Genome Biology最新文献

筛选
英文 中文
SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues SMORE:空间图案揭示了复杂组织的细胞结构模式
IF 12.3 1区 生物学
Genome Biology Pub Date : 2025-01-03 DOI: 10.1186/s13059-024-03467-5
Zainalabedin Samadi, Kai Hao, Amjad Askary
{"title":"SMORE: spatial motifs reveal patterns in cellular architecture of complex tissues","authors":"Zainalabedin Samadi, Kai Hao, Amjad Askary","doi":"10.1186/s13059-024-03467-5","DOIUrl":"https://doi.org/10.1186/s13059-024-03467-5","url":null,"abstract":"Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells. Structural signatures detected by SMORE also form a basis for classifying tissues. Together, our method provides a new framework for uncovering spatial complexity in tissue organization and offers novel insights into tissue function.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"83 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spatiotemporal dynamics of early oogenesis in pigs 猪早期卵发生的时空动态
IF 12.3 1区 生物学
Genome Biology Pub Date : 2025-01-02 DOI: 10.1186/s13059-024-03464-8
Wei Ge, Yi-Lin Niu, Yu-Kang Li, Li Li, Han Wang, Wen-Wen Li, Tian Qiao, Yan-Ni Feng, Yu-Qing Feng, Jing Liu, Jun-Jie Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Wei Shen
{"title":"Spatiotemporal dynamics of early oogenesis in pigs","authors":"Wei Ge, Yi-Lin Niu, Yu-Kang Li, Li Li, Han Wang, Wen-Wen Li, Tian Qiao, Yan-Ni Feng, Yu-Qing Feng, Jing Liu, Jun-Jie Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Wei Shen","doi":"10.1186/s13059-024-03464-8","DOIUrl":"https://doi.org/10.1186/s13059-024-03464-8","url":null,"abstract":"In humans and other mammals, the process of oogenesis initiates asynchronously in specific ovarian regions, leading to the localization of dormant and growing follicles in the cortex and medulla, respectively; however, the current understanding of this process remains insufficient. Here, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to comprehend spatial–temporal gene expression profiles and explore the spatial organization of ovarian microenvironments during early oogenesis in pigs. Projection of the germ cell clusters at different stages of oogenesis into the spatial atlas unveils a “cortical to medullary (C-M)” distribution of germ cells in the developing porcine ovaries. Cross-species analysis between pigs and humans unveils a conserved C-M distribution pattern of germ cells during oogenesis, highlighting the utility of pigs as valuable models for studying human oogenesis in a spatial context. RNA velocity analysis with ST identifies the molecular characteristics and spatial dynamics of granulosa cell lineages originating from the cortical and medullary regions in pig ovaries. Spatial co-occurrence analysis and intercellular communication analysis unveils a distinct cell–cell communication pattern between germ cells and somatic cells in the cortex and medulla regions. Notably, in vitro culture of ovarian tissues verifies that intercellular NOTCH signaling and extracellular matrix (ECM) proteins played crucial roles in initiating meiotic and oogenic programs, highlighting an underappreciated role of ovarian microenvironments in orchestrating germ cell fates. Overall, our work provides insight into the spatial characteristics of early oogenesis and the regulatory role of ovarian microenvironments in germ cell fate within a spatial context.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"83 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells SiCLAT:活细胞中染色质环和活性转录的同时成像
IF 12.3 1区 生物学
Genome Biology Pub Date : 2025-01-02 DOI: 10.1186/s13059-024-03463-9
Xin Wan, Jie Kong, Xiaodi Hu, Lulu Liu, Yuanping Yang, Hu Li, Gaoao Liu, Xingchen Niu, Fengling Chen, Dan Zhang, Dahai Zhu, Yong Zhang
{"title":"SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells","authors":"Xin Wan, Jie Kong, Xiaodi Hu, Lulu Liu, Yuanping Yang, Hu Li, Gaoao Liu, Xingchen Niu, Fengling Chen, Dan Zhang, Dahai Zhu, Yong Zhang","doi":"10.1186/s13059-024-03463-9","DOIUrl":"https://doi.org/10.1186/s13059-024-03463-9","url":null,"abstract":"We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately labeled chromatin loop anchor interactions and associated gene transcription during myogenic differentiation. This imaging system offers a novel means of directly observing cis-element interactions and the corresponding gene transcription in living primary cells, thus providing real-time imaging for comprehensive mechanistic investigations of dynamic enhancer-promoter or enhancer-enhancer interactions in regulating transcription activation within living cells.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"16 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis 启动子捕获Hi-C在拟南芥中鉴定启动子相关环和喷泉结构
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-31 DOI: 10.1186/s13059-024-03465-7
Dingyue Wang, Suxin Xiao, Jiayue Shu, Lingxiao Luo, Minqi Yang, Myriam Calonje, Hang He, Baoxing Song, Yue Zhou
{"title":"Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis","authors":"Dingyue Wang, Suxin Xiao, Jiayue Shu, Lingxiao Luo, Minqi Yang, Myriam Calonje, Hang He, Baoxing Song, Yue Zhou","doi":"10.1186/s13059-024-03465-7","DOIUrl":"https://doi.org/10.1186/s13059-024-03465-7","url":null,"abstract":"Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete. Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes. We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"26 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular dependencies and genomic consequences of a global DNA damage tolerance defect 全球DNA损伤耐受缺陷的分子依赖性和基因组后果
