To Generate biological hypotheses based on the specific genetic abnormalities of the cancer cell lines.

Question

[David_emir]

Hello All,

I am hoping to work on publicly-available cell lines with the IC50 data in order to generate biological hypotheses based on the specific genetic abnormalities of the cancer cell lines.

I want to generate hypothesis or build a model which suggests a particular genetic mutations/changes linked to disease and IC50 data has some role in it.

Kindly let me know if any process available or any method for doing this work. I appreciate any suggestions.

Thanks a lot for your valuable time and Help.

-Ateeq Khaliq

[David_emir]

the data is from gene expression profile of cell line panel (CCLE) (h133...) Affy platform

[Sean Davis]

A simple approach is to compare presence/absence of mutation to IC50 on a per-gene basis. This will not get you far, but you will likely find the true positives (eg., BRAF and vemurafenib).

Answer 1

[mikhail.shugay]

A bit of off-topic, but a very interesting paper on your question: Inconsistency in large pharmacogenomic studies. So basically you need not only a high number of cell lines, but reproducible IC50 data for each cell line. The paper also contains references to datasets.

Good luck!