Bringing in BEAT AML Data

[ychae]

Moving the email thread conversation here for tracking.

Ilya suggested that we consider Beat AML for neoantigen calls. "they have the first two waves published and we (Guangrong) are working with Jeff Tyner (OHSU) and we have access to Wave 3 and 4 (prepublication)".

--

Ben noted that "we could look at how antigens associate with response not just survival".

--

Ilya:
I am pulling in Guangrong Qin into this thread. :-) (Guangrong -- this is our iAtlas team)
She has been working with Beat AML (Jeff Tyner's group) through our CTD^2 network participation.
We have Beat AML (1.0) data already on ISB-CGC: https://isb-cgc.appspot.com/cohorts/filelist/
(click on Program to see Beat AML)

--

Guangrong provided a "link to Beat AML wave 1/2 dataset" -- @vthorsson please let me know if that file can be shared in a public repo as is, I didn't want to accidentally link sensitive data.

"All raw and processed sequencing data, along with relevant clinical annotations, have been submitted to dbGaP and Genomic Data Commons. The dbGaP study ID is 30641 and accession ID is phs001657.v1.p1. The raw data for clinical annotations, variant calls, gene expression counts and drug sensitivity that underlie Figs. 1–3 and Extended Data Figs. 1–9 are provided as Source Data.

We can check it first in the dbGaP."

"... isb-cgc has hosted these dataset, which means we could download the bam files"

"Just to give you an update about the dataset (bam files).
They can be used in the GCP platform. As they are controlled datasets, there is some authorization process for each member who will be directly working on these datasets. "

--

Ben will "apply for the dbGap permissions and the registered ppl from my group can work with the data then - I will do that and let you know when permission is granted."

---

BEAT AML DREAM Challenge