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Table 2 Summary of cancer types and bacterial presence

From: Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Cancer type Total no. of seq. runs Seq. runs with any bacterial read pair Total no. of patients Patients with any bacterial read pair Samples1 Samples with any bacterial read pair
Tumor Normal Tumor Normal
Solid tissue Blood Solid tissue Blood
AML 553 197 (36%) 187 117 (63%) 192 0 0 117 (61%) NA2 NA
BRCA 754 90 (12%) 430 90 (21%) 425 26 0 87 (20%) 3 (12%) NA
GBM 1476 600 (41%) 83 72 (87%) 78 0 78 68 (87%) NA 59 (76%)
KIRC 647 72 (11%) 401 72 (18%) 398 22 0 72 (18%) 0 (0%) NA
KIRP 15 9 (60%) 15 9 (60%) 15 0 0 9 (60%) NA NA
LUAD 76 10 (13%) 76 10 (13%) 76 0 0 10 (13%) NA NA
LUSC 306 20 (7%) 174 20 (11%) 172 2 0 20 (12%) 0 (0%) NA
OV 1991 561 (28%) 160 127 (79%) 154 20 136 105 (68%) 15 (75%) 93 (68%)
STAD 143 142 (99%) 71 71 (100%) 71 0 0 71 (100%) NA NA
  1. 1 There can be multiple tumor and normal samples for each patient. A sample is defined as each tumor or normal sample. It should be noted that a tumor sample may have DNA and RNA extracted for sequencing and as such may result in more than one analysis per sample.
  2. 2NA = not applicable