μCaler DNA Full Screen System Comprehensive Solution

Figure 1. μCaler DNA Full Screen System can stably and efficiently cut the unmethylated sites across different sample types. A. Simulated samples with varying methylation levels and different initial input amounts of human genomic DNA standard (Promega, G1471); B. Clinical FFPE and cfDNA samples.

Note: The samples were simulated DNA by using human 100% Methylated DNA standard (zymo, D5014-2) positive control and 0% Methylated DNA standard (zymo, D5014-1) negative control to mimic different methylation levels (0%, 10%, and 50%). The initial input amounts for both simulated samples with different methylation levels and clinical FFPE and cfDNA samples were 10 ng.

Figure 2. μCaler DNA Full Screen System can increase the effective coverage depth of CpG sites several times that of the BS treatment. A. Average coverage depth of 13 CpG sites in simulated samples with different methylation levels at the initial inputs of 10 ng and B. simulated samples with a methylation level of 5% at different initial input amounts. The simulated samples were processed to hybridization capture using the μCaler DNA Full Screen System Comprehensive Solution (Full Screen) and the μCaler targeted methylation capture solution (BS), respectively. The sequencing mode was Illumina® Novaseq 6000, PE150; 1 M reads pair were randomly selected for data analysis.

Figure 3. Consistency of detection values obtained with the μCaler DNA Full Screen System: A. Detection values compared to theoretical values for samples with different methylation levels, and B. Consistency between two measurements of one randomly selected clinical colorectal cancer tissue sample. 1 M reads pair were randomly selected for data analysis.

Note: Traditional_BS utilized NadPrep Hybrid Capture Reagents (overnight hybridization) for capture.

Figure 4. Performance of μCaler DNA Full Screen System for synchronous detection of ultra-low-frequency mutation and low-abundance methylation. A total of 80 ng of simulated samples were analyzed using μCaler DNA Full Screen System with the μCaler Full Screen LF Custom Panel (< 5 Kb, covering 31 CpG sites) for hybrid capture. 3 Gb were randomly selected for data analysis. A. Mutation frequencies at different sites corresponded closely with the nominal frequencies of the standard [pre-libraries containing UMI, with analytical filtering criteria set to duplex consensus sequences (DCS211)]; B. Average number of unique reads supporting mutation detection (DCS211); C. Methylation levels of different simulated samples.

Figure 5. Performance ofμCaler DNA Full Screen System applied to cfDNA detection in clinical colorectal cancer Patients and healthy individuals. A. Methylation levels at CpG sites within the target regions; B. Z-score analysis.
Note: The initial input amount was 10 ng. T: Plasma cfDNA from clinical colorectal cancer patients, with T-1 to T-4 representing early-stage patients and T-5 representing a late-stage patient; N: Plasma cfDNA from healthy individuals.