In comparison, there were 100%, 62%, and 31% of CTC samples having ≥3%, 5%, and 10% tumor fractions, respectively (Fig. 1c, green panel).
Methods for the analysis of CTCs in clinical samples should be designed to detect both epithelial and mesenchymal-like subpopulations.
In univariate analysis of CTC levels and conventional prognostic factors (Table 2), none showed significant effect on overall survival, though analyses were limited by small sample sizes; no further multivariate analysis was performed.
Additionally, repeated sampling and molecular analysis of CTCs could help to uncover traits of cancer cells selected under therapy early on and could enable physicians to rapidly adapt treatment strategies.
For 46,467 probes, fewer than 4 out of 6 CTC samples gave present detection calls and therefore these probes were omitted from further analysis (Additional file 1).
However, most of what is discussed will apply to any multiplex analysis of CTCs, irrespective of the enrichment method.
In general, analysis of CTCs involves primary enrichment followed by CTC detection.
Six ECM protein genes were highly expressed in human CTCs (>100 rpm in >15% of all CTC samples).
Applying to 139 samples, we detected a tumor fraction of >0.10 in 17% and 21% of the cfDNA and CTC samples, respectively, sufficient for WES.
We also detected >0.03 tumor fraction (the limit of detection for ichorCNA using ULP-WGS data) in 58% and 96% of the cfDNA and CTC samples, respectively.
Among 70 cfDNA and 39 CTC samples of overt myeloma samples (newly diagnosed or relapsed), there were 76%, 41%, and 24% of cfDNA samples with ≥3%, 5%, and 10% tumor fractions, respectively (Fig. 1c, blue panel).
