Table 1.
Positive for cancer but negative by conventional testing (cytology/flow cytometry)
| 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 |
aNew Dx (diagnosis): either no history of the cancer or no treatment of a newly diagnosed cancer
bBody fluid is correlated with cancer tissue (see Fig. 2G, H for PC63 and Additional file 1 for all other cases)
cPlasma NGS (same protocol) 1 day prior shows a lower tumor fraction at 27% (versus 40% in the BAL)