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Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy

Rico Rueedi, Roger Mallol, Johannes Raffler, David Lamparter, Nele Friedrich, Peter Vollenweider, Gérard Waeber, Gabi Kastenmüller, Zoltán Kutalik, Sven Bergmann, Christos A. Ouzounis
2017 PLoS Computational Biology  
Metabomatching: Using genetic association to identify metabolites in 1 H NMR spectroscopy PLOS Computational Biology | https://doi.  ...  When the metabolome is measured by proton NMR spectroscopy, genetically associated features tend to correspond to peaks in the NMR spectrum of the underlying metabolites.  ...  However, whereas the aim of metabolite spiking is to determine an unknown spectrum for a known metabolite, we developed metabomatching to use genetic spiking to identify an unknown metabolite from a known  ... 
doi:10.1371/journal.pcbi.1005839 pmid:29194434 pmcid:PMC5711027 fatcat:u4gtowscuzd7xi2rasbyczuggu

Untargeted metabolome- and transcriptome-wide association study identifies causal genes modulating metabolite concentrations in urine [article]

Reyhan Sonmez Flitman, Bita Khalili, Rico Rueedi, Zoltan Kutalik, Sven Bergmann
2020 bioRxiv   pre-print
In this study we investigate the results of a metabolome- and transcriptome-wide association study to identify genes influencing the human metabolome.  ...  As for the metabolome we took an untargeted approach using binned features from 1H nuclear magnetic resonance spectroscopy (NMR) of urine samples from the same subjects allowing for data-driven discovery  ...  In the present study we use metabomatching to identify metabolites that are associated with gene expression.  ... 
doi:10.1101/2020.05.22.110197 fatcat:xnou3r2fkrb33f3wybee24yqe4

Automated analysis of large-scale NMR data generates metabolomic signatures and links them to candidate metabolites [article]

Bita Khalili, Mattia Tomasoni, Mirjam Mattei, Roger Mallol Parera, Reyhan Sonmez, Daniel Krefl, Rico Rueedi, Sven Bergmann
2019 bioRxiv   pre-print
We used our previously developed metabomatching method to match the sets generated by these algorithms to NMR spectra of individual metabolites available in public databases.  ...  In this work, we test the capacity of three analysis tools to extract metabolite signatures from 968 NMR profiles of human urine samples.  ...  ACP: Averaged Correlation Profile We devised the following greedy approach to populate a list L of feature pairs and their corresponding correlation profiles c as input for metabomatching: (1) We compute  ... 
doi:10.1101/613935 fatcat:a5gu3b6cejhgbiqjueoc43vgsq

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links

Rico Rueedi, Mirko Ledda, Andrew W. Nicholls, Reza M. Salek, Pedro Marques-Vidal, Edgard Morya, Koichi Sameshima, Ivan Montoliu, Laeticia Da Silva, Sebastiano Collino, François-Pierre Martin, Serge Rezzi (+11 others)
2014 PLoS Genetics  
They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome.  ...  Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9610 244 ) and lysine (rs8101881, P = 1.2610 233 ), respectively.  ...  Encouraged by these findings, we decided to use metabomatching to identify the metabolites (or metabolite families) underlying some of our associations.  ... 
doi:10.1371/journal.pgen.1004132 pmid:24586186 pmcid:PMC3930510 fatcat:kzs6wrnvwffsphjsihb4jhgh3e

Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality

Johannes Raffler, Nele Friedrich, Matthias Arnold, Tim Kacprowski, Rico Rueedi, Elisabeth Altmaier, Sven Bergmann, Kathrin Budde, Christian Gieger, Georg Homuth, Maik Pietzner, Werner Römisch-Margl (+9 others)
2015 PLoS Genetics  
In the largest genetic study on urinary metabolites to date, we identified 15 additional loci. Most of the 26 loci also affect blood metabolite levels.  ...  Two-thirds of the urinary loci also have a metabolite association in blood.  ...  Acknowledgments We thank all participants in the SHIP and KORA studies for donating their blood, urine and time. We also thank all SHIP and KORA study personnel that made this work possible.  ... 
doi:10.1371/journal.pgen.1005487 pmid:26352407 pmcid:PMC4564198 fatcat:m66xta4ybbbyxo2dtehbibjgke

From Metabonomics to Pharmacometabonomics: The Role of Metabolic Profiling in Personalized Medicine

Jeremy R. Everett
2016 Frontiers in Pharmacology  
John Lindon, and Professor Ian Wilson in the Department of Surgery and Cancer at Imperial.  ...  I would also like to acknowledge the stimulating support of my students and post-doctoral research assistants, Ms. Beatriz Sanchon Lopez, Ms. Dorna Varshavi, and Dr. Dorsa Varshavi.  ...  Out of 139 discovered associations, 56 replicated and the identity of the underlying metabolites was sought from the NMR features using a new metabomatching method.  ... 
doi:10.3389/fphar.2016.00297 pmid:27660611 pmcid:PMC5014868 fatcat:hchlrug36ncwbioj7xdtjmcqsi

A New Paradigm for Known Metabolite Identification in Metabonomics/Metabolomics: Metabolite Identification Efficiency

Jeremy R. Everett
2015 Computational and Structural Biotechnology Journal  
A new paradigm is proposed for assessing confidence in the identification of known metabolites in metabonomics studies using NMR spectroscopy approaches.  ...  These indices, together with some guidelines, can be used to provide a better indication of known metabolite identification confidence in metabonomics studies than existing methods.  ...  the 600 MHz NMR facilities; Dr.  ... 
doi:10.1016/j.csbj.2015.01.002 pmid:25750701 pmcid:PMC4348432 fatcat:26kycrqz7nconpappjvvvrqetu

Metabolic profiling of maternal serum of women at high-risk of spontaneous preterm birth using NMR and mGWAS approach

Juhi Gupta, Angharad Care, Laura Goodfellow, Zarko Alfirevic, Lu-Yun Lian, Bertram Müller-Myhsok, Ana Alfirevic, Marie Phelan
2021 Bioscience Reports  
MGWAS identified several metabolite bins with strong genetic associations.  ...  This study aimed to investigate the metabolic biomarkers of PTB in early pregnancy and the association of significant metabolites with participant genotypes.  ...  , S., Stern, V.L., Parker, J.L., Stafford, G.P., Paley, M.N. et al. (2016) 410 Identifying metabolite markers for preterm birth in cervicovaginal fluid by magnetic resonance 411 spectroscopy.  ... 
doi:10.1042/bsr20210759 pmid:34402867 pmcid:PMC8415214 fatcat:aaes5gwx7jcv5ilpai7l4xlhue

48th European Mathematical Genetics Meeting (EMGM) 2020

Zoltan Kutalik
2020 Human Heredity  
In contrast, genetic variants that are associated with the expression of multiple target genes in trans, have the potential to directly identify the cellular processes affected by disease variants.  ...  A major challenge in human genetics is translating non-coding GWAS loci to mechanistic understanding about the disease causing processes.  ...  Next, we used metabomatching to identify most likely metabolites underlying these novel associations.  ... 
doi:10.1159/000507248 pmid:32268327 fatcat:3aneluafpnes3a2ayzn53uffca