Table 1 The list of biased batch IDs
From: Pan-cancer analysis of systematic batch effects on somatic sequence variations
Cancer type | #Total Variants | MAF | Batch ID | #Biased Variants |
|---|---|---|---|---|
KIRC | 25,372 | KIRC-broad.mit.edu_GA_automated | plate_id ~ 0886 | 577 |
KIRC-broad.mit.edu_GA_automated | plate_id ~ 0966 | 4 | ||
LUAD | 188,695 | LUAD-broad.mit.edu_GA | plate_id ~ 0928 | 313 |
LUAD-broad.mit.edu_GA | plate_id ~ 1040 | 5 | ||
LUAD-broad.mit.edu_GA | plate_id ~ 0969 | 4 | ||
LUAD-broad.mit.edu_GA | plate_id ~ 2284 | 1 | ||
UCEC | 52,789 | UCEC-broad.mit.edu_GA | plate_id ~ A10C | 56 |
UCEC-broad.mit.edu_GA | plate_id ~ A10M | 1 | ||
COAD | 106,434 | COAD-hgsc.bcm.edu_GA | plate_id ~ 1719 | 22 |
COAD-hgsc.bcm.edu_GA | tss_id_AA | 1 | ||
LGG | 45,851 | LGG-broad.mit.edu_GA_automated | plate_id ~ A289 | 4 |
LGG-broad.mit.edu_GA_automated | plate_id ~ 1705 | 1 | ||
LIHC | 71,536 | LIHC-bcgsc.ca_HiSeq_automated | plate_id ~ A12Z | 3 |
STAD | 135,407 | STAD-broad.mit.edu_GA | plate_id ~ 2340 | 2 |
142,498 | STAD-broad.mit.edu_GA_curated | plate_id ~ 2340 | 1 | |
BRCA | 84,908 | BRCA-genome.wustl.edu_GA_curated | plate_id ~ A071 | 1 |
45,607 | BRCA-genome.wustl.edu_GA | plate_id ~ A188 | 1 | |
KIRP | 15,061 | KIRP-hgsc.bcm.edu__Mixed_curated | plate_id ~ 1252 | 1 |
PRAD | 23,023 | PRAD-broad.mit.edu_GA_automated | plate_id ~ 2114 | 1 |