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-31 DOI: 10.1186/s13059-024-03451-z
Daniel de Groot, Aldo Spanjaard, Ronak Shah, Maaike Kreft, Ben Morris, Cor Lieftink, Joyce J. I. Catsman, Shirley Ormel, Matilda Ayidah, Bas Pilzecker, Olimpia Alessandra Buoninfante, Paul C. M. van den Berk, Roderick L. Beijersbergen, Heinz Jacobs
{"title":"Molecular dependencies and genomic consequences of a global DNA damage tolerance defect","authors":"Daniel de Groot, Aldo Spanjaard, Ronak Shah, Maaike Kreft, Ben Morris, Cor Lieftink, Joyce J. I. Catsman, Shirley Ormel, Matilda Ayidah, Bas Pilzecker, Olimpia Alessandra Buoninfante, Paul C. M. van den Berk, Roderick L. Beijersbergen, Heinz Jacobs","doi":"10.1186/s13059-024-03451-z","DOIUrl":"https://doi.org/10.1186/s13059-024-03451-z","url":null,"abstract":"DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiquitinated PCNA, respectively. To determine the molecular and genomic impact of a global DDT defect, we studied PcnaK164R/−;Rev1−/− compound mutants in mouse cells. Double-mutant cells display increased replication stress, hypersensitivity to genotoxic agents, replication speed, and repriming. A whole-genome CRISPR-Cas9 screen revealed a strict reliance of double-mutant cells on the CST complex, where CST promotes fork stability. Whole-genome sequencing indicated that this double-mutant DDT defect favors the generation of large, replication-stress inducible deletions of 0.4–4.0 kbp, defined as type 3 deletions. Junction break sites of these deletions reveal microhomology preferences of 1–2 base pairs, differing from the smaller type 1 and type 2 deletions. These differential characteristics suggest the existence of molecularly distinct deletion pathways. Type 3 deletions are abundant in human tumors, can dominate the deletion landscape, and are associated with DNA damage response status and treatment modality. Our data highlight the essential contribution of the DDT system to genome maintenance and type 3 deletions as mutational signature of replication stress. The unique characteristics of type 3 deletions implicate the existence of a novel deletion pathway in mice and humans that is counteracted by DDT. ","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"35 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142905021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
vmrseq: probabilistic modeling of single-cell methylation heterogeneity Vmrseq:单细胞甲基化异质性的概率建模
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-30 DOI: 10.1186/s13059-024-03457-7
Ning Shen, Keegan Korthauer
{"title":"vmrseq: probabilistic modeling of single-cell methylation heterogeneity","authors":"Ning Shen, Keegan Korthauer","doi":"10.1186/s13059-024-03457-7","DOIUrl":"https://doi.org/10.1186/s13059-024-03457-7","url":null,"abstract":"Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on predefined regions or sliding windows and report regions insensitive to heterogeneity level present in input. We present vmrseq, a statistical method that overcomes these challenges to detect VMRs with increased accuracy in synthetic benchmarks and improved feature selection in case studies. vmrseq also highlights context-dependent correlations between methylation and gene expression, supporting previous findings and facilitating novel hypotheses on epigenetic regulation. vmrseq is available at https://github.com/nshen7/vmrseq .","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"5 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromatin-based memory as a self-stabilizing influence on cell identity 基于染色质的记忆对细胞身份的自稳定影响
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-30 DOI: 10.1186/s13059-024-03461-x
Charles C. Bell, Geoffrey J. Faulkner, Omer Gilan
{"title":"Chromatin-based memory as a self-stabilizing influence on cell identity","authors":"Charles C. Bell, Geoffrey J. Faulkner, Omer Gilan","doi":"10.1186/s13059-024-03461-x","DOIUrl":"https://doi.org/10.1186/s13059-024-03461-x","url":null,"abstract":"Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through pervasive, local, feedback loops, chromatin memory enables cell states that were initially unstable to become stable. Deeper appreciation of this self-stabilizing role for chromatin broadens our perspective of Waddington’s epigenetic landscape from a static surface with islands of stability shaped by evolution, to a plasticine surface molded by experience. With implications for the evolution of cell types, stabilization of resistant states in cancer, and the widespread plasticity of complex life.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"3 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations 一种检测细胞间相关性的空间染色质可及性模式的方法
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-30 DOI: 10.1186/s13059-024-03458-6
Xiaoyang Chen, Keyi Li, Xiaoqing Wu, Zhen Li, Qun Jiang, Xuejian Cui, Zijing Gao, Yanhong Wu, Rui Jiang
