Tumour region identification guided scoring (TRIGS) and foundation model-based Tumour Infiltrating Lymphocyte scoring are prognostic for pathological complete response/event free survival in the triple negative patients in the PARTNER randomized controlled trial

@misc{schouten2026tumour,
  title = {{Tumour region identification guided scoring (TRIGS) and foundation model-based Tumour Infiltrating Lymphocyte scoring are prognostic for pathological complete response/event free survival in the triple negative patients in the PARTNER randomized controlled trial}},
  author = {P. C. Schouten and M. O. Irfan and Z. Kinsella and A. Sionakidis and A. Riddell and J. R. Worley and J. Lay and S. Casford and K. Pinilla and J. Kane and D. Whitehorn and S. Tarantino and A. Dayimu and N. Demiris and H. M. Earl and N. Simidjievski and E. Provenzano and J. E. Abraham},
  howpublished = {medRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.15.26363116},
  url = {https://www.medrxiv.org/content/10.64898/2026.09.15.26363116v1},
  note = {CC BY-ND},
}

TY  - UNPB
TI  - Tumour region identification guided scoring (TRIGS) and foundation model-based Tumour Infiltrating Lymphocyte scoring are prognostic for pathological complete response/event free survival in the triple negative patients in the PARTNER randomized controlled trial
AU  - P. C. Schouten
AU  - M. O. Irfan
AU  - Z. Kinsella
AU  - A. Sionakidis
AU  - A. Riddell
AU  - J. R. Worley
AU  - J. Lay
AU  - S. Casford
AU  - K. Pinilla
AU  - J. Kane
AU  - D. Whitehorn
AU  - S. Tarantino
AU  - A. Dayimu
AU  - N. Demiris
AU  - H. M. Earl
AU  - N. Simidjievski
AU  - E. Provenzano
AU  - J. E. Abraham
PY  - 2026
DA  - 2026/09/15
PB  - medRxiv
DO  - 10.64898/2026.09.15.26363116
UR  - https://www.medrxiv.org/content/10.64898/2026.09.15.26363116v1
AB  - Assessment of tumour infiltrating lymphocytes (TILs) is a robust prognostic biomarker for HER2-positive and triple negative breast cancer. We aimed to update a previously established pipeline for automated TIL assessment to align to clinical scoring guidelines (tumour region identification guided scoring), foundation model-based lymphocyte detection (SAM-TIL) and compare with alternative methods (HoVerNet, muTILs) and gold standard clinical assessment.  TRIGS and SAM-TIL had an odds ratio of 1.95 (95% confidence interval(ci): 1.22-3.03, p=0.005) and 2.32 (95% ci:1.43-3.77, p=0.001) for predicting pathological complete response (pCR) rate in 166 neoadjuvantly treated patients in the TransNEO cohort. Hazard ratios for overall survival in 277 triple negative and HER2-positive patients in The Cancer Genome Atlas were 0.79 (95% ci: 0.63-1.00, p=0.05) and 0.80 (95% ci: 0.67-0.97, p=0.02) for TRIGS and SAM-TIL. Comparator methods showed similar results. Correlation with gold standard clinical assessment in 285 patients from the PARTNER randomized trial ranged from 0.59-0.69, which is substantially more than interobserver variability for the gold standard. Despite differences with gold standard assessment, no substantial difference in predicting pCR (AUC 0.60-0.64) or event free survival (Integrated Brier score approximately 0.10) were observed between the tested methods and gold standard assessment, suggesting AI tools that do not follow manual scoring guidelines could be validated and subsequently used.  Although we reached prognostic performance similar to published literature and gold standard assessment, the lymphocyte detections produced by the models are not interchangeable with gold standard clinical assessment (correlation 0.59-0.69) and therefore cannot support pathologist assessment. Further studies to validate independent use and/or to improve prognostication are required.
ER  -