CSF H3F3A K27M circulating tumor DNA copy number quantifies tumor growth and in vitro treatment response

[...]less invasive and more rapid diagnostic tests are needed to detect actionable brain cancer mutations. H3K27M detection in CSF by a combination of nested PCR and Sanger sequencing in DIPG patients [6] as well as by ddPCR in older diffuse midline glioma patients has been reported [11]. [...]far, there have been no extensive studies using ddPCR to quantify ctDNA in the CSF of younger pediatric DIPG patients. Fig. 1 Fig. 1 a CSF ddPCR results from experimental samples correlated with contrast-enhancing and total tumor cross-sectional area on MRI. b ddPCR of multi-focal sampling shows K27M copy number varies between tumor (purple) and CSF (orange) regions c Co-culture scheme of bioluminescent human DIPG007 cells with NHAs. d DIPG007 cells release ctDNA in proportion to their proliferation. e 8 Gy radiation results in an increase in mutant ctDNA from DIPG007 cells We found that ddPCR was able to detect the K27M mutation in patient CSF and that the closest relationship emerged between mutant K27M copies per ng of total DNA (hereafter K27M copies) and contrast-enhancing cross-sectional tumor area on MRI (Fig. 1a). (DOCX 268 kb) Authors’ Affiliations (1) Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, 3520D MSRB I, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA (2) SciGency Science Communications, Ann Arbor, MI 48104, USA (3) Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA (4) Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA (5) Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA (6) Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA (7) Department of Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain (8) Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA Chen WW, Balaj L, Liau LM, Samuels ML, Kotsopoulos SK, Maguire CA, Loguidice L, Soto H, Garrett M, Zhu LD et al (2013) BEAMing and droplet digital PCR analysis of mutant IDH1 mRNA in glioma patient serum and cerebrospinal fluid extracellular vesicles.