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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 1000 Genomes Project (1000G) (1000 Genomes Project Consortium et al., Nature 2015). Prior to 1000G stranding, all palindromic SNPs were removed and 1000G stranding was done using an in-house tool (courtesy of Scott Huntsman) which compares genotyping alleles to stated alleles from 1000G Phase 3 (version 5) legend files leaving 678,304 correctly matched variants for 10,128 unique individuals for imputation.

Please see: Sayaman, Saad et al., Immunity 2021 for details on the pre-processing steps. The 1000G imputed genotyping data was not used in the manuscript, but the pre-processed and stranded file is provided for convenience.