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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)