Fig. 1
From: Brush swab as a noninvasive surrogate for tissue biopsies in epigenomic profiling of oral cancer
(A) We compared depth of coverage in all CpGs and determined an inflection point at 10x coverage. (B) Using 10x read depth as a cutoff, we determined the number of quantified CpG sites in each sample. Average number of quantified CpGs meeting our criteria was 2,716,674 for swab samples and 2,904,261 for tissue samples, with no significant difference between the two sample types. (C) The average mapping efficiency was 89.45% for brush swabs and 90% for tissues, with no significant difference between the two sampling methods. (D) The pie charts detail the relative genic locations of the CpGs profiled by MC-Seq (left) and CpGs covered by the EPIC array that were profiled (right). MC-Seq provided more robust coverage of functional gene regions than the EPIC array