Low-coverage whole-genome sequencing of cerebrospinal-fluid-derived cell-free DNA in brain tumor patients.

Abstract

This protocol summarizes the pipeline for analysis of tumor-derived cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) using low-coverage whole-genome sequencing (lcWGS). This approach enables resolution of chromosomal and focal copy-number variations (CNVs) as oncologic signatures, particularly for patients with central nervous system tumors. Our strategy tolerates sub-nanogram cfDNA input and is thus optimized for CSF samples where cfDNA yields are typically low. Overall, the detection of tumor-specific signatures in CSF-derived cfDNA is a promising biomarker for personalization of brain-tumor therapy. For complete details on the use and execution of this protocol, please refer to Liu et al. (2021).

• Authors: Anthony P Y Liu, Kyle S Smith, Rahul Kumar, Giles W Robinson, Paul A Northcott
• Journal: STAR protocols (STAR Protoc) Vol. 3 Issue 2 Pg. 101292 (06 17 2022) ISSN: 2666-1667 [Electronic] United States
• PMID: 35463474 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: © 2022 The Author(s).

Chemical References

• Cell-Free Nucleic Acids

Topics

• Brain Neoplasms (cerebrospinal fluid, genetics)
• Cell-Free Nucleic Acids (cerebrospinal fluid, genetics)
• DNA Copy Number Variations (genetics)
• Humans
• Whole Genome Sequencing