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Table 3 Relative Mycobacterium spp. read pairs and sequencing center for each sample

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

Cancer type Sequencing centers
Total samples1 Samples with bacteria Samples with a log10 (Myco./total reads) ratio ≥ −7 Samples with a log10 (Myco./total reads) ratio ≥ −4
Baylor2 BCGSC Broad UNC Wash. Baylor BCGSC Broad UNC Wash. Baylor BCGSC Broad UNC Wash. Baylor BCGSC Broad UNC Wash.
AML 3 192 117 33 0
BRCA 340 393 0 90 0 40 0 0
GBM 1 154 3 0 125 3 0 29 1 0 0 0
KIRC 397 248 0 72 0 26 0 0
KIRP 15 9 2 0
LUAD 58 18 0 10 0 3 0 0
LUSC 136 167 0 20 0 4 0 0
OV 3 262 97 0 197 20 0 106 0 0 1 0
STAD 71 71 22 0
  1. 1 Total samples and samples with bacteria are defined as an analyte from each sample, so if one tumor sample had DNA and RNA sequenced or had RNA sequenced at multiple centers, each analysis of each nucleic acid is counted individually. For example, while there were only 451 BRCA samples (Table 1), most samples were sequenced at two sequencing centers, resulting in a total of 733 entries in the “Total samples” column of this table.
  2. 2Baylor = Baylor College of Medicine Human Genome Sequencing Center; BCGSC = British Columbia Genome Sequencing Center; Broad = The Broad Institute; UNC = University of North Carolina, Chapel Hill; Wash. = Washington University in St. Louis.
  3. 3​Sequencing centers that did not sequence any samples of a specific cancer type are denoted by a "–"