Summary of study ST001403

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000962. The data can be accessed directly via it's Project DOI: 10.21228/M8BM3B This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001403
Study TitleOntogeny related changes in the pediatric liver metabolome (part-II)
Study SummaryA major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent.
Institute
Moffitt Cancer Center
Last NameFridley
First NameBrooke
Address12902 Magnolia Drive
Emailbrooke.fridley@moffitt.org
Phone813-745-1461
Submit Date2020-06-02
Analysis Type DetailLC-MS
Release Date2020-09-10
Release Version1
Brooke Fridley Brooke Fridley
https://dx.doi.org/10.21228/M8BM3B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000962
Project DOI:doi: 10.21228/M8BM3B
Project Title:Ontogeny related changes in the pediatric liver metabolome
Project Summary:A major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent.
Institute:Moffitt Cancer Center
Last Name:Fridley
First Name:Brooke
Address:12902 USF Magnolia Dr
Email:brooke.fridley@moffitt.org
Phone:813-745-1461

Subject:

Subject ID:SU001477
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:0-18 years old
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id GROUP_DESCRIPTION
SA113975CMH7099412 to 18 years
SA113976CMH891012 to 18 years
SA113977CMH890612 to 18 years
SA113978CMH88512 to 18 years
SA113979CMH893512 to 18 years
SA113980CMH902712 to 18 years
SA113981CMH912712 to 18 years
SA113982CMH7128112 to 18 years
SA113983CMH6412 to 18 years
SA113984CMH903212 to 18 years
SA113961CMH90111 to 5.99 years
SA113962CMH89261 to 5.99 years
SA113963CMH6891 to 5.99 years
SA113964CMH90231 to 5.99 years
SA113965CMH7921 to 5.99 years
SA113966CMH91011 to 5.99 years
SA113967CMH96121 to 5.99 years
SA113968CMH96091 to 5.99 years
SA113969CMH96081 to 5.99 years
SA113970CMH6771 to 5.99 years
SA113971CMH90361 to 5.99 years
SA113972CMH8721 to 5.99 years
SA113973CMH3461 to 5.99 years
SA113974CMH6171 to 5.99 years
SA113985CMH90036 to 11.99 years
SA113986CMH96116 to 11.99 years
SA113987CMH18606 to 11.99 years
SA113988CMH89256 to 11.99 years
SA113989CMH90136 to 11.99 years
SA113990CMH90066 to 11.99 years
SA113991CMH89206 to 11.99 years
SA113992CMH708986 to 11.99 years
SA113993CMH710006 to 11.99 years
SA113994CMH89026 to 11.99 years
SA113995CMH89176 to 11.99 years
SA113996CMH1325< 1 year of age
SA113997CMH1296< 1 year of age
SA113998CMH1281< 1 year of age
SA113999CMH1157< 1 year of age
SA114000CMH1547< 1 year of age
SA114001CMH774< 1 year of age
SA114002CMH435< 1 year of age
SA114003CMH1055< 1 year of age
SA114004CMH86< 1 year of age
SA114005CMH825< 1 year of age
SA114006CMH569< 1 year of age
SA114007CMH780< 1 year of age
SA114008CMH759< 1 year of age
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001472
Collection Summary:Postmortem pediatric human liver tissue samples were obtained through the Brain and Tissue Bank for Developmental Disorders at the University of Maryland (Baltimore, MD), the Liver Tissue Cell Distribution System (LTCDS; University of Pittsburgh and University of Minnesota), and XenoTech LLC (Lenexa, KS). The use of these tissues was classified as nonhuman subject research by the Children's Mercy Hospital Pediatric Institutional Review Board A replication set of post-mortem liver tissue samples from autopsy of fetuses (from therapeutic abortions or stillbirths) and infants was provided by the Erasmus Medical Center Tissue Bank, Sophia Children’s Hospital, Rotterdam, The Netherlands. Tissue was procured at the time of autopsy within 24 h after death and snap-frozen at −80 °C for later research use. The Erasmus Medical Center Research Ethics Board waived the need for formal ethics approval according to the Dutch Law on Medical Research in Humans. Tissue was collected when parental written informed consent for both autopsy and the explicit use of the tissue for research was present. Samples were selected based on the absence of a clinical diagnosis or medications affecting the liver (CMH and Erasmus), and tissue that was histologically normal (Erasmus). Samples were stratified into four age groups: less than one year of age (age group 1), one to less than six years (age group 2), six to less than 12 years (age group 3), and 12 to 18 years of age (age group 4). In total 98 liver samples were available for metabolomic analysis.
Sample Type:Liver

Treatment:

Treatment ID:TR001492
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP001485
Sampleprep Summary:Given that the metabolomic platform changed between the first analysis and the sample set containing the replication samples, the second experiment examined the entire set of 98 samples. The same 48 samples previously processed in Experiment 1 and designated as “batch 1” above were re-analyzed on the new platform, with the results designated “batch 2”. The replication samples from Erasmus/Sophia Children’s Hospital and additional samples from CMH (N=50) are designated as “batch 3”. Following the sample extraction, the resulting extract was analyzed using a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution (Evans et al., 2014). Four methods were utilized: two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), RP/UPLC-MS/MS with negative ion mode ESI, and HILIC/UPLC-MS/MS with negative ion mode ESI. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slightly between methods but covered 70-1000 m/z. The final experiment 2 metabolomic dataset comprised a total of 971 biochemicals, 779 compounds of known identity (named biochemicals) and 192 compounds of unknown structural identity.

Combined analysis:

Analysis ID AN002345
Analysis type MS
Chromatography type GC
Chromatography system Waters Acquity
Column Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units m/z

Chromatography:

Chromatography ID:CH001718
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Chromatography Type:GC

MS:

MS ID:MS002187
Analysis ID:AN002345
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon
Ion Mode:UNSPECIFIED
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