Table 1.
Amount of samples used for target selection and sequencing experiments.
| Repeatability | Selection of CpG sites* | Multi-cancer assay° | ddPCR validation° | ||||||
|---|---|---|---|---|---|---|---|---|---|
| (Tumor) tissue type | Mortality rank | # Tumor | # Normal | # Tumor | # Normal | # Tumor | # Normal | # Tumor | # Normal |
| Lung cancer (LUAD + LUSC) | 1 | 3 | 2 | 370 + 473 | 42 + 32 | 9 + 13 | 11 + 11 | 20 | 22 |
| Colorectal adenocarcinoma (CRC) | 2 | 3 | 2 | 411 | 45 | 7 | 10 | 7 | 10 |
| Liver hepatocellular carcinoma (LIHC) | 4 | 2 | 2 | 377 | 50 | 13 | 11 | 12 | 10 |
| Breast invasive carcinoma (BRCA) | 5 | 2 | 0 | 791 | 96 | 10 | 9 | 10 | 7 |
| Pancreatic adenocarcinoma (PAAD) | 6 | 2 | 2 | 184 | 10 | 21 | 24 | 17 | 23 |
| Head & neck squamous cell carcinoma (HNSC) | 7 | 2 | 1 | 528 | 50 | 13 | 8 | 13 | 8 |
| Esophageal carcinoma (ESCA) | 8 | 2 | 1 | 185 | 16 | 10 | 5 | 10 | 5 |
| Prostate adenocarcinoma (PRAD) | 9 | 2 | 1 | 502 | 50 | 15 | 25 | 14 | 24 |
| Blood | - | - | - | - | 140 | - | 35 | - | 22 |
| Total | 18 | 11 | 3821 | 531 | 111 | 149 | 103 | 109 | |
Stomach cancer ranks 3rd in mortality but was left out of the analysis due to a lack of normal samples in the public dataset at the time of analysis.
LUAD Lung adenocarcinoma, LUSC Lung squamous cell carcinoma.
*CpG sites were selected from online available 450 K methylation array datasets. Tumor and normal tissue sample data were retrieved from The Cancer Genome Atlas (TCGA). Blood datasets, retrieved from the Gene Expression Omnibus (GEO), originate from 18 peripheral blood mononuclear cells (PBMC) (GSE111942), 4 left atrium (GSE62727), 30 erythrocyte progenitors from bone marrow (GSE63409), 6 whole blood, 6 PBMCs, 6 granulocytes, 6 CD4 + T cells, 6 CD8 + T cells, 6 CD56 + NK cells, 6 CD19 + B cells, 6 CD14+ monocytes, 6 neutrophils and 6 eosinophils (GSE35069) and 28 peripheral blood (GSE113012).
°For the multi-cancer assay, we used both matched and unmatched tissue samples. Matched samples are tumor and adjacant normal tissue samples from the same patient. We used 8 matched samples for LUAD, 10 for LUSC, 6 for CRC, 7 for LIHC, 4 for BRCA, 7 for PAAD, 5 for HNSC, 2 for ESCA, and 10 for PRAD. Fot the ddPCR assay, we used most of these samples again.