A correlation study of the methylation proportion of DNA in serum versus cancerous and normal breast tissue revealed a correlation between tumor tissue and serum for BMP6, BRCA1, CST6, GSTP1, P16 and TIMP3 genes but not with the matched normal tissue (Dataset S2).
Having confirmed high EVADR expression in the colorectal tumors in two independent datasets, we also validated the cancer association of EVADR in a non-colorectal tumor and matched normal control tissue dataset.
To compare the sensitivity of PathWave with other, common approaches we used the RPKM expression values of 77 lung adenocarcinomas and their matched normal tissue, which was the larger dataset of our case studies.
We analyzed a large dataset of tumor and matched normal samples of BRCA profiled for both gene and miRNA expression, obtained from TCGA.
We applied the method to predict CNAs in mate-pair datasets for the melanoma cell line COLO-829 and matched normal cell line COLO-829BL (Pleasance et al., 2010), a paired-end dataset for the small-cell lung cancer cell line NCI-H2171 (Campbell et al., 2008) and a single-end dataset for the breast cancer cell line HCC1143 (Chiang et al., 2009).
Hydra-Multi was originally developed to explore the mechanisms driving complex genomic rearrangements among 129 whole genome sequencing datasets (64 tumors and 65 matched normal tissues, Supplementary Table S1) from TCGA (Malhotra et al., 2013).
This dataset included 326 PCa and 50 matched normal patient samples.
Because none of the tumor datasets processed in this study included matched normal profiles for each tumor, as required by the Clarke method, we used Spearman rank correlation to identify the most similar normal profile b r for each input tumor sample, and used that normal profile as the matched normal for input into the method.
HCA of MassARRAY methylation data in the UNC tumor/matched normal dataset, followed by validation of methylation patterns in TCGA tumors and matched normal tissues revealed the six methylation patterns described herein.
The dataset included 62 primary tumor tissues, 41 matched normal prostate tissues, and 9 unmatched pelvic lymph node metastases.
