Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials

Yuanting Zheng, Yaqing Liu, Jingcheng Yang, Lianhua Dong, Rui Zhang, Sha Tian, Ying Yu, Luyao Ren, Wanwan Hou, Feng Zhu, Yuanbang Mai, Jinxiong Han, Lijun Zhang, Hui Jiang, Ling Lin, Jingwei Lou, Ruiqiang Li, Jingchao Lin, Huafen Liu, Ziqing KongDepeng Wang, Fangping Dai, Ding Bao, Zehui Cao, Qiaochu Chen, Qingwang Chen, Xingdong Chen, Yuechen Gao, He Jiang, Bin Li, Bingying Li, Jingjing Li, Ruimei Liu, Tao Qing, Erfei Shang, Jun Shang, Shanyue Sun, Haiyan Wang, Xiaolin Wang, Naixin Zhang, Peipei Zhang, Ruolan Zhang, Sibo Zhu, Andreas Scherer, Jiucun Wang, Jing Wang, Yinbo Huo, Gang Liu, Chengming Cao, Li Shao, Joshua Xu, Huixiao Hong, Wenming Xiao, Xiaozhen Liang, Daru Lu, Li Jin, Weida Tong, Chen Ding, Jinming Li, Xiang Fang, Leming Shi

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Sammanfattning

Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
Originalspråkengelska
TidskriftNature Biotechnology
Antal sidor38
ISSN1087-0156
DOI
StatusPublicerad - 2023
MoE-publikationstypA1 Tidskriftsartikel-refererad

Bibliografisk information

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© 2023, The Author(s).

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  • 217 Medicinsk teknik

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