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

Table 1 List of cancer types analyzed, their TCGA designated abbreviations, and the sequencing type analyzed

Cancer type	Abbreviation	Sequencing type¹
Acute myeloid leukemia	AML	RNA-Seq (192)
Breast cancer	BRCA	RNA-Seq (451)
Glioblastoma multiforme	GBM	RNA-Seq (1), DNA (10), WGA (147)
Kidney clear cell carcinoma	KIRC	RNA-Seq (420)
Kidney papillary carcinoma	KIRP	RNA-Seq (15)
Lung adenocarcinoma	LUAD	RNA-Seq (76)
Lung squamous cell carcinoma	LUSC	RNA-Seq (174)
Ovarian serous cystadenocarcinoma	OV	WGA (310), DNA (13)
Stomach adenocarcinoma	STAD	RNA-Seq (71)

¹ As denoted by the TCGA barcode, the sequencing types are RNA-Seq, DNA, or whole genome amplified (WGA). The number of samples analyzed for each sequencing type is denoted in the parentheses and is not the number of samples where bacterial read pairs were identified

ISSN: 2049-2618