Cell-free DNA as a diagnostic analyte for molecular diagnosis of vascular malformations

Kaitlyn Zenner, Dana M. Jensen, Tori T. Cook, Victoria Dmyterko, Randall A. Bly, Sheila Ganti, Ghayda M. Mirzaa, William B. Dobyns, Jonathan A. Perkins, James T. Bennett

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Purpose: Vascular malformations (VM) are primarily caused by somatic activating pathogenic variants in oncogenes. Targeted pharmacotherapies are emerging but require molecular diagnosis. Since variants are currently only detected in malformation tissue, patients may be ineligible for clinical trials prior to surgery. We hypothesized that cell-free DNA (cfDNA) could provide molecular diagnoses for patients with isolated VM. Methods: cfDNA was isolated from plasma or cyst fluid from patients with arteriovenous malformations (AVM), venous malformations (VeM), or lymphatic malformations (LM), and assayed for known pathogenic variants using droplet digital polymerase chain reaction (ddPCR). Cyst fluid cfDNA from an independent cohort of LM patients was prospectively screened for variants using a multiplex ddPCR assay. Results: Variants were detected in plasma cfDNA in patients with AVM (2/8) and VeM (1/3). Variants were detected in cyst fluid cfDNA (7/7) but not plasma (0/26) in LM patients. Prospective testing of cyst fluid cfDNA with multiplex ddPCR identified variants in LM patients who had never undergone surgery (4/5). Conclusion: Variants were detected in plasma from AVM and VeM patients, and in cyst fluid from patients with LM. These data support investigation of cfDNA-based molecular diagnostics for VM patients, which may provide opportunities to initiate targeted pharmacotherapies without prior surgery.

Original languageEnglish (US)
Pages (from-to)123-130
Number of pages8
JournalGenetics in Medicine
Issue number1
StatePublished - Jan 2021
Externally publishedYes

Bibliographical note

Funding Information:
We thank the affected individuals, their families, and referring physicians for their important contribution to our ongoing work on these disorders. This study was funded by the US National Institutes of Health under National Heart, Lung, and Blood Institute (NHLBI) grants F32HL147398 (to K.Z.) and 1RO1HL103996 (to W.B.D.), a Seattle Children’s Hospital Guild Association Funding Focus Award (to J.A.P.), and Burroughs Wellcome Career Award for Medical Scientists 1014700 (to J.T.B.). We thank the Brotman Baty Institute for Precision Medicine for sharing their protocols and expertise on cfDNA isolation. We also acknowledge the Seattle Children’s Vascular Anomalies Program and especially the interventional radiology team for their support in sample collection. The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of the funding sources.

Publisher Copyright:
© 2020, American College of Medical Genetics and Genomics.


  • PIK3CA
  • cell-free DNA
  • droplet digital PCR
  • multiplexing
  • vascular malformations

PubMed: MeSH publication types

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


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