Literature DB >> 23151027

Subset optimization by reference matching (STORM): an optimized statistical approach for recovery of metabolic biomarker structural information from 1H NMR spectra of biofluids.

Joram M Posma1, Isabel Garcia-Perez, Maria De Iorio, John C Lindon, Paul Elliott, Elaine Holmes, Timothy M D Ebbels, Jeremy K Nicholson.   

Abstract

We describe a new multivariate statistical approach to recover metabolite structure information from multiple (1)H NMR spectra in population sample sets. Subset optimization by reference matching (STORM) was developed to select subsets of (1)H NMR spectra that contain specific spectroscopic signatures of biomarkers differentiating between different human populations. STORM aims to improve the visualization of structural correlations in spectroscopic data by using these reduced spectral subsets containing smaller numbers of samples than the number of variables (n ≪ p). We have used statistical shrinkage to limit the number of false positive associations and to simplify the overall interpretation of the autocorrelation matrix. The STORM approach has been applied to findings from an ongoing human metabolome-wide association study on body mass index to identify a biomarker metabolite present in a subset of the population. Moreover, we have shown how STORM improves the visualization of more abundant NMR peaks compared to a previously published method (statistical total correlation spectroscopy, STOCSY). STORM is a useful new tool for biomarker discovery in the "omic" sciences that has widespread applicability. It can be applied to any type of data, provided that there is interpretable correlation among variables, and can also be applied to data with more than one dimension (e.g., 2D NMR spectra).

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Year:  2012        PMID: 23151027     DOI: 10.1021/ac302360v

Source DB:  PubMed          Journal:  Anal Chem        ISSN: 0003-2700            Impact factor:   6.986


  25 in total

Review 1.  Can NMR solve some significant challenges in metabolomics?

Authors:  G A Nagana Gowda; Daniel Raftery
Journal:  J Magn Reson       Date:  2015-08-18       Impact factor: 2.229

Review 2.  Applications of NMR spectroscopy to systems biochemistry.

Authors:  Teresa W-M Fan; Andrew N Lane
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2016-02-06       Impact factor: 9.795

3.  Identifying unknown metabolites using NMR-based metabolic profiling techniques.

Authors:  Isabel Garcia-Perez; Joram M Posma; Jose Ivan Serrano-Contreras; Claire L Boulangé; Queenie Chan; Gary Frost; Jeremiah Stamler; Paul Elliott; John C Lindon; Elaine Holmes; Jeremy K Nicholson
Journal:  Nat Protoc       Date:  2020-07-17       Impact factor: 13.491

Review 4.  Metabolic phenotyping for discovery of urinary biomarkers of diet, xenobiotics and blood pressure in the INTERMAP Study: an overview.

Authors:  Queenie Chan; Ruey Leng Loo; Timothy M D Ebbels; Linda Van Horn; Martha L Daviglus; Jeremiah Stamler; Jeremy K Nicholson; Elaine Holmes; Paul Elliott
Journal:  Hypertens Res       Date:  2016-12-22       Impact factor: 3.872

5.  Nutriome-metabolome relationships provide insights into dietary intake and metabolism.

Authors:  Joram M Posma; Isabel Garcia-Perez; Gary Frost; Ghadeer S Aljuraiban; Queenie Chan; Linda Van Horn; Martha Daviglus; Jeremiah Stamler; Elaine Holmes; Paul Elliott; Jeremy K Nicholson
Journal:  Nat Food       Date:  2020-06-22

6.  Urinary metabolic signatures of human adiposity.

Authors:  Paul Elliott; Joram M Posma; Queenie Chan; Isabel Garcia-Perez; Anisha Wijeyesekera; Magda Bictash; Timothy M D Ebbels; Hirotsugu Ueshima; Liancheng Zhao; Linda van Horn; Martha Daviglus; Jeremiah Stamler; Elaine Holmes; Jeremy K Nicholson
Journal:  Sci Transl Med       Date:  2015-04-29       Impact factor: 17.956

7.  A new paradigm for known metabolite identification in metabonomics/metabolomics: metabolite identification efficiency.

Authors:  Jeremy R Everett
Journal:  Comput Struct Biotechnol J       Date:  2015-01-27       Impact factor: 7.271

8.  A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments.

Authors:  Anthony C Dona; Michael Kyriakides; Flora Scott; Elizabeth A Shephard; Dorsa Varshavi; Kirill Veselkov; Jeremy R Everett
Journal:  Comput Struct Biotechnol J       Date:  2016-03-09       Impact factor: 7.271

9.  Modifying gut integrity and microbiome in children with severe acute malnutrition using legume-based feeds (MIMBLE): A pilot trial.

Authors:  Nuala Calder; Kevin Walsh; Peter Olupot-Olupot; Tonny Ssenyondo; Rita Muhindo; Ayub Mpoya; Jerusa Brignardello; Xuedan Wang; Eleanor McKay; Douglas Morrison; Elaine Holmes; Gary Frost; Kathryn Maitland
Journal:  Cell Rep Med       Date:  2021-05-18

10.  Statistical HOmogeneous Cluster SpectroscopY (SHOCSY): an optimized statistical approach for clustering of ¹H NMR spectral data to reduce interference and enhance robust biomarkers selection.

Authors:  Xin Zou; Elaine Holmes; Jeremy K Nicholson; Ruey Leng Loo
Journal:  Anal Chem       Date:  2014-05-13       Impact factor: 6.986

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