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.

Study ID	ST001404
Study Title	Ontogeny related changes in the pediatric liver metabolome (part-III)
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:	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
SA114016	CMH71187	12 to 18 years
SA114017	CMH71008	12 to 18 years
SA114018	CMH70779	12 to 18 years
SA114019	CMH326	12 to 18 years
SA114020	CMH71294	12 to 18 years
SA114021	CMH71032	12 to 18 years
SA114022	CMH71065	12 to 18 years
SA114023	CMH71512	12 to 18 years
SA114024	CMH9005	12 to 18 years
SA114025	CMH8912	12 to 18 years
SA114026	CMH71514	12 to 18 years
SA114009	CMH260	1 to 5.99 years
SA114010	CMH71839	1 to 5.99 years
SA114011	CMH71002	1 to 5.99 years
SA114012	CMH551	1 to 5.99 years
SA114013	CMH211	1 to 5.99 years
SA114014	CMH866	1 to 5.99 years
SA114015	CMH70943	1 to 5.99 years
SA114027	CMH9028	6 to 11.99 years
SA114028	CMH99377	6 to 11.99 years
SA114029	CMH70915	6 to 11.99 years
SA114030	CMH70921	6 to 11.99 years
SA114031	CMH4	6 to 11.99 years
SA114032	CMH8924	6 to 11.99 years
SA114033	CMH307	6 to 11.99 years
SA114034	CMH71058	6 to 11.99 years
SA114035	CMH8909	6 to 11.99 years
SA114036	CMH71414	6 to 11.99 years
SA114037	CMH8901	6 to 11.99 years
SA114038	CMH432	< 1 year of age
SA114039	CMH227	< 1 year of age
SA114040	CMH234	< 1 year of age
SA114041	CMH249	< 1 year of age
SA114042	CMH258	< 1 year of age
SA114043	CMH218	< 1 year of age
SA114044	CMH214	< 1 year of age
SA114045	CMH203	< 1 year of age
SA114046	CMH207	< 1 year of age
SA114047	CMH213	< 1 year of age
SA114048	CMH259	< 1 year of age
SA114049	CMH268	< 1 year of age
SA114050	CMH316	< 1 year of age
SA114051	CMH318	< 1 year of age
SA114052	CMH320	< 1 year of age
SA114053	CMH298	< 1 year of age
SA114054	CMH290	< 1 year of age
SA114055	CMH283	< 1 year of age
SA114056	CMH284	< 1 year of age
SA114057	CMH289	< 1 year of age
SA114058	CMH202	< 1 year of age

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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.

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

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