Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures
Abstract Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introduce Melody, a framework that generates, harmonizes,...
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| Format: | Article |
| Language: | English |
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BMC
2025-08-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03721-4 |
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| _version_ | 1849735898208403456 |
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| author | Zhoujingpeng Wei Guanhua Chen Zheng-Zheng Tang |
| author_facet | Zhoujingpeng Wei Guanhua Chen Zheng-Zheng Tang |
| author_sort | Zhoujingpeng Wei |
| collection | DOAJ |
| description | Abstract Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introduce Melody, a framework that generates, harmonizes, and combines study-specific summary association statistics to powerfully and robustly identify microbial signatures in meta-analysis. Comprehensive and realistic simulations demonstrate that Melody substantially outperforms existing approaches in prioritizing true signatures. In the meta-analyses of five studies on colorectal cancer and eight studies on the gut metabolome, we showcase the superior stability, reliability, and predictive performance of Melody-identified signatures. |
| format | Article |
| id | doaj-art-939bb7b894824bcfa8a2fda5ff0184a6 |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-939bb7b894824bcfa8a2fda5ff0184a62025-08-20T03:07:25ZengBMCGenome Biology1474-760X2025-08-0126112010.1186/s13059-025-03721-4Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signaturesZhoujingpeng Wei0Guanhua Chen1Zheng-Zheng Tang2Department of Biostatistics and Medical Informatics, University of Wisconsin-MadisonDepartment of Biostatistics and Medical Informatics, University of Wisconsin-MadisonDepartment of Biostatistics and Medical Informatics, University of Wisconsin-MadisonAbstract Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introduce Melody, a framework that generates, harmonizes, and combines study-specific summary association statistics to powerfully and robustly identify microbial signatures in meta-analysis. Comprehensive and realistic simulations demonstrate that Melody substantially outperforms existing approaches in prioritizing true signatures. In the meta-analyses of five studies on colorectal cancer and eight studies on the gut metabolome, we showcase the superior stability, reliability, and predictive performance of Melody-identified signatures.https://doi.org/10.1186/s13059-025-03721-4Absolute abundanceBest subset selectionCompositional dataMeta-analysisQuasi-multinomial modelRelative abundance |
| spellingShingle | Zhoujingpeng Wei Guanhua Chen Zheng-Zheng Tang Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures Genome Biology Absolute abundance Best subset selection Compositional data Meta-analysis Quasi-multinomial model Relative abundance |
| title | Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures |
| title_full | Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures |
| title_fullStr | Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures |
| title_full_unstemmed | Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures |
| title_short | Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures |
| title_sort | melody meta analysis of microbiome association studies for discovering generalizable microbial signatures |
| topic | Absolute abundance Best subset selection Compositional data Meta-analysis Quasi-multinomial model Relative abundance |
| url | https://doi.org/10.1186/s13059-025-03721-4 |
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