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Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics.

ABSTRACT: BACKGROUND:Quantitative molecular data from urine are rare in epidemiology and genetics. NMR spectroscopy could provide these data in high throughput, and it has already been applied in epidemiological settings to analyse urine samples. However, quantitative protocols for large-scale applications are not available. METHODS:We describe in detail how to prepare urine samples and perform NMR experiments to obtain quantitative metabolic information. Semi-automated quantitative line shape fitting analyses were set up for 43 metabolites and applied to data from various analytical test samples and from 1004 individuals from a population-based epidemiological cohort. Novel analyses on how urine metabolites associate with quantitative serum NMR metabolomics data (61 metabolic measures; n?=?995) were performed. In addition, confirmatory genome-wide analyses of urine metabolites were conducted (n?=?578). The fully automated quantitative regression-based spectral analysis is demonstrated for creatinine and glucose (n?=?4548). RESULTS:Intra-assay metabolite variations were mostly <5%, indicating high robustness and accuracy of urine NMR spectroscopy methodology per se. Intra-individual metabolite variations were large, ranging from 6% to 194%. However, population-based inter-individual metabolite variations were even larger (from 14% to 1655%), providing a sound base for epidemiological applications. Metabolic associations between urine and serum were found to be clearly weaker than those within serum and within urine, indicating that urinary metabolomics data provide independent metabolic information. Two previous genome-wide hits for formate and 2-hydroxyisobutyrate were replicated at genome-wide significance. CONCLUSION:Quantitative urine metabolomics data suggest broad novelty for systems epidemiology. A roadmap for an open access methodology is provided.

SUBMITTER: Tynkkynen T

PROVIDER: S-EPMC6659374 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics.

Tynkkynen Tuulia T Wang Qin Q Ekholm Jussi J Anufrieva Olga O Ohukainen Pauli P Vepsäläinen Jouko J Männikkö Minna M Keinänen-Kiukaanniemi Sirkka S Holmes Michael V MV Goodwin Matthew M Ring Susan S Chambers John C JC Kooner Jaspal J Järvelin Marjo-Riitta MR Kettunen Johannes J Hill Michael M Davey Smith George G Ala-Korpela Mika M

International journal of epidemiology 20190601 3

<h4>Background</h4>Quantitative molecular data from urine are rare in epidemiology and genetics. NMR spectroscopy could provide these data in high throughput, and it has already been applied in epidemiological settings to analyse urine samples. However, quantitative protocols for large-scale applications are not available.<h4>Methods</h4>We describe in detail how to prepare urine samples and perform NMR experiments to obtain quantitative metabolic information. Semi-automated quantitative line sh ...[more]

PMID: 30689875

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Project description:IntroductionIn orbital reconstruction, the optimal location of a predefined implant can be planned preoperatively. Surgical results can be assessed intraoperatively or postoperatively. A novel method for quantifying orbital implant position is introduced. The method measures predictability of implant placement: transformation parameters between planned and resulting implant position are quantified.MethodsThe method was tested on 3 human specimen heads. Computed Tomography scans were acquired at baseline with intact orbits (t0), after creation of the defect (t1) and postoperatively after reconstruction of the defect using a preformed implant (t2). Prior to reconstruction, the optimal implant position was planned on the t0 and t1 scans. Postoperatively, the planned and realized implant position were compared. The t0 and t2 scans were fused using iPlan software and the resulting implant was segmented in the fused t2 scan. An implant reference frame was created (Orbital Implant Positioning Frame); the planned implant was transformed to the reference position using an Iterative Closest Point approach. The segmentation of the resulting implant was also registered on the reference position, yielding rotational (pitch, yaw, roll) as well as translational parameters of implant position.ResultsMeasurement with the Orbital Implant Positioning Frame proved feasible on all three specimen. The positional outcome provided more thorough and accurate insight in resulting implant position than could be gathered from distance measurements alone. Observer-related errors were abolished from the process, since the method is largely automatic.ConclusionA novel method of quantifying surgical outcome in orbital reconstructive surgery was presented. The presented Orbital Implant Positioning Frame assessed all parameters involved in implant displacement. The method proved to be viable on three human specimen heads. Clinically, the method could provide direct feedback intraoperatively and could improve postoperative evaluation of orbital reconstructive surgery.

Dataset Information

Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics.

Publications

Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics.

Similar Datasets

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