How does heterogeneity and/or clonal diversity in the true population affect the amount of information we obtain
from samples of the true population?
It is currently unknown how statistically representative the biopsy is
of the full tumor or tumors present and how biopsy representativeness
changes as a function of features of the biopsy or the cancer itself.
Agent-based models (ABMs) present an opportunity to provide the
necessary data to answer this question.
The data for this project is from ARCADE
v2.2 POPULATION_HETEROGENEITY simulations, produced in November 2019. Simulations conditions include
context, population mixture, population heterogeneity, and background heterogeneity.
More information on ARCADE can be found at the ARCADE GitHub
repository and the paper.
Simulations are labeled as: `[context]_[populations]_[population heterogeneity]_[background heterogeneity]`
For data analysis, this project analyze data from simulation with varied cell line permutation and heterogeneity levels across the two contxt.
Below, we describe the specific features we looked at in the data. Namely, discrete and continuous features.
Index | Cell State Name |
---|---|
0 | NECRO_FRAC |
1 | SENES_FRAC |
2 | ENERGY_THRESHOLD |
3 | MAX_HEIGHT |
4 | ACCURACY |
5 | AFFINITY |
6 | DEATH_AGE_AVG |
7 | DIVISION_POTENTIAL |
8 | META_PREF |
9 | MIGRA_THRESHOLD |
Index | Cell State Name |
---|---|
0 | Neutral |
1 | Apoptotic |
2 | Quiescent |
3 | Migratory |
4 | Proliferative |
5 | Senescent |
6 | Necrotic |
We have cancer cell lines X, A, B, and C.
Cell Line | Index | Property |
---|---|---|
X | 0 | Cancerous cell population with basal parameters |
A | 1 | MAX_HEIGHT 8.7 -> 13.4 |
B | 2 | META_PREF 0.3 -> 0.45 |
C | 3 | MIGRA_THRESHOLD 3.0 -> 1.5 |
H | 4 | Healthy cells |
Heteoreneity is an intrinsic property of biological systems, even within clonal populations. In our model, all internal cell parameters are drawn from a normal distribution where mean (µ) = parameter value and standard deviation (σ) = heterogeneity (H) · µ. There are 5 intracellular heterogeneity levels varied at 0, 10, 20, 30, 40, and 50%.