Towards the DNA methylation haplotype map of 11 common solid cancers

Aberrant DNA methylation is an epigenetic hallmark of cancer, known to play an essential role in cancer initiation, progression and drug resistance. Traditional analyses focus on mean methylation that measures the aggregated signal across a group of cells and neglect intra-sample heterogeneity. Sequencing-based techniques such as whole genome bisulfite sequencing (WGBS) are now widely used to measure DNA methylation on each read at single-nucleotide resolution. A single read fragment stems from a single chromosome of a single cell and represents a DNA methylation haplotype (mHap). In this study, we have profiled 110 fresh frozen tumor samples that cover 11 most common solid cancer types using WGBS and constructed a comprehensive DNA methylation haplotype map. We have focused on 11 most common solid cancer types, i.e., head and neck squamous cell carcinoma (HNSC), Thyroid carcinoma (THCA), Non-small cell lung cancer (NSCLC), Breast carcinoma (BRCA), Esophageal carcinoma (ESCA), liver hepatocellular carcinoma (LIHC), Stomach adenocarcinoma (STAD), Pancreatic carcinoma (PAAD), Colon adenocarcinoma (COAD), Ovarian serous adenocarcinoma (OV), Cervical and endocervical cancers (CESC). These cancer types cumulatively represent 85% of all cancer cases worldwide. Whole-genome bisulfite sequencing (30x) was performed on 9 to 11 fresh-frozen tumor samples for each cancer type, resulting in 110 WGBS samples covering 11 cancer types. **Raw data not provided due to patient privacy concerns**