Seq-ing the SINEs of Central Nervous System Tumors in Cerebrospinal Fluid DNA

Lesions within the brain cavity pose critical challenges for diagnostics, particularly distinction between cancerous and non-cancerous lesions. We here introduce an analytic technique called Real-CSF to detect cancers of the central nervous system from evaluation of DNA in the cerebrospinal fluid (CSF). Short interspersed nuclear elements (SINEs) from throughout the genome are PCR-amplified with a single primer pair and the PCR products are evaluated by next generation sequencing. Real-CSF uses machine learning to assess three features from the sequencing data – gains or losses of 39 chromosome arms, focal amplifications, and somatic nucleotide variants. Real-CSF was applied to 282 CSF samples and correctly classified 71 % of 187 cancers and misclassified only 4.2% of 95 non-neoplastic lesions in the brain. ### Competing Interest Statement BV, KWK, & NP are founders of Thrive Earlier Detection, an Exact Sciences Company. KWK, NP, & CD are consultants to Thrive Earlier Detection. BV, KWK, NP, and CD hold equity in Exact Sciences. BV, KWK, & NP are founders of Thrive Earlier Detection, an Exact Sciences Company. KWK, NP, & CD are consultants to Thrive Earlier Detection. BV, KWK, and NP are founders of and own equity in ManaT Bio. KWK and NP are consultants to and own equity in Haystack Oncology, Neophore and Personal Genome Diagnostics. KWK, BV, and NP, hold equity in and are consultants to CAGE Pharma. BV is a consultant to and holds equity in Catalio Capital Management and may be a consultant to and hold equity in Haystack Oncology. BV owns equity in CAGE, Neophore, and Personal Genome Diagnostics. CB is a consultant to Depuy-Synthes, Bionaut Labs, Haystack Oncology and Galectin Therapeutics. CB is a co-founder of OrisDx. The companies named above, as well as other companies, have licensed previously described technologies related to the work described in this paper from Johns Hopkins University. BV, KWK, NP, CB, and CD, are inventors on some of these technologies. Licenses to these technologies are or will be associated with equity or royalty payments to the inventors as well as to Johns Hopkins University. Patent applications on the work described in this paper may be filed by Johns Hopkins University. The terms of all these arrangements are being managed by Johns Hopkins University in accordance with its conflict of interest policies. MH is on the Data Safety Monitoring Board for Parexel, Advarra, and has received an Honorarium from Pfizer. KS received an honorarium from Springworks Therapeutics and receives research funding from Springworks Therapeutics. JN receives research funding from Merck, AstraZeneca, BMS, Amgen, Novartis, Roche/Genetech and is a consulting/advisory board for Merck, AstraZeneca, BMS, Amgen, Novartis, Roche/Genetech, Takeda, Pfizer, Daiichi Sankyo, and NGM Biosciences. CJ is a cofounder with equity interest in Egret Therapeutics and receives research support from Biohaven. ### Funding Statement The full funding statement is included in the manuscript ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was cross-sectional in design. Patients were recruited as part of an Institutional Review Board-approved, multi-institutional study to develop biomarkers for central nervous system tumors using cerebrospinal fluid. The four institutions involved (Johns Hopkins, University of Michigan, Pennsylvania State University, Children Tissue Brain Tumor Tissue Consortium (CBTTC)) are tertiary centers that care for patients referred for management of central nervous system tumors. The Johns Hopkins Institutional Review Board gave ethical approval of the study. The University of Michigan Institutional Review Board Approved gave ethical approval of the study. The Pennsylvania State University Institutional Review board gave ethical approval of the study. The Children Tissue Brain Tumor Tissue Consortium (CBTTC)) Institutional Review Board gave ethical approval of the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The bioinformatic methods and pipeline used to process the raw sequencing data are available at ().