The AIM assay makes up part of the CMI-Flu prediction challenge. An overview of all the data, including links to more detailed descriptions of the other data, may be found at https://cmi-x.org/prediction-challenges/

Experimental protocol

PBMC were thawed and stimulated for 24h with (last 4h of stimulation with Golgi Stop/Plug):

  • DMSO: negative control
  • GLO: HA universal peptide pool: overlapping 15-mer covering the HA proteins from the virus strains contained in vaccines spanning 2017-2019 seasons + epitopes with experimental data available in IEDB.
  • PR8 backbone pool : overlapping 15-mer peptides covering all non-HA and non-NA proteins of the H1N1 A/Puerto Rico/8/1934 (PR8) strain (8 proteins total: M1, M2, NP, NEP, NS1, PA, PB1, PB2).
  • CON: Conserved HA/NA pool: overlapping 15-mer peptides covering conserved HA/NA epitopes from H1N1 and H3N2 vaccine strains from the past 10 flu seasons, starting in 2024/2025 season
  • SEA: Seasonal HA/NA pool: overlapping 15-mer peptides covering novel (i.e., absent from the conserved HA/NA pool) HA/NA epitopes from H1N1 and H3N2 strains in the 2025/2026 flu season.
  • POL: Polyclonal stimulation: antiCD3+anti-CD28, positive control Following stimulation, cells were stained with a 23-color surface and intracellular panel, and analyzed on a Cytek Aurora spectral analyzer. Antigen-specific CD4 T cells were defined as Live/CD14-CD19-/CD3+/CD4+CD8-/OX40+CD137+. DMSO (negative control) frequencies were subtracted from cell frequencies and values <0.01 were assigned to 0.01

The Data

Data tables

The AIM data consists of 1 table : 2025LJI_AIM.tsv (which contains pre-vaccination data).

Antigen-reactive T cell Assay (AIM)
Data dictionary
Column Description
participant_id Donor ID, one for each subject in each study, in the format studyID.subjectID (links to participants.tsv)
timepoint Days relative to influenza vaccination (-14 or 0), or 'Pre-vacc' for the mean of the two pre-vaccination timepoints.
stimulation Peptide pool used to stimulate the PBMC: Global (GLO), Conserved (CON), Seasonal (SEA), PR8_backbone (PR8), or Polyclonal (POL, positive control).
name Measured cell population: Antigen-reactive CD4 T cells.
value Frequency of the measured population as a percentage of parent_population, after subtraction of the matched DMSO control. Values below 0.01 are floored at 0.01.
unit Unit of measurement (percent).
parent_population Denominator population for value: CD4 T cells.
population_definition Gating strategy.
material Antigen-specific CD4 T cells.
comments Batch in which the sample was acquired (Round 1 - Round 8).
study_accession Study identifier.
subject subject ID.
  • Pre-vaccination data : Day0 timepoints are available.

Across all assay data, we also provide a “Pre-vacc” measure, which is the mean of all pre-vaccination timepoints for each subject and each cytokine. In the case of the cytokine data, “Pre-vacc” measures will be the same as Day 0 measures since there are no other pre-vaccination timepoints.

TBC

Data exploration

library(tidyverse)
aim = read_tsv('../datasets/260512/train/2025LJI_aim.tsv')
head(aim)
## # A tibble: 6 × 12
##   participant_id  timepoint stimulation  name      value unit  parent_population
##   <chr>           <chr>     <chr>        <chr>     <dbl> <chr> <chr>            
## 1 2025LJI.SUB1829 -14       Polyclonal   Antigen-… 18.6  perc… CD4 T cells      
## 2 2025LJI.SUB1829 -14       Conserved    Antigen-…  0.16 perc… CD4 T cells      
## 3 2025LJI.SUB1829 -14       Seasonal     Antigen-…  0.01 perc… CD4 T cells      
## 4 2025LJI.SUB1829 -14       Global       Antigen-…  0.12 perc… CD4 T cells      
## 5 2025LJI.SUB1829 -14       PR8_backbone Antigen-…  0.13 perc… CD4 T cells      
## 6 2025LJI.SUB2491 -14       Polyclonal   Antigen-… 24.5  perc… CD4 T cells      
## # ℹ 5 more variables: population_definition <chr>, material <chr>,
## #   comments <chr>, study_accession <chr>, subject <chr>

TBC

Prediction Task

Task 1.4 asks contestants to predict the frequency of antigen-reactive CD4+ T cells (conserved pool), for the 40 donors found in the 2025LJI challenge dataset.

More details about all tasks are available here: https://docs.google.com/spreadsheets/d/1mmnSfJ2t24-AfBugTbLcAwcIdg3-I_v1X93WFWS3HxY/edit?gid=0#gid=0

#TBC