DNA 甲基化与人类身高的关系以及基于 DNA 甲基化的身高预测前瞻性模型。

IF 3.8 2区 生物学 Q2 GENETICS & HEREDITY
Human Genetics Pub Date : 2024-03-01 Epub Date: 2024-03-20 DOI:10.1007/s00439-024-02659-0
Zhonghua Wang, Guangping Fu, Guanju Ma, Chunyan Wang, Qian Wang, Chaolong Lu, Lihong Fu, Xiaojing Zhang, Bin Cong, Shujin Li
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引用次数: 0

摘要

作为重要的人体测量特征,人类身高信息不仅有助于了解整体发育状况和遗传风险因素,而且对法医 DNA 表型分析也很重要。我们利用线性回归分析检验了每个 CpG 探针与身高表型之间的关联。接下来,我们设计了一个针对 959 个 CpGs 的甲基化测序面板,并随后构建了中国人群的身高推断模型。共鉴定出 11,730 个身高相关位点。通过使用 KPCA 和深度神经网络,我们建立了一个预测模型,其交叉验证 RMSE、MAE 和 R2 分别为 5.62 厘米、4.45 厘米和 0.64。遗传因素可以解释身高推断模型中所用位点甲基化水平变异的 39.4%。总之,我们通过 EWAS 分析证明了身高与 DNA 甲基化状态之间的关系。对仅有的 959 个 CpGs 进行靶向甲基化测序并结合深度学习技术,可以提供一个估计人类身高的模型,其准确性高于基于 SNP 的预测模型。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

The association between DNA methylation and human height and a prospective model of DNA methylation-based height prediction.

The association between DNA methylation and human height and a prospective model of DNA methylation-based height prediction.

As a vital anthropometric characteristic, human height information not only helps to understand overall developmental status and genetic risk factors, but is also important for forensic DNA phenotyping. We utilized linear regression analysis to test the association between each CpG probe and the height phenotype. Next, we designed a methylation sequencing panel targeting 959 CpGs and subsequent height inference models were constructed for the Chinese population. A total of 11,730 height-associated sites were identified. By employing KPCA and deep neural networks, a prediction model was developed, of which the cross-validation RMSE, MAE and R2 were 5.62 cm, 4.45 cm and 0.64, respectively. Genetic factors could explain 39.4% of the methylation level variance of sites used in the height inference models. Collectively, we demonstrated an association between height and DNA methylation status through an EWAS analysis. Targeted methylation sequencing of only 959 CpGs combined with deep learning techniques could provide a model to estimate human height with higher accuracy than SNP-based prediction models.

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来源期刊
Human Genetics
Human Genetics 生物-遗传学
CiteScore
10.80
自引率
3.80%
发文量
94
审稿时长
1 months
期刊介绍: Human Genetics is a monthly journal publishing original and timely articles on all aspects of human genetics. The Journal particularly welcomes articles in the areas of Behavioral genetics, Bioinformatics, Cancer genetics and genomics, Cytogenetics, Developmental genetics, Disease association studies, Dysmorphology, ELSI (ethical, legal and social issues), Evolutionary genetics, Gene expression, Gene structure and organization, Genetics of complex diseases and epistatic interactions, Genetic epidemiology, Genome biology, Genome structure and organization, Genotype-phenotype relationships, Human Genomics, Immunogenetics and genomics, Linkage analysis and genetic mapping, Methods in Statistical Genetics, Molecular diagnostics, Mutation detection and analysis, Neurogenetics, Physical mapping and Population Genetics. Articles reporting animal models relevant to human biology or disease are also welcome. Preference will be given to those articles which address clinically relevant questions or which provide new insights into human biology. Unless reporting entirely novel and unusual aspects of a topic, clinical case reports, cytogenetic case reports, papers on descriptive population genetics, articles dealing with the frequency of polymorphisms or additional mutations within genes in which numerous lesions have already been described, and papers that report meta-analyses of previously published datasets will normally not be accepted. The Journal typically will not consider for publication manuscripts that report merely the isolation, map position, structure, and tissue expression profile of a gene of unknown function unless the gene is of particular interest or is a candidate gene involved in a human trait or disorder.
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