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

doi:10.1038/s41436-020-00943-8

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 journal › Article › peer-review

34 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	123-130
Number of pages	8
Journal	Genetics in Medicine
Volume	23
Issue number	1
DOIs	https://doi.org/10.1038/s41436-020-00943-8
State	Published - Jan 2021
Externally published	Yes

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.

Keywords

PIK3CA
cell-free DNA
droplet digital PCR
multiplexing
vascular malformations

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title = "Cell-free DNA as a diagnostic analyte for molecular diagnosis of vascular malformations",

abstract = "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.",

keywords = "PIK3CA, cell-free DNA, droplet digital PCR, multiplexing, vascular malformations",

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

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{\textquoteright}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{\textquoteright}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: {\textcopyright} 2020, American College of Medical Genetics and Genomics.",

year = "2021",

month = jan,

doi = "10.1038/s41436-020-00943-8",

language = "English (US)",

volume = "23",

pages = "123--130",

journal = "Genetics in Medicine",

issn = "1098-3600",

publisher = "Elsevier B.V.",

number = "1",

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TY - JOUR

T1 - Cell-free DNA as a diagnostic analyte for molecular diagnosis of vascular malformations

AU - Zenner, Kaitlyn

AU - Jensen, Dana M.

AU - Cook, Tori T.

AU - Dmyterko, Victoria

AU - Bly, Randall A.

AU - Ganti, Sheila

AU - Mirzaa, Ghayda M.

AU - Dobyns, William B.

AU - Perkins, Jonathan A.

AU - Bennett, James T.

N1 - 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.

PY - 2021/1

Y1 - 2021/1

N2 - 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.

AB - 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.

KW - PIK3CA

KW - cell-free DNA

KW - droplet digital PCR

KW - multiplexing

KW - vascular malformations

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

Abstract

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