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Table 1 Positive for cancer but negative by conventional testing (cytology/flow cytometry)

From: Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

Sample ID Sample type Presentation Cancer type New Dxa Cytology (Flow cytometry if available) Confirmation NGS Pos for CNVs and EBV CNV count by NGS Tumor Fraction
PC37 BAL New lung nodules after chemotherapy, fever Anaplastic large cell lymphoma n/a EBUS/FNA 0 0.00
PC38b Pleural Exudative pleural effusion, fever Sarcoma Benign Tissue CNV correlation, clinical suspicion + 5+ 0.62
PC39b Pleural Lung masses (history of Leiomyosarcoma on chemotherapy), exudative pleural effusion, tachycardia, leukocytosis, dyspnea Leiomyosarcoma Benign Tissue CNV correlated with NGS CNVs; imaging; clinical history + 5+ 0.28
PC40 Peritoneal Lung and liver metastasis, peritonitis (low SAAG/low protein), fever Poorly differentiated carcinoma most consistent with neuroendocrine carcinoma Benign Autopsy + 5+ 0.12
PC41b Pleural Lung masses, pleural effusion, lymphadenopathy, hypotension, dyspnea Undifferentiated carcinoma + Benign (negative) Tissue based FoundationONE testing: MET amplification correlated with NGS amplification + 5+ 0.056
PC42 Pleural lymphadenopathy (cervical/thoracic), non-diagnostic biopsies (2), hypercalcemia, weight loss (history of disseminated coccidioidomycosis, breast cancer) Unknown—presumptive lymphoproliferative disorder + Benign (negative) Probable: High clinical suspicion of lymphoproliferative disorder +/− tuberculosis (working diagnosis) +/EBV+ 5+ 0.32
PC43 Pleural Liver masses, exudative pleural effusions, dyspnea, fatigue, weight loss Unknown—presumptive hepatocellular carcinoma + Benign Probable: High clinical suspicion + 5+ 0.31
PC44b Pleural Chest mass, pleural based lesions, dyspnea Rhabdomyosarcoma Benign (negative) Tissue based UCSF500 testing: CNVs correlated + 1 0.66
PC45 Pleural Exudative effusion, lymphadenopathy (recent diagnosis of Hodgkin lymphoma, untreated), weight loss Hodgkin lymphoma + Benign (negative) Clinical suspicion, recent tissue diagnosis without treatment, CNV decrease after therapy, and EBV decrease after therapy +/EBV+ 4 0.35
PC46b Pleural Chronic pleural effusion requiring repeated drainage with known malignancy Hodgkin lymphoma Benign (negative) Probable: High clinical suspicion + 5+ 0.26
PC47 Peritoneal Known relapsed malignancy Diffuse large B cell lymphoma Benign (negative) Probable: High clinical suspicion of known DLBCL with suggestive imaging 0 0.00
PC48 Peritoneal Hepatic mass, ascites Intrahepatic cholangiocarcinoma + Benign Core Biopsy of liver: Adenocarcinoma + 5+ 0.31
PC49 Pleural Pleural effusion, recently treated community acquired pneumonia, recurrent fever Invasive ductal carcinoma + Benign Breast core biopsy shows invasive ductal carcinoma 0 0.00
PC50 Pleural Suspected malignant pleural effusion Anal squamous cell carcinoma Benign Probable: High clinical suspicion for malignant effusion + 5+ 0.61
PC51 Pleural Lung mass, exudative effusion Unknown—suspected cancer + Benign Probable: High clinical suspicion 0 0.00
PC52 Pleural Known pulmonary metastasis Colon adenocarcinoma Benign Probable: High clinical suspicion + 5+ 0.52
PC53 BAL Lung mass, pancreatic mass, night sweats, weight loss Melanoma + Benign FNA: Melanoma + 4 0.15
PC54 BAL Lung mass, lymphadenopathy Lung adenocarcinoma + Benign FNA: Lung adenocarcinoma + 5+ 0.11
PC55 Peritoneal Ascites Breast cancer Benign (negative) Probable: High clinical suspicion + 2 0.31
PC56 Pericardial Effusions, fever, weakness Castleman’s + Benign Lymph node biopsy 0 0.00
PC57 Pleural Effusions, fever, weakness Castleman’s + Benign Lymph node biopsy 0 0.00
PC58 BAL Lung nodules, fever (known AML) Acute myeloid leukemia Benign Cytogenetics (bone marrow) correlated with NGS CNVs +c 5+ 0.40
PC59 Peritoneal Liver masses, ascites Cholangiocarcinoma Benign FNA: adenocarcinoma + 5+ 0.55
PC60 Peritoneal Liver masses, ascites Hepatocellular carcinoma Benign FNA: Metastatic hepatocellular carcinoma + 5+ 0.55
PC61 Pleural Liver masses, exudative pleural effusion, lung nodules Colon cancer Benign Probable: High clinical suspicion 0 0.00
PC62 Peritoneal Liver masses, ascites Cholangiocarcinoma Benign FNA: adenocarcinoma 0 0.00
PC63b BAL Lung nodules, lymphadenopathy, non-diagnostic biopsies (5), eosinophilia, hypercalcemia Myeloid neoplasm + Benign (negative) Tissue FISH and cytogenetics (bone marrow) correlated with NGS CNVs: see Fig. 2 + 5+ 0.96
PC64 FNA Lymphadenopathy, splenomegaly, fever Hodgkin lymphoma + Scant atypical lymphoid cells Core Biopsy: Hodgkin lymphoma 0 0.00
PC65 BAL Lymphadenopathy Lung adenocarcinoma + Benign FNA: adenocarcinoma 0 0.00
  1. aNew Dx (diagnosis): either no history of the cancer or no treatment of a newly diagnosed cancer
  2. bBody fluid is correlated with cancer tissue (see Fig. 2G, H for PC63 and Additional file 1 for all other cases)
  3. cPlasma NGS (same protocol) 1 day prior shows a lower tumor fraction at 27% (versus 40% in the BAL)