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


ABSTRACT: 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.

SUBMITTER: Zheng Y 

PROVIDER: S-EPMC11252085 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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

Zheng Yuanting Y   Liu Yaqing Y   Yang Jingcheng J   Dong Lianhua L   Zhang Rui R   Tian Sha S   Yu Ying Y   Ren Luyao L   Hou Wanwan W   Zhu Feng F   Mai Yuanbang Y   Han Jinxiong J   Zhang Lijun L   Jiang Hui H   Lin Ling L   Lou Jingwei J   Li Ruiqiang R   Lin Jingchao J   Liu Huafen H   Kong Ziqing Z   Wang Depeng D   Dai Fangping F   Bao Ding D   Cao Zehui Z   Chen Qiaochu Q   Chen Qingwang Q   Chen Xingdong X   Gao Yuechen Y   Jiang He H   Li Bin B   Li Bingying B   Li Jingjing J   Liu Ruimei R   Qing Tao T   Shang Erfei E   Shang Jun J   Sun Shanyue S   Wang Haiyan H   Wang Xiaolin X   Zhang Naixin N   Zhang Peipei P   Zhang Ruolan R   Zhu Sibo S   Scherer Andreas A   Wang Jiucun J   Wang Jing J   Huo Yinbo Y   Liu Gang G   Cao Chengming C   Shao Li L   Xu Joshua J   Hong Huixiao H   Xiao Wenming W   Liang Xiaozhen X   Lu Daru D   Jin Li L   Tong Weida W   Ding Chen C   Li Jinming J   Fang Xiang X   Shi Leming L  

Nature biotechnology 20230907 7


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  ...[more]

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