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

Gu, Wei; Talevich, Eric; Hsu, Elaine; Qi, Zhongxia; Urisman, Anatoly; Federman, Scot; Gopez, Allan; Arevalo, Shaun; Gottschall, Marc; Liao, Linda; Tung, Jack; Chen, Lei; Lim, Harumi; Ho, Chandler; Kasowski, Maya; Oak, Jean; Holmes, Brittany J.; Yeh, Iwei; Yu, Jingwei; Wang, Linlin; Miller, Steve; DeRisi, Joseph L.; Prakash, Sonam; Simko, Jeff; Chiu, Charles Y.

BACKGROUND: Metagenomic next-generation sequencing (mNGS) of body fluids is an emerging approach to identify occult pathogens in undiagnosed patients. We hypothesized that metagenomic testing can be simultaneously used to detect malignant neoplasms in addition to infectious pathogens. METHODS: From two independent studies (n = 205), we used human data generated from a metagenomic sequencing pipeline to simultaneously screen for malignancies by copy number variation (CNV) detection. In the first case-control study, we analyzed body fluid samples (n = 124) from patients with a clinical diagnosis of either malignancy (positive cases, n = 65) or infection (negative controls, n = 59). In a second verification cohort, we analyzed a series of consecutive cases (n = 81) sent to cytology for malignancy workup that included malignant positives (n = 32), negatives (n = 18), or cases with an unclear gold standard (n = 31). RESULTS: The overall CNV test sensitivity across all studies was 87% (55 of 63) in patients with malignancies confirmed by conventional cytology and/or flow cytometry testing and 68% (23 of 34) in patients who were ultimately diagnosed with cancer but negative by conventional testing. Specificity was 100% (95% CI 95–100%) with no false positives detected in 77 negative controls. In one example, a patient hospitalized with an unknown pulmonary illness had non-diagnostic lung biopsies, while CNVs implicating a malignancy were detectable from bronchoalveolar fluid. CONCLUSIONS: Metagenomic sequencing of body fluids can be used to identify undetected malignant neoplasms through copy number variation detection. This study illustrates the potential clinical utility of a single metagenomic test to uncover the cause of undiagnosed acute illnesses due to cancer or infection using the same specimen. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-021-00912-z.