AML Resistance Networks

This package supports a series of projects that analyze various aspects of AML progression, drug sensitivity and drug resistance.

Currently there are four ongoing projects, each with different PIs. They are in varying states of analysis and publication. The BeatAML and early resistance projects already have one paper each. The other projects are still underway. The individual project files now listed in separate repositories to contribute to the analysis of the data and subsequent publication. These are supported through the NCI CPTAC PTRC work shared by OHSU and PNNL.

All data for this project is stored on Synapse. To gain access to the data you must request access until it is made available for publication. All data for this project should be uploaded into a folder.

BEAT AML Proteogenomic Project.

This project is the primary driver of methods development, as it uses diverse omics measurements to ascertain the impact that proteomics can have in drug response prognosis. THis project is located at the BEAT AML Proteomics Site. This work will support two publications. The first paper is a pilot project studying the analysis of a subset of the patient data, the second will be a broader analysis of the full cohort.

Some of the data ingest code can be found in the bin directory in this repository.

Pilot project

This project is underway and is nearly ready to be submitted.

Full patient cohort

This project needs to be processed and added to Synapse tables, then analyzed.

Studying the effect of drug combinations in cell lines

This study (also known as the cell line study) will focus on the the immediate effect of drugs on AML cell lines to determine how they could act in concert. The data ingeset for this project as well as the subsequent analysis will be at the AML Drug Combination site.

Early vs. Late Resistance in AML

This work compares the effects of gilteritinib and quizartinib in models of early and late resistance in AML. Most of the data ingest is in the bin directory here but most of the analysis is in the Early Late Resistance repository.

First paper

This paper is currently under review at Cancer Cell.

PTRC Pilot project

This data is currently being ingested.

Effects of Cytokines on drug resistance

This project led by the Agarwal lab is currently in process. Most of the data ingest can be found in the bin directory but the analysis has been moved to its own repository. The Cytokine drug resistance.