoffs #383

Open cgpreston opened 1 week ago

cgpreston commented 1 week ago

This project will need to be synchronized with the SOP 12 release, expected in late summer 2025.

For the GCI classification the current logic for the points that equal classifications is stated in the GCI:

Screenshot 2024-11-18 at 2 41 26 PM

This stated logic matches the SOP 11 logic, however:

   if (totalPoints >= 0.1 && totalPoints <= 6) {
      autoClassification = "Limited";
    } else if (totalPoints > 6 && totalPoints <= 11) {
      autoClassification = "Moderate";
    } else if (totalPoints > 11 && totalPoints <= 18 && !replicatedOverTime) {
      autoClassification = "Strong";
    } else if (totalPoints > 11 && totalPoints <= 18 && replicatedOverTime) {
      autoClassification = "Definitive";

The goal would be to do the following:

  1. Update the logic in all three places (GCI summary table, GCI logic, SOP) at the same time
  2. Update it as follows:
    • Between 0.1 and up to 6.5 is "Limited"
    • Between 6.5 and up to 11.5 is "Moderate"
    • Equal to or above 11.5 without "Replicated over time" is "Strong"
    • Equal to or above 11.5 with "Replicated over time" is "Definitive"
      if (totalPoints >= 0.1 && totalPoints < 6.5) {
      autoClassification = "Limited";
      } else if (totalPoints >= 6.5 && totalPoints < 11.5) {
      autoClassification = "Moderate";
      } else if (totalPoints >= 11.5 && totalPoints <= 18 && !replicatedOverTime) {
      autoClassification = "Strong";
      } else if (totalPoints >= 11.5 && totalPoints <= 18 && replicatedOverTime) {
      autoClassification = "Definitive";

SP ticket: https://broadinstitute.atlassian.net/browse/CGSP-795