TY  - JOUR
AU  - Brix, Nikko
AU  - Samaga, Daniel
AU  - Gehr, Katharina
AU  - Dankó, Benedek
AU  - Schumann, Mohamed
AU  - Drexler, Guido
AU  - Alnatsha, Ahmed
AU  - Beyer, Georg
AU  - Mahajan, Ujjwal
AU  - Selmansberger, Martin
AU  - Mayerle, Julia
AU  - Belka, Claus
AU  - Zitzelsberger, Horst
AU  - Lauber, Kirsten
TI  - LDAcoop: Integrating non-linear population dynamics into the analysis of clonogenic growth in vitro.
JO  - Molecular oncology
VL  - nn
SN  - 1574-7891
CY  - Hoboken, NJ
PB  - John Wiley & Sons, Inc.
M1  - DKFZ-2025-03060
SP  - nn
PY  - 2025
N1  - epub
AB  - The limiting dilution assay (LDA) is a key method to quantify clonogenic cells with self-renewing capacity in vitro, crucial for preclinical cancer research and therapy response assessment. It estimates the frequency of individual clonogenic, stem-like cells within a population based on their ability to form colonies with ≥50 cells at limiting cell numbers. Standard LDA analysis relies on linear, single-hit Poisson models, yet clonogenic growth under single-cell conditions often involves cooperative or competitive dynamics, violating this linearity assumption. Here, we present a modeling framework incorporating non-linear population dynamics into LDA analysis and introduce LDAcoop, an R-based tool for universal quantification of clonogenic cells in LDA formats. Across multiple cancer cell types, we benchmarked LDA against the colony formation assay (CFA) and show that LDA outperforms CFA, especially for patient-derived organoids, suspension cultures, and higher throughput applications. This renders the LDA format particularly suitable for larger-scale pharmacogenomic screening and drug sensitivity testing in complex models. Our results establish LDA and LDAcoop as versatile, scalable tools for robust quantification of clonogenic growth, supporting preclinical drug development and molecular precision oncology research.
KW  - Allee effect (Other)
KW  - cellular competition (Other)
KW  - cellular cooperation (Other)
KW  - clonogenic growth (Other)
KW  - clonogenic survival (Other)
KW  - limiting dilution assay (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:41454442
DO  - DOI:10.1002/1878-0261.70185
UR  - https://inrepo02.dkfz.de/record/307461
ER  -