Summary of study ST001404

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 IDST001404
Study TitleOntogeny related changes in the pediatric liver metabolome (part-III)
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:SU001478
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
SA114016CMH7118712 to 18 years
SA114017CMH7100812 to 18 years
SA114018CMH7077912 to 18 years
SA114019CMH32612 to 18 years
SA114020CMH7129412 to 18 years
SA114021CMH7103212 to 18 years
SA114022CMH7106512 to 18 years
SA114023CMH7151212 to 18 years
SA114024CMH900512 to 18 years
SA114025CMH891212 to 18 years
SA114026CMH7151412 to 18 years
SA114009CMH2601 to 5.99 years
SA114010CMH718391 to 5.99 years
SA114011CMH710021 to 5.99 years
SA114012CMH5511 to 5.99 years
SA114013CMH2111 to 5.99 years
SA114014CMH8661 to 5.99 years
SA114015CMH709431 to 5.99 years
SA114027CMH90286 to 11.99 years
SA114028CMH993776 to 11.99 years
SA114029CMH709156 to 11.99 years
SA114030CMH709216 to 11.99 years
SA114031CMH46 to 11.99 years
SA114032CMH89246 to 11.99 years
SA114033CMH3076 to 11.99 years
SA114034CMH710586 to 11.99 years
SA114035CMH89096 to 11.99 years
SA114036CMH714146 to 11.99 years
SA114037CMH89016 to 11.99 years
SA114038CMH432< 1 year of age
SA114039CMH227< 1 year of age
SA114040CMH234< 1 year of age
SA114041CMH249< 1 year of age
SA114042CMH258< 1 year of age
SA114043CMH218< 1 year of age
SA114044CMH214< 1 year of age
SA114045CMH203< 1 year of age
SA114046CMH207< 1 year of age
SA114047CMH213< 1 year of age
SA114048CMH259< 1 year of age
SA114049CMH268< 1 year of age
SA114050CMH316< 1 year of age
SA114051CMH318< 1 year of age
SA114052CMH320< 1 year of age
SA114053CMH298< 1 year of age
SA114054CMH290< 1 year of age
SA114055CMH283< 1 year of age
SA114056CMH284< 1 year of age
SA114057CMH289< 1 year of age
SA114058CMH202< 1 year of age
Showing results 1 to 50 of 50

Collection:

Collection ID:CO001473
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:TR001493
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP001486
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 AN002346
Analysis type MS
Chromatography type UPLC
Chromatography system Waters Acquity
Column Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units m/z

Chromatography:

Chromatography ID:CH001719
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)
Chromatography Type:UPLC

MS:

MS ID:MS002188
Analysis ID:AN002346
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon
Ion Mode:UNSPECIFIED
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