Volcano plot substeam kickoff meeting 03-25-2021

[xni7]

Attendees

• Dennis O'Brien
• Scott Wong
• Asli Memisoglu
• Xiao Ni

Meeting minutes

• Team discussed roadmap toward Volcano plot V 1.0 release, prioritization and aligned on the following
  • Postpone the User Guide development until a stable prototype is ready
  • The focus now is to determine the requirements for a minimal viable product for Version 1 release this year
• Team reviewed two prototypes shared by Xiao and discussed the main features for V1
  • "Review by" - MEDDRA hierarchy and SMQ could be useful. Would be helpful to keep "Other" but allow users to designate a custom name. Note the "other" classification would require user to provide the grouping in the AE data.
  • "Period" - it would useful to allow user to designate a numerical window to define "TEAE". Consider last dose date + X days
  • "Measure of Association". Need to add statistical guide on the choices.
  • Treatment Group Selection. It seems useful to allow users to select multiple active treatment doses to pool them. Selecting high dose vs. low dose arm may provide an assessment of dose-dependency.
  • "Subgroup Variable" - would be useful to correlation medical history and other patient characteristics with AE findings to help causality assessment and better understand the etiology. Another idea is to capture / save a list of patient IDs.
  • "Y-axis reference line" it could be confusing to have two horizontal reference lines, unadjusted p = 0.05 and corresponding adj p threshold. Consider having one single reference line by default.
  • "p value option" It is okay to keep existing implementation of unadj + FDR adj. Need some statistical documentation to educate non-stats users.
• Desirable Interactivity and Drill down capabilities
  • Linking Volcano plot to AE Explorer to show % of PTs
  • Click on a SOC dot to expand into PT clusters
  • Displaying two linked Volcano plots, e.g., Plot1 = SOC, Plot2 = PT. Clicking SOC dot will highlight PT cluster on the other
  • Displaying two linked Volcano plots, e.g., Plot1 = High dose vs. Placebo, Plot2 = Low dose vs. Placebo. Clicking one dot will highlight corresponding event on the other

Actions

• Asli to provide statistical guidance for "Measure of Association" and "p value option"
• Xiao provided the links to the two prototype apps (see below)
• Xiao pushed a dev branch to safetyGraphics/volcanoPlot
• Team to review the prototypes and minutes. Log new issues on Github. next meeting in ~2wks

Prototypes

• BI initial version
  • https://xiao-ni.shinyapps.io/volcano-plot/
• ISG dev version
  • https://git866.shinyapps.io/volcano-plot/