Table 1.
Prediction results in CUP patients
| ID | Sex | Biopsy site | Histology | Path Diag. | Stand of Ref | LDA Pred | Outlier score |
|---|---|---|---|---|---|---|---|
| 14. | F | LN neck | PDC | Lung | Lung (CD) | Lung | 975 |
| 17. | F | LN neck | Adenoc. | Lower GI | Colon (RD) | Colon | 746 |
| 22. | M | LN neck | Adenoc. | CUP | Stomach (RD) | Normal | 934 |
| 23. | M | LN retro | PDC | CUP | Kidney (RD) | Kidney | 1085 |
| 28. | F | Peritoneum | PDA | Ovary | Ovary (RD) | Ovary | 810 |
| 31. | F | LN neck | PDA | CUP | Lung (CD) | Stomach | 985 |
| 34 | M | Skin | PDA | Lung | Lung (RD) | Lung | 898 |
| 39. | M | Liver | Adenoc. | CUP | Pancreas (CD) | Pancreas | 1097 |
| 40. | F | Liver | Adenoc. | Colon | Colon (RD) | Colon | 729 |
| 44. | F | Kidney | Carc. | CUP | Bladder (RD) | Bladder | 1286 |
| 49. | M | LN neck | PDA | Kidney | Kidney (RD) | Kidney | 1223 |
| 51. | F | LN pelvis | SCC | CUP-SCC | Cervical (RD) | Cervix | 828 |
| 52. | M | Liver | PDA | CUP | CCC (RD) | CCC | 923 |
| 53. | M | Liver | Adenoc. | Lung | Lung (RD) | Lung | 1047 |
| 57. | M | Liver | Adenoc. | CCC | CCC (RD) | HCC | 965 |
| 66. | F | Liver | PDA | CUP | CCC (RD) | Cervix | 1100 |
| 70. | M | Peritoneum | Adenoc. | Stomach | Stomach (CD) | Colon | 842 |
| 74. | M | Leg | Carc. | Adnex tumor | Adnex tumor (RD) | Normal | 1010 |
| 76. | M | Liver | Adenoc. | Lower GI | Small intestine (RD) | Colon | 912 |
| 77. | M | LN axilla | PDC | CUP | Lung (CD) | Breast | 978 |
| 86. | F | LN axilla | Adenoc. | CUP | Lung (RD) | Stomach | 1108 |
| 88. | F | Peritoneum | Adenoc. | Ovary | Ovary (RD) | Cervix | 1033 |
| 89. | F | Liver | PDA | CCC | CCC (RD) | CCC | 916 |
| 90. | F | Peritoneum | Adenoc | Ovary | Ovary (RD) | Ovary | 781 |
| 92. | M | Liver | Malignant tumor | Angiosarcoma | Angiosarcoma (RD) | Normal | 1097 |
| 95. | M | Peritoneum | PDC | DSRCT | DSRCT (RD) | Breast | 1098 |
| 71 + 72 | M | Bone + Kidney | PDC | Kidney | Kidney (RD) | Kidney | 1096 |
| 1277 | |||||||
| 75 + 87 | F/43 | Liver | PDA | CCC | CCC (RD) | CCC | 925 |
| 1030 | |||||||
| ID | Sex | Biopsy site | Histology | Path Diag. | Stand of Ref | LDA Pred | Outlier score |
| 11. | F | LN neck | PDA | CUP | CUP (SD) | Ovary | 756 |
| 13. | F | Peritoneum | PDA | CUP | CUP (NSD) | Pancreas | 1193 |
| 21. | M | LN neck | PDC | CUP | CUP (NSD) | Breast | 1108 |
| 26. | F | Skin | PDA | CUP | CUP (NSD) | Breast | 971 |
| 32. | M | LN neck | PDSCC | CUP-SCC | CUP (NSD) | Normal | 926 |
| 33. | M | Skin | PDA | CUP | CUP (NSD) | Colon | 1098 |
| 41. | M | Liver | PDA | Pancreas | CUP (NSD) | Stomach | 1040 |
| 42. | M | Liver | Adenoc. | CUP | CUP (NSD) | Pancreas | 994 |
| 43. | F | LN retro | PDA | CUP | CUP (NSD) | Stomach | 797 |
| 45. | M | Liver | PDC | CUP | CUP (NSD) | Colon | 1245 |
| 46. | F | Liver | Adenoc. | CUP | CUP (NSD) | Normal | 1027 |
| 47. | F | Liver | Adenoc. | CUP | CUP (SD) | CCC | 932 |
| 48. | F | LN neck | PDC | CUP | CUP (NSD) | Ovary | 1032 |
| 54. | F | Liver | Adenoc. | CUP | CUP (NSD) | Normal | 1068 |
| 55 | F | Liver | Adenoc. | CUP | CUP (NSD) | Normal | 962 |
| 58. | F | Liver | PDC | CUP | CUP (SD) | CCC | 995 |
| 61. | M | Liver | Carc. | HCC | CUP (NSD) | CCC | 1102 |
| 64. | F | LN inguien | PDA | CUP | CUP (SD) | Lung | 1168 |
| 65. | M | LN neck | PDSCC | CUP-SCC | CUP (NSD) | Breast | 929 |
| 73. | M | LN retro | PDC | CUP | CUP (NSD) | Normal | 1020 |
| 78. | F | Lung | Adenoc. | Lower GI | CUP (NSD) | Lung | 1062 |
| 80. | F | Liver | Adenoc. | CUP | CUP (SD) | CCC | 1111 |
| 81. | F | Liver | PDA | CUP | CUP (NSD) | Breast | 1212 |
| 82. | F | Bone | Adenoc. | CUP | CUP (NSD) | CCC | 1209 |
| 83. | F | Liver | PDA | CUP | CUP (SD) | CCC | 1061 |
| 91. | F | LN axilla | Adenoc. | CUP | CUP (SD) | Lung | 939 |
| 93. | M | Bone | PDSCC | CUP-SCC | CUP (NSD) | Breast | 940 |
| 94. | F | Liver | PDA | CUP | CUP (NSD) | Normal | 984 |
| 50. + 68 | M | Adr gl | PDC | CUP | CUP (NSD) | Stomach | 978 |
| Pancreas | 1079 |
A validation of the LDA predicted diagnoses was performed by comparing with a Standard of Reference (SR). SR was established by an experienced pathologist and two experienced oncologists. In addition to the 23 patients where a primary tumor site was identified (Reference Diagnosis (RD)) within the study period, the Standard of Reference reached a Consensus Diagnosis (CD) in 5 patients based on patient demographics, metastatic pattern, results of clinical and laboratory tests, imaging data and pathologic evaluations (Samples labeled in red). In the 29 remaining CUP labeled in blue, the results from gene expression profiling were compared with clinicopathological features and the predictions were categorized as Supportive (SD) or Non-Supportive (NSD). LN: lymph node; n: neck LN; m: mediastinal LN; a: axilla LN; r: retroperitoneal LN; p: pelvis LN; adr gl: adrenal gland; Adenoc: adenocarcinoma, PDA: poorly differentiated adenocarcinoma; Carc: carcinoma; PDC: poorly differentiated carcinoma; SCC: squamous cell carcinoma; PDSCC: poorly differentiated SCC; CCC: cholangiocarcinoma; HCC: hepatocelluar carcinoma; DSRCT: desmoplastic small round cell tumor.Path Diag: pathological diagnosis; Stand of ref: Standard of reference; LDA pred: Linear discriminant analysis prediction; RD: Reference Diagnosis; CD: Consensus Diagnosis, SD: Supportive Diagnosis; NSD: Non-Supportive Diagnosis.