{"title":"Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations","authors":"Xiaoyang Chen, Keyi Li, Xiaoqing Wu, Zhen Li, Qun Jiang, Xuejian Cui, Zijing Gao, Yanhong Wu, Rui Jiang","doi":"10.1186/s13059-024-03458-6","DOIUrl":"https://doi.org/10.1186/s13059-024-03458-6","url":null,"abstract":"Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the key analytic task for characterizing the spatial chromatin accessibility landscape of complex tissues. Here, we propose an efficient and iterative model, Descart, for spatially variable peaks identification based on the graph of inter-cellular correlations. Through the comprehensive benchmarking, we demonstrate the superiority of Descart in revealing cellular heterogeneity and capturing tissue structure. Utilizing the graph of inter-cellular correlations, Descart shows its potential to denoise data, identify peak modules, and detect gene-peak interactions.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"25 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy 多组学方法显示弥漫性中线胶质瘤存在DNA复制改变,易受复制应激治疗的影响
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-20 DOI: 10.1186/s13059-024-03460-y
Anastasia E. Hains, Kashish Chetal, Tsunetoshi Nakatani, Joana G. Marques, Andreas Ettinger, Carlos A. O. Biagi Junior, Adriana Gonzalez-Sandoval, Renjitha Pillai, Mariella G. Filbin, Maria-Elena Torres-Padilla, Ruslan I. Sadreyev, Capucine Van Rechem
{"title":"Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy","authors":"Anastasia E. Hains, Kashish Chetal, Tsunetoshi Nakatani, Joana G. Marques, Andreas Ettinger, Carlos A. O. Biagi Junior, Adriana Gonzalez-Sandoval, Renjitha Pillai, Mariella G. Filbin, Maria-Elena Torres-Padilla, Ruslan I. Sadreyev, Capucine Van Rechem","doi":"10.1186/s13059-024-03460-y","DOIUrl":"https://doi.org/10.1186/s13059-024-03460-y","url":null,"abstract":"The fatal diffuse midline gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling differentiation. The identification of targetable pathways remains very poorly explored. Toward this goal, we undertake a multi-omics approach to evaluate replication timing profiles, transcriptomics, and cell cycle features in DMG cells from both H3.1K27M and H3.3K27M subgroups and perform a comparative, integrative data analysis with healthy brain tissue. DMG cells present differential replication timing in each subgroup, which, in turn, correlates with significant differential gene expression. Differentially expressed genes in S phase are involved in various pathways related to DNA replication. We detect increased expression of DNA replication genes earlier in the cell cycle in DMG cell lines compared to normal brain cells. Furthermore, the distance between origins of replication in DMG cells is smaller than in normal brain cells and their fork speed is slower, a read-out of replication stress. Consistent with these findings, DMG tumors present high replication stress signatures in comparison to normal brain cells. Finally, DMG cells are specifically sensitive to replication stress therapy. This whole genome multi-omics approach provides insights into the cell cycle regulation of DMG via the H3K27M mutations and establishes a pharmacologic vulnerability in DNA replication, which resolves a potentially novel therapeutic strategy for this non-curable disease.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"20 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA 基于甲基化的无浆细胞DNA细胞型反褶积方法的系统评价
IF 12.3 1区 生物学
Genome Biology Pub Date : 2024-12-19 DOI: 10.1186/s13059-024-03456-8
Tongyue Sun, Jinqi Yuan, Yacheng Zhu, Jingqi Li, Shen Yang, Junpeng Zhou, Xinzhou Ge, Susu Qu, Wei Li, Jingyi Jessica Li, Yumei Li
{"title":"Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA","authors":"Tongyue Sun, Jinqi Yuan, Yacheng Zhu, Jingqi Li, Shen Yang, Junpeng Zhou, Xinzhou Ge, Susu Qu, Wei Li, Jingyi Jessica Li, Yumei Li","doi":"10.1186/s13059-024-03456-8","DOIUrl":"https://doi.org/10.1186/s13059-024-03456-8","url":null,"abstract":"Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur during disease progression or in response to treatment. Consequently, cfDNA has emerged as a valuable noninvasive biomarker for disease detection and treatment monitoring. Although there are many methylation-based methods for cfDNA cell type deconvolution, a comprehensive and systematic evaluation of these methods has yet to be conducted. In this study, we benchmark five methods: MethAtlas, cfNOMe toolkit, CelFiE, CelFEER, and UXM. Utilizing deep whole-genome bisulfite sequencing data from 35 human cell types, we generate in silico cfDNA samples with ground truth cell type proportions to assess the deconvolution performance of the five methods under multiple scenarios. Our findings indicate that multiple factors, including reference marker selection, sequencing depth, and reference atlas completeness, jointly influence the deconvolution performance. Notably, an incomplete reference with missing markers or cell types leads to suboptimal results. We observe performance differences among methods under varying conditions, underscoring the importance of tailoring cfDNA deconvolution analyses. To increase the clinical relevance of our findings, we further evaluate each method’s performance in potential clinical applications using real-world datasets. Based on the benchmark results, we propose general guidelines to choose the suitable methods based on sequencing depth of the cfDNA data and completeness of the reference atlas to maximize the performance of methylation-based cfDNA cell type deconvolution.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"87 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信