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Prediction and mode...
Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
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- Brunius, Carl, 1974 (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för Molekylära vetenskaper,Department of Molecular Sciences,Chalmers University of Technology
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- Pedersen, Anders, 1976 (författare)
- Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University,University of Gothenburg
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- Malmodin, Daniel, 1974 (författare)
- Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University,University of Gothenburg
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- Karlsson, B Göran, 1962 (författare)
- Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University,University of Gothenburg
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- Andersson, L. I. (författare)
- Karolinska Institutet
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- Tybring, G. (författare)
- Karolinska Institutet
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- Landberg, Rikard, 1981 (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för Molekylära vetenskaper,Department of Molecular Sciences,Chalmers University of Technology,Karolinska Institute
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(creator_code:org_t)
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- 2017-07-14
- 2017
- Engelska.
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059 .- 1367-4811. ; 33:22, s. 3567-3574
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Abstract
Ämnesord
Stäng
- Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples. This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1-36 h pre-centrifugation delay time at 4 A degrees C and 22 A degrees C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 A degrees C. Moreover, pre-centrifugation delay at 4 A degrees C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 A degrees C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology (hsv//eng)
- NATURVETENSKAP -- Matematik (hsv//swe)
- NATURAL SCIENCES -- Mathematics (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik -- Medicinsk bioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology -- Medical Biotechnology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- quality assessment
- cross-validation
- human blood
- metabonomics
- urine
- serum
- Biochemistry & Molecular Biology
- Biotechnology & Applied Microbiology
- Computer Science
- Mathematical & Computational Biology
- Mathematics
- urine
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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