molecular-subtyping-ATRT

Molecular Subtyping ATRT

Module authors: Zhuangzhuang Geng and Jo Lynne Rokita

Note: the previous files/scripts can be find in Archive folder

Usage

To run all of the Rscripts in this module from the command line sequentially, use:

bash run-molecular-subtyping-ATRT.sh

run-molecular-subtyping-ATRT.sh is designed to be run as if it was called from this module directory even when called from outside of this directory.

Molecular subtyping ATRT workflow

Folder content

This folder contains scripts tasked to molecularly subtype ATRT samples in the PBTA dataset. Methylation classification is used during subtyping. The DKFZ v12b6 data are available in dkfz_v12_methylation_subclass and subtypes with dkfz_v12_methylation_subclass_score >= 0.8 are considered high-confidence and used here. The NIH Bethesda classifier v2 data are available in NIH_v2_methylation_Class and subtypes with NIH_v2_methylation_Class_mean_score >= 0.9 and NIH_methylation_Superfamily_mean_score >= 0.9 are considered high-confidence and used here.

00-ATRT_subtyping.R selects samples from histologies-base.tsv and subtypes all PBTA and/or DGD tumor biospecimens into three subtypes, (ATRT, MYC, ATRT, SHH and ATRT, TYR).

• Filter the samples with dkfz_v12_methylation_subclass_score >=0.8 and if dkfz_v12_methylation_subclass is one of the three ATRT subtypes ->
  • ATRT, MYC
  • ATRT, SHH
  • ATRT, TYR If dkfz_v12_methylation_subclass_score < 0.8 but NIH_v2_methylation_Class_mean_score >= 0.9 and NIH_methylation_Superfamily_mean_score >= 0.9, and NIH_v2_methylation_Class is one of the three ATRT subtypes ->
  • ATRT, MYC
  • ATRT, SHH
  • ATRT, TYR
• All remaining samples -> ATRT, To be clasified

Final results is a table with sample_id, Kids_First_Biospecimen_ID_meth, Kids_First_Biospecimen_ID_DNA, Kids_First_Biospecimen_ID_RNA, and molecular_subtype, and saved as ATRT-molecular-subtypes.tsv