Soluble IL-2R × ICI

Soluble IL-2 receptor draws before and after immune checkpoint inhibitors

Project overview

This site publishes the Quarto pipeline behind a cohort count for the soluble IL-2 receptor (sIL2R, CD25) project: of everyone at Mass General Brigham with an sIL2R drawn, who had already received an immune checkpoint inhibitor (ICI) when the level was drawn, and how many were measured more than once afterwards.

Stage	File	Role
Data management	`data_management.qmd`	Read the RPDR extract and the ICI pull; rename `EMPI MRN` → `EMPI`; convert `SCHEDULEDSTARTDTS` to a date; classify every IL2R result; linkage QC
Analysis	`analysis.qmd`	Cohort flow, the three requested counts, RPDR medication / diagnosis cross-check, sensitivity analyses

The requests

Table 1: Headline counts (primary definitions; see Analysis for definitions, sensitivity analyses and caveats).

Request	N
RPDR patient set (sIL2R lab result OR Epic sIL2R order code)	3,171
… with >= 1 sIL2R row in the RPDR Lab file	2,321
… with >= 1 numeric sIL2R Result on/after 2015-01-01 (all-pre-2015 excluded)	2,202
Request 1: had an ICI (any dose) before the sIL2R was drawn	464
Request 2: … and had at least 2 measurements after the ICI	117
Request 3: post-2015 patients NOT found in the ICI cohort	1,711
No IL2R result row (no draw date), not in the ICI cohort	682

Data privacy

Patient-level identifiers (EMPI, MRN, names, dates of birth) never appear in any rendered output. Tables contain only aggregate counts; counts from 1 to 10 are shown as <11, with a second cell hidden where a total would reveal it.

The raw RPDR extract, the ICI pull, the EMPI-keyed cache and the chart-review workbook stay on the local machine and are excluded from this repository by .gitignore. Only the code and the aggregate results are published here.

Data sources (local only, not in this repo)

ICI_data_pull_07172026.csv: ICI administrations (Epic MAR, one row per bag hung)
RPDR extract MES98_20260811_112907 (Mrn / Lab / Med / Dia): Mass General Brigham Research Patient Data Registry, pulled 2026-08-11 under IRB 2022P001091

Reproducing

cp R/paths_template.R R/paths_local.R   # then edit the local file paths
Rscript R/build.R                       # local PHI step -> cache/ and output/
quarto render                           # aggregate-only site -> _site/

Dependencies

R packages: data.table, knitr, writexl.