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.

Study ID	ST001403
Study Title	Ontogeny related changes in the pediatric liver metabolome (part-II)
Study 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 Magnolia Drive
Email	brooke.fridley@moffitt.org
Phone	813-745-1461
Submit Date	2020-06-02
Analysis Type Detail	LC-MS
Release Date	2020-09-10
Release Version	1

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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
SA113975	CMH70994	12 to 18 years
SA113976	CMH8910	12 to 18 years
SA113977	CMH8906	12 to 18 years
SA113978	CMH885	12 to 18 years
SA113979	CMH8935	12 to 18 years
SA113980	CMH9027	12 to 18 years
SA113981	CMH9127	12 to 18 years
SA113982	CMH71281	12 to 18 years
SA113983	CMH64	12 to 18 years
SA113984	CMH9032	12 to 18 years
SA113961	CMH9011	1 to 5.99 years
SA113962	CMH8926	1 to 5.99 years
SA113963	CMH689	1 to 5.99 years
SA113964	CMH9023	1 to 5.99 years
SA113965	CMH792	1 to 5.99 years
SA113966	CMH9101	1 to 5.99 years
SA113967	CMH9612	1 to 5.99 years
SA113968	CMH9609	1 to 5.99 years
SA113969	CMH9608	1 to 5.99 years
SA113970	CMH677	1 to 5.99 years
SA113971	CMH9036	1 to 5.99 years
SA113972	CMH872	1 to 5.99 years
SA113973	CMH346	1 to 5.99 years
SA113974	CMH617	1 to 5.99 years
SA113985	CMH9003	6 to 11.99 years
SA113986	CMH9611	6 to 11.99 years
SA113987	CMH1860	6 to 11.99 years
SA113988	CMH8925	6 to 11.99 years
SA113989	CMH9013	6 to 11.99 years
SA113990	CMH9006	6 to 11.99 years
SA113991	CMH8920	6 to 11.99 years
SA113992	CMH70898	6 to 11.99 years
SA113993	CMH71000	6 to 11.99 years
SA113994	CMH8902	6 to 11.99 years
SA113995	CMH8917	6 to 11.99 years
SA113996	CMH1325	< 1 year of age
SA113997	CMH1296	< 1 year of age
SA113998	CMH1281	< 1 year of age
SA113999	CMH1157	< 1 year of age
SA114000	CMH1547	< 1 year of age
SA114001	CMH774	< 1 year of age
SA114002	CMH435	< 1 year of age
SA114003	CMH1055	< 1 year of age
SA114004	CMH86	< 1 year of age
SA114005	CMH825	< 1 year of age
SA114006	CMH569	< 1 year of age
SA114007	CMH780	< 1 year of age
SA114008	CMH759	< 1 year of age

Showing results 1 to 48 of 48

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.

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	Reversed phase
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:	Reversed phase

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