Supplementary Materials and Methods, Figures 1 -9, Tables 1 - 4 from Novel Methylated Biomarkers and a Robust Assay to Detect Circulating Tumor DNA in Metastatic Breast Cancer

PDF file - 1559KB, This file contains detailed methods, tables of study samples and source, primer and probe sequences,and genes belonging to the panel. Supplementary Table 1. Patient sample sets used in this study. Supplementary Table 2. 10-gene marker panel and its performance. Supplementary Table 3A. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 3B. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 3C. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 4. Comparison and reproducibility of the cMethDFNA assay using three DNA purification methods. Supplementary Figure 1. Infinium Human Methylation27 tissue DNA methylation array profile of the 10-gene marker panel. Supplementary Figure 2. Illumina Infinium Human Methylation27 serum DNA array profile of the 10-gene marker panel. Supplementary Figure 3. cMethDNA assay using a 6-gene marker panel. Supplementary Figure 4. Scatter plot and data analysis of cumulative methylation of the 10-gene panel in normal serum DNA. Supplementary Figure 5. Monitoring of treatment response by the cMethDNA assay. Supplementary Figure 6. Methylation Profiles in serum, primary, and metastatic tumor DNA. Supplementary Figure 7. Methylation profiles of serum, primary tumor and/or metastasis in patients with Stage 4 breast cancer. Supplementary Figure 8A. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8B. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8C. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8D. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8E. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8F. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 9. Representative examples of amplification plots of cMethDNA real-time PCR.