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Treffer: Bootstrap Evaluation of Association Matrices (BEAM) for Integrating Multiple Omics Profiles with Multiple Outcomes.

Title:
Bootstrap Evaluation of Association Matrices (BEAM) for Integrating Multiple Omics Profiles with Multiple Outcomes.
Authors:
Seffernick AE; Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA., Cao X; Department of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis, TN, USA., Cheng C; Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA., Yang W; Department of Pharmacy & Pharmaceutical Services, St. Jude Children's Research Hospital, Memphis, TN, USA.; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA., Autry RJ; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.; Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany., Yang JJ; Department of Pharmacy & Pharmaceutical Services, St. Jude Children's Research Hospital, Memphis, TN, USA.; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA., Pui CH; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA., Teachey DT; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.; Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Lamba JK; Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA., Mullighan CG; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA., Pounds SB; Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA.
Source:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 03. Date of Electronic Publication: 2024 Aug 03.
Publication Type:
Journal Article; Preprint
Language:
English
Journal Info:
Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
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Grant Information:
P30 CA021765 United States CA NCI NIH HHS; R01 CA132946 United States CA NCI NIH HHS; R01 CA270120 United States CA NCI NIH HHS; T32 CA236748 United States CA NCI NIH HHS
Entry Date(s):
Date Created: 20240812 Latest Revision: 20241023
Update Code:
20250114
PubMed Central ID:
PMC11312528
DOI:
10.1101/2024.07.31.605805
PMID:
39131398
Database:
MEDLINE

Weitere Informationen

Motivation: Large datasets containing multiple clinical and omics measurements for each subject motivate the development of new statistical methods to integrate these data to advance scientific discovery.
Model: We propose bootstrap evaluation of association matrices (BEAM), which integrates multiple omics profiles with multiple clinical endpoints. BEAM associates a set omic features with clinical endpoints via regression models and then uses bootstrap resampling to determine statistical significance of the set. Unlike existing methods, BEAM uniquely accommodates an arbitrary number of omic profiles and endpoints.
Results: In simulations, BEAM performed similarly to the theoretically best simple test and outperformed other integrated analysis methods. In an example pediatric leukemia application, BEAM identified several genes with biological relevance established by a CRISPR assay that had been missed by univariate screens and other integrated analysis methods. Thus, BEAM is a powerful, flexible, and robust tool to identify genes for further laboratory and/or clinical research evaluation.
Availability: Source code, documentation, and a vignette for BEAM are available on GitHub at: https://github.com/annaSeffernick/BEAMR. The R package is available from CRAN at: https://cran.r-project.org/package=BEAMR.
Contact: Stanley.Pounds@stjude.org.
Supplementary Information: Supplementary data are available at the journal's website.