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

STAR Protoc. 2022 Apr 12;3(2):101292. doi: 10.1016/j.xpro.2022.101292. eCollection 2022 Jun 17.

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).

Keywords: Bioinformatics; Cancer; Clinical Protocol; Genomics; Health Sciences; Molecular Biology; Neuroscience; Sequence analysis; Sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brain Neoplasms* / cerebrospinal fluid
  • Brain Neoplasms* / genetics
  • Cell-Free Nucleic Acids* / cerebrospinal fluid
  • Cell-Free Nucleic Acids* / genetics
  • DNA Copy Number Variations / genetics
  • Humans
  • Whole Genome Sequencing

Substances

  • Cell-Free Nucleic Acids