Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
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15 months ago
E-HR • 0

We came across a project in our lab that no one exactly knows how to approach. Since I know a little bit of Python programming, this project was assigned to me.

There is a data from a randomised controlled clinical trial with 60 participants. Half (30) are control and the other half are actual patients (case). From each group, biopsy samples were taken before (pre) and after (post) treatment with drug A that targets cell type B in the tissue.

In each biopsy sample, the B cells were detected and classified either as “normal” or “malignant”.

Associated metadata for each biopsy are displayed here (I have only included 12 records for this file):

name    patient_id  arm treatment
111     0       control     pre
112     1       control     pre
113     2       control     pre
121     0       control     post
122     1       control     post
123     2       control     post
211     75      case        pre
212     76      case        pre
213     77      case        pre
221     75      case        post
222     76      case        post
223     77      case        post
  • name: spreadsheet file name
  • patient_id: patient identity number
  • arm: trial arm (‘case’ or ‘control)
  • treatment: treatment condition (‘pre’ or ‘post’ treatment)

Other files (I have only included 20 records for each file: 10 normal and 10 malignant) contain cell detection results from a single biopsy, and each row in a spreadsheet represents an individual detected cell:

  • x: x coordinate
  • y: y coordinate
  • label: classified label (‘normal’ or ‘malignant’)

Just showing an example, file 111 looks like this:

x   y   label
730 724 normal
1962 450 normal
1511 817 normal
1244 455 normal
2529 397 normal
1878 262 normal
2248 369 normal
2007 273 normal
1531 878 normal
1729 834 normal
931  1270 malignant
1282 314 malignant
1630 839 malignant
1543 460 malignant
2493 237 malignant
1311 744 malignant
1999 366 malignant
737 1361 malignant
2252 448 malignant
2620 398 malignant

The rest can be found here, but probably they will not be necessary: https://www.mediafire.com/file/ka7r59kf0swnbnd/OtherFiles.rar/file

I am trying to answer 3 questions here (if you can think of other questions, please let me know):

  • identifying post-treatment morphological changes due to the effect of drug A.
  • proposing measures to quantify the changes.
  • Using appropriate statistical analysis tools to provide insight whether the changes are due to chance or not.
drug-effect statistical-analysis • 628 views
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The linchpin is what features you are interested in; can you describe them in plain English? Something like "how many of the cells are malignant" or "how interspersed malignant cells are with normal cells" or "how diffuse malignant cells are from each other"?

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Had not thought about these questions.

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Are the x and y coordinates important for calculating i.e. some general area/density of cells or something like that? Otherwise you have few data columns: patient_id, arm, treatement, cells_norm, cells_malignant, cells_total

Assuming the control arm patients also have biopsies at two time points you can estimate variation due to a fact that biopsies are from different spots and sometime apart.

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