10.6084/m9.figshare.7012307.v1 Ishihara H. Ishihara H. Yamashita S. Yamashita S. Amano R. Amano R. Kimura K. Kimura K. Hirakawa K. Hirakawa K. Ueda T. Ueda T. Murakami Y. Murakami Y. Tamori A. Tamori A. Tanabe K. Tanabe K. Kawada N. Kawada N. Hagihara A. Hagihara A. Ushijima T. Ushijima T. Supplementary Material for: Pancreatic Cancer Cell Fraction Estimation in a DNA Sample Karger Publishers 2018 DNA methylation Pancreatic cancer Cancer cell fraction Epigenetics Intraductal papillary mucinous neoplasm 2018-08-27 11:25:20 Dataset https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Pancreatic_Cancer_Cell_Fraction_Estimation_in_a_DNA_Sample/7012307 <b><i>Objective:</i></b> Pancreatic cancers are characterized by dense stroma. To estimate the degree of interference by coexisting noncancer cells in molecular analyses, we aimed to develop a DNA methylation marker that assesses a cancer cell fraction in DNA samples. <b><i>Methods:</i></b> The microarray data of 22 pancreatic cancer tissues from the The Cancer Genome Atlas database and 9 noncancer tissues were used for genome-wide screening. Thirty-one surgical tumor samples (10 intraductal papillary mucinous neoplasms [IPMNs] and 21 pancreatic cancers), 4 normal, and 26 nontumor samples were used for validation. Gene-specific methylation analysis was conducted by bisulfite pyrosequencing. <b><i>Results:</i></b> Genome-wide screening isolated <i>SIM1</i>, <i>MIR129-2</i>, <i>NR1I2</i>, and <i>HOXB-AS4</i>, as specifically methylated in pancreatic cancer cells. Bisulfite pyrosequencing validated that one or more of three genes (<i>SIM1</i>, <i>MIR129-2</i>, and <i>NR1I2</i>) were methylated in 22 (71.0%) tumor samples (8 IPMNs and 14 cancers), and all showed low levels of methylation in 26 (86.7%) normal and nontumor samples. Therefore, the three genes collectively constituted one marker for a pancreatic cancer cell fraction. The cancer cell fraction estimated by the marker was highly correlated with that estimated using the <i>KRAS</i> mutant allele frequency (<i>R</i> = 0.79). <b><i>Conclusion:</i></b> The DNA methylation marker is useful to estimate the pancreatic cancer cell fraction in DNA samples.