Recent GDC Data Updating Parameters

Question

[Aqsa]

I was performing analysis on different cancers data using 2019 data, but recently GDC, TCGA data is updated. I am unable to understand on what basis the data is updated or what are the updating parameters. If someone can answer me I will be thankful and it would be really helpful for me. Thank You.

Answer 1

[Zhenyu Zhang]

The main reason behind the change is that the gene model has been updated from GENCODE v22 to GENCODE v36. If you are looking at the somatic mutation data (MAF) in TCGA, another big change is that TCGA has adopted similar workflows to other GDC projects: now instead of single-called project-level MAFs, TCGA now has aliquot-level multiple caller ensemble MAF.