READ ME
Sayaman et al TCGA QC HRC Imputed Genotyping Data
v20210209


DATA AVAILABILITY
Access to the pre-processed quality controlled (QC), stranded and imputed genotyping data ("Sayaman et al TCGA QC HRC Imputed Genotyping Data") requires GDC controlled access permission approval. 

The quality controlled and HRC imputed genotyping data were contributed towards ancestry analyses in Carrot-Zhang et al., Cancer Cell 2020, and are accessible at the GDC publication page (https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020). 


Please cite Sayaman, Saad et al., Immunity 2021 when using the quality controlled, stranded and HRC imputed genotyping data. 

FULL CITATION
Sayaman, Saad, et al., Germline genetic contribution to the immune landscape of cancer, Immunity (2021), https://doi.org/10.1016/j.immuni.2021.01.011



LEAD CONTACT 
Rosalyn W. Sayaman, rwsayaman@gmail.com

CORRESPONDING AUTHORS
Rosalyn W. Sayaman, rwsayaman@gmail.com
Elad Ziv, elad.ziv@ucsf.edu
Davide Bedognetti, dbedognetti@sidra.org



DESCRIPTION

The quality-controlled genotyping file was stranded and imputed against the Haplotype Reference Consortium (HRC) (McCarthy et al., Nat. Genet. 2016). Prior to HRC stranding, all palindromic SNPs (A/T or G/C) were removed. Stranding was then performed using the McCarthy Group tools (HRC-1000G-check-bim-NoReadKey.pl)(https://www.well.ox.ac.uk/~wrayner/tools/), which compares our data genotyping alleles to the corresponding SNP alleles from HRC (v1.1 HRC.r1-1.GRCh37.wgs.mac5.sites.tab), leaving 680,389 correctly matched variants for 10,128 unique individuals for imputation.

Please see: Sayaman, Saad et al., Immunity 2021 for full details.