Table 1 List of classes used within CUPiD, with the number of methylation arrays for each class and regrouping
From: A cfDNA methylation-based tissue-of-origin classifier for cancers of unknown primary
CUPiD class | Class details | Total number | Source (TCGA abbreviation or GEO accession) | Number |
|---|---|---|---|---|
ACC | Adrenocortical carcinoma | 79 | TCGA (ACC) | 79 |
BLCA | Bladder urothelial carcinoma | 409 | TCGA (BLCA) | 409 |
BRCA | Breast invasive carcinoma | 777 | TCGA (BRCA) | 777 |
CervSq | Cervical squamous cell carcinoma | 254 | TCGA (CESC) | 254 |
CHOL | Cholangiocarcinoma | 256 | TCGA (CHOL) | 36 |
GEO (GSE32079) | 50 | |||
GEO (GSE49656) | 32 | |||
GEO (GSE89803) | 138 | |||
DLBC | Diffuse large B-cell lymphoma | 48 | TCGA (DLBC) | 48 |
GBM | Glioblastoma multiforme | 139 | TCGA (GBM) | 139 |
Gynae | Non-squamous gynaelogical carcinomas (endocervical adenocarcinoma, ovarian cystadenocarcinoma, endometrial carcinoma, uterine carcinosarcomas) | 531 | TCGA (CESC) | 46 |
TCGA (OV) | 10 | |||
TCGA (UCEC) | 418 | |||
TCGA (UCS) | 57 | |||
KICH | Kidney chromophobe | 65 | TCGA (KICH) | 65 |
KIRC | Kidney renal clear cell carcinoma | 312 | TCGA (KIRC) | 312 |
KIRP | Kidney renal papillary cell carcinoma | 271 | TCGA (KIRP) | 271 |
LAML | Acute myeloid leukaemia | 194 | TCGA (LAML) | 194 |
LGG | Brain lower grade glioma | 514 | TCGA (LGG) | 514 |
LIHC | Liver hepatocellular carcinoma | 366 | TCGA (LIHC) | 366 |
LowerGI | Colon and rectum adenocarcinomas | 382 | TCGA (COAD) | 288 |
TCGA (READ) | 94 | |||
LUAD | Lung adenocarcinoma | 456 | TCGA (LUAD) | 456 |
LUSC | Lung squamous cell carcinoma | 364 | TCGA (LUSC) | 364 |
MESO | Mesothelioma | 87 | TCGA (MESO) | 87 |
PAAD | Pancreatic adenocarcinoma | 156 | TCGA (PAAD) | 156 |
PCPG | Pheochromocytoma and Paraganglioma | 178 | TCGA (PCPG) | 178 |
PRAD | Prostate adenocarcinoma | 495 | TCGA (PRAD) | 495 |
SARC | Sarcoma | 257 | TCGA (SARC) | 257 |
SKCM | Skin cutaneous melanoma | 472 | TCGA (SKCM) | 472 |
TGCT | Testicular germ cell tumours | 149 | TCGA (TGCT) | 149 |
THCA | Thyroid carcinoma | 503 | TCGA (THCA) | 503 |
THYM | Thymoma | 124 | TCGA (THYM) | 124 |
UpperGI | Stomach and oesophageal adenocarcinoma | 481 | TCGA (ESCA) | 88 |
TCGA (STAD) | 393 | |||
UpperSq | Head and neck and oesophageal squamous cell carcinoma | 618 | TCGA (ESCA) | 95 |
TCGA (HNSC) | 523 | |||
UVM | Uveal melanoma | 80 | TCGA (UVM) | 80 |
NCC | Non-cancer controls (patient matched adjacent normal liver) | 49 | TCGA (LIHC) | 49 |
