Comparison of Circulating Tumor Cell Derived DNA and Circulating Cell-Free DNA from Simultaneous Blood Sampling of Patients with Metastatic Breast Cancer

Circulating tumor DNA is usually read from plasma alone; this AACR 2020 poster compares CTC-derived DNA against cell-free DNA drawn at the same moment from patients with metastatic breast cancer, and reports where the two disagree.

Presented by Mayo Clinic and RareCyte.

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• Both analytes came out of the same blood collection, and the plasma arm was checked against the standard tube before anything was compared. CTC enumeration and phenotyping were completed for 36 subjects and CTCs were detected in 25; the 10 subjects with more than 2 CTCs per 3.75 mL went on to paired sequencing of CTC-DNA, white blood cell DNA and cfDNA through one 65-gene panel and one informatics pipeline. Plasma drawn into RareCyte AccuCyte tubes and plasma drawn into Streck tubes tracked each other closely across the variants tested (R² = 0.9948), so the cfDNA arm was not handicapped by its collection tube.
• Most mutations appeared in both compartments, but several the authors call actionable were detected in CTC-DNA only. PIK3CA H1047R read 54.1% variant allele frequency in one patient’s pooled CTCs against 0.0% in the paired RareCyte plasma, EGFR T790M read 31.6% against 0.0%, and EGFR R521K read 10.2% in the CTCs while both of that patient’s plasma tubes read 0.0%. The discordance ran the other way as well, with DNMT3A S714C at 0.0% in CTCs and 16.0% in cfDNA. These are case-level observations from 10 subjects with only 3 to 5 CTCs pooled per patient, not a detection rate.
• The intact cells also carried receptor phenotype, which has no counterpart in plasma DNA. ER and HER2 were scored on every CTC by immunofluorescence, and one patient’s 113 CTCs fell into all four receptor combinations at once — 56 scored ER+/HER2+ and 44 ER+/HER2- — while that same patient’s tissue biopsy had been called ER positive (>75%) and HER2 negative (IHC 1+). The poster reports this heterogeneity within a single blood sample and states that its clinical and theranostic relevance is unclear and warrants further investigation.