Zhao Jianmei, Zhao Zeyu, Li Hongfei, Yu Haojie, Lin Hao, Chen Hanqi, Li Xuecang, Liu Di, Wang Yiming, Wang Guohua
College of Life Sciences, Northeast Forestry University, Harbin, China.
Big Data Management and Application, College of Management, Beijing University of Chinese Medicine, Beijing, China.
BMC Genomics. 2025 Jul 9;26(1):648. doi: 10.1186/s12864-025-11849-7.
Allele-specific DNA methylation (ASM) provides critical insights into the complex genetic and epigenetic mechanisms regulating gene transcription. Emerging evidence suggests that ASM is particularly enriched in gene enhancer regions, and recent studies have demonstrated that ASM is increased in cancer tissues compared with normal tissues. Despite the increasing recognition of ASM as a potential biomarker in tumorigenesis, systematic resources dedicated to identifying and annotating ASMs in cancer contexts remain limited. In this study, we developed CanASM ( https://bioinfor.nefu.edu.cn/CanASM/ ), the first comprehensive database specifically designed to identify and annotate ASM in cancer. In CanASM, ASM sites identified from bisulfite sequencing (BS-Seq) data across 31 cancer types and their matched normal tissue samples are cataloged. Importantly, CanASM includes extensive regulatory annotations for ASMs, including associated genes, cis-regulatory elements and transcription factor binding colocalizations, transcription factor affinity changes, etc. Users can query and explore ASMs using various parameters, such as single-nucleotide variations (SNVs), chromosomal coordinates, and gene names. The current version of CanASM includes 5,003,877 unique SNV-CpG pairs, including 3,056,776 index SNVs, of which 2,634,406 are single-nucleotide polymorphisms (SNPs), and 4,157,508 CpGs. With an intuitive interface for browsing, querying, analyzing, and downloading, CanASM serves as a valuable resource for researchers investigating cancer-associated genetic variations and epigenetic regulation in cancer.
等位基因特异性DNA甲基化（ASM）为调控基因转录的复杂遗传和表观遗传机制提供了关键见解。新出现的证据表明，ASM在基因增强子区域特别富集，最近的研究表明，与正常组织相比，癌症组织中的ASM增加。尽管人们越来越认识到ASM作为肿瘤发生中的潜在生物标志物，但专门用于在癌症背景下识别和注释ASM的系统资源仍然有限。在本研究中，我们开发了CanASM（https://bioinfor.nefu.edu.cn/CanASM/），这是第一个专门设计用于识别和注释癌症中ASM的综合数据库。在CanASM中，对从31种癌症类型及其匹配的正常组织样本的亚硫酸氢盐测序（BS-Seq）数据中识别出的ASM位点进行了编目。重要的是，CanASM包括对ASM的广泛调控注释，包括相关基因、顺式调控元件和转录因子结合共定位、转录因子亲和力变化等。用户可以使用各种参数，如单核苷酸变异（SNV）、染色体坐标和基因名称来查询和探索ASM。CanASM的当前版本包括5,003,877个独特的SNV-CpG对，其中包括3,056,776个索引SNV，其中2,634,406个是单核苷酸多态性（SNP），以及4,157,508个CpG。CanASM具有直观的浏览、查询、分析和下载界面，是研究癌症相关遗传变异和癌症表观遗传调控的研究人员的宝贵资源。
