PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines.
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines.
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DOI：
10.1093/database/baad042
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发表时间：
2023-06-10
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表观遗传修饰在基因调控和疾病病理生物学中起着重要作用。包括微阵列和基于测序的方法在内的高度敏感的使能技术允许对临床样本中dna中的胞嘧啶修饰进行全基因组分析，以促进发现用于疾病诊断和预后的表观遗传生物标志物。然而，从历史上看，许多先前的研究并没有将研究最多的5-甲基胞嘧啶（5mC）与其他修饰的胞嘧啶区分开来，特别是生物化学稳定的5-羟甲基胞嘧啶（5hmC），它们已被证明具有与5mC不同的基因组分布和调节作用。值得注意的是，在过去几年中，5hmC- seal是一种高度敏感的化学标记技术，已被证明是在临床可行的生物标本（例如几毫升血浆或血清）中进行5hmC全基因组分析的有力工具。5hmC- seal技术已被我们的团队用于利用循环无细胞DNA （cfDNA）发现人类癌症和其他复杂疾病的生物标志物，以及首个5hmC人类组织图谱的表征。方便地访问累积的5hmC-Seal数据将使研究界能够验证和重复使用这些结果，可能为一系列人类疾病的表观遗传贡献提供新的见解。这里我们介绍PETCH-DB，这是一个集成数据库，用于提供使用5hmC-Seal技术生成的5hmc相关结果。我们的目标是PETCH-DB成为一个中央门户网站，它将为科学界提供定期更新的临床样本中的5hmC数据，以反映该领域的当前进展。数据库地址http://petch-db.org/
Epigenetic modifications play critical roles in gene regulation and disease pathobiology. Highly sensitive enabling technologies, including microarray- and sequencing-based approaches have allowed genome-wide profiling of cytosine modifications in DNAs in clinical samples to facilitate discovery of epigenetic biomarkers for disease diagnosis and prognosis. Historically, many previous studies, however, did not distinguish the most investigated 5-methylcytosines (5mC) from other modified cytosines, especially the biochemically stable 5-hydroxymethylcytosines (5hmC), which have been shown to have a distinct genomic distribution and regulatory role from 5mC. Notably, during the past several years, the 5hmC-Seal, a highly sensitive chemical labeling technique, has been demonstrated to be a powerful tool for genome-wide profiling of 5hmC in clinically feasible biospecimens (e.g. a few milliliter of plasma or serum). The 5hmC-Seal technique has been utilized by our team in biomarker discovery for human cancers and other complex diseases using circulating cell-free DNA (cfDNA), as well as the characterization of the first 5hmC Human Tissue Map. Convenient access to the accumulating 5hmC-Seal data will allow the research community to validate and re-use these results, potentially providing novel insights into epigenetic contribution to a range of human diseases. Here we introduce the PETCH-DB, an integrated database that was implemented to provide 5hmC-related results generated using the 5hmC-Seal technique. We aim the PETCH-DB to be a central portal, which will be available to the scientific community with regularly updated 5hmC data in clinical samples to reflect current advances in this field. Database URL http://petch-db.org/
DOI：
10.20517/evcna.2021.22
发表时间：
2022
期刊：
Extracellular vesicles and circulating nucleic acids
影响因子：
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作者：
Zhang Z;Zeng C;Zhang W
通讯作者：
Zhang W