Fig 1.
Summary of total number of patients within each sample group for the different phases of the experiment.
Fig 2.
Comparison of RSEQC results from two plasma tube types (phase 1).
Samples from LBgard tubes consistently had poor quality metrics (low mapping rates and low number of reads mapped to annotated genes) compared to EDTA preserved samples.
Fig 3.
Unsupervised clustering of expressed genes dendrogram (phase 1).
There was no clear separation between cancers and controls and between different stages of cancer (0 for controls) although in certain sub-clusters cancers and controls were separated.
Fig 4.
Plasma RNA composition (phase 2).
(a) Plasma RNA yield (ng) for the different sample groups. There was a tendency for cancer patients to have increased cfRNA yields, Kruskal-Wallis test (Mean ± SEM) (b) Plasma RNA yield (ng) by cancer stage. There was no difference in total RNA yield among different stages of cancer, Kruskal-Wallis test (Mean ± SEM).
Fig 5.
Targeted capture sequencing principal component analysis plot (phase 2).
There was a lack of clustering observed among sample groups (AD/Cancer: red, adenoma: blue, and CTR/control: green).
Table 1.
Clinical characteristics of cancer and control patients for phase 3 study.
Table 2.
Differentially expressed transcripts validated by RT-qPCR.