Summary of Study ST002332

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 PR001496. The data can be accessed directly via it's Project DOI: 10.21228/M8BX3F 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 IDST002332
Study TitlePlasma metabolomic profiling of individuals with autism spectrum disorder and their family members.
Study SummaryAutism spectrum disorder (ASD) is a common neurodevelopmental condition affecting 2.3% of 8-year-old children and is attributable to polygenic risks in most cases. Gene discovery studies catalogued >1000 genes with de novo, rare and common genetic variants that are likely associated with ASD; however, the candidate genes are rarely translated to diagnostic and treatment biomarkers. As such no pharmacological treatment option is available for targeting core symptoms. Neural circuits involved in verbal/nonverbal communications and social interaction are likely changed, which may be caused by an excitatory-inhibitory (E-I) imbalance in individuals with ASD. To date, clinical trials targeting excitatory glutamatergic or inhibitory GABAergic receptors showed mixed results. These early clinical trials highlight the unmet need of biomarkers for target populations and outcome indicators. We investigated whether plasma biomarkers would be associated with genetic risk factors and core symptoms of ASD. Plasma samples were collected for metabolomics profiling from the Autism Genetics Resource Exchange (AGRE). Detailed phenotype information is available at NIMH Data Archive (Collection ID: 4214) and can be accessed using NDAR GUID for the individuals.
Institute
Boston Children's Hospital
DepartmentComputational Health informatics Program
LaboratoryKong Lab
Last NameKong
First NameSek Won
Address401 Park Drive, LM5528.4
Emailsekwon.kong@childrens.harvard.edu
Phone6179192689
Submit Date2022-10-14
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-10-14
Release Version1
Sek Won Kong Sek Won Kong
https://dx.doi.org/10.21228/M8BX3F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001496
Project DOI:doi: 10.21228/M8BX3F
Project Title:Plasma metabolomic profiling of individuals with autism spectrum disorder and their family members.
Project Summary:Autism spectrum disorder (ASD) is a common neurodevelopmental condition affecting 2.3% of 8-year-old children and is attributable to polygenic risks in most cases. Gene discovery studies catalogued >1000 genes with de novo, rare and common genetic variants that are likely associated with ASD; however, the candidate genes are rarely translated to diagnostic and treatment biomarkers. As such no pharmacological treatment option is available for targeting core symptoms. Neural circuits involved in verbal/nonverbal communications and social interaction are likely changed, which may be caused by an excitatory-inhibitory (E-I) imbalance in individuals with ASD. To date, clinical trials targeting excitatory glutamatergic or inhibitory GABAergic receptors showed mixed results. These early clinical trials highlight the unmet need of biomarkers for target populations and outcome indicators. We investigated whether plasma biomarkers would be associated with genetic risk factors and core symptoms of ASD. Plasma samples were collected for metabolomics profiling from the Autism Genetics Resource Exchange (AGRE). Detailed phenotype information is available at NIMH Data Archive (Collection ID: 4214) and can be accessed using NDAR GUID for the individuals.
Institute:Boston Childrens Hospital
Department:Computational Health informatics Program
Laboratory:Kong Lab
Last Name:Kong
First Name:Sek Won
Address:401 Park Drive, LM5528.4
Email:sekwon.kong@childrens.harvard.edu
Phone:6179192689
Funding Source:NIMH R01MH107205

Subject:

Subject ID:SU002419
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Status
SA230667VT_181127_M338_229case
SA230668VT_181127_M338_146case
SA230669VT_181009_M338_242case
SA230670VT_181009_M338_241case
SA230671VT_181023_M338_092case
SA230672VT_181111_M338_085case
SA230673VT_181023_M338_091case
SA230674VT_181127_M338_145case
SA230675VT_181011_M338_152case
SA230676VT_181011_M338_151case
SA230677VT_181111_M338_086case
SA230678VT_181028_M338_043case
SA230679VT_181030_M338_019case
SA230680VT_181030_M338_049case
SA230681VT_181030_M338_050case
SA230682VT_181023_M338_080case
SA230683VT_181023_M338_079case
SA230684VT_181023_M338_230case
SA230685VT_181030_M338_097case
SA230686VT_181030_M338_098case
SA230687VT_181028_M338_044case
SA230688VT_181127_M338_230case
SA230689VT_181208_M338_050case
SA230690VT_181208_M338_049case
SA230691VT_181030_M338_020case
SA230692VT_181028_M338_182case
SA230693VT_181111_M338_164case
SA230694VT_181111_M338_109case
SA230695VT_181111_M338_163case
SA230696VT_181127_M338_122case
SA230697VT_181127_M338_121case
SA230698VT_181111_M338_110case
SA230699VT_181207_M338_182case
SA230700VT_181208_M338_242case
SA230701VT_181208_M338_241case
SA230702VT_181208_M338_152case
SA230703VT_181208_M338_151case
SA230704VT_181021_M338_145case
SA230705VT_181011_M338_218case
SA230706VT_181021_M338_038case
SA230707VT_181029_M338_163case
SA230708VT_181202_M338_164case
SA230709VT_181202_M338_163case
SA230710VT_181023_M338_229case
SA230711VT_181029_M338_164case
SA230712VT_181021_M338_037case
SA230713VT_181011_M338_217case
SA230714VT_181011_M338_032case
SA230715VT_181011_M338_031case
SA230716VT_181021_M338_146case
SA230717VT_181028_M338_181case
SA230718VT_181022_M338_098case
SA230719VT_181026_M338_217case
SA230720VT_181026_M338_218case
SA230721VT_181203_M338_031case
SA230722VT_181203_M338_032case
SA230723VT_181130_M338_056case
SA230724VT_181026_M338_139case
SA230725VT_181026_M338_140case
SA230726VT_181031_M338_188case
SA230727VT_181031_M338_187case
SA230728VT_181031_M338_146case
SA230729VT_181031_M338_145case
SA230730VT_181130_M338_055case
SA230731VT_181130_M338_044case
SA230732VT_181031_M338_224case
SA230733VT_181110_M338_103case
SA230734VT_181031_M338_223case
SA230735VT_181031_M338_014case
SA230736VT_181031_M338_013case
SA230737VT_181110_M338_104case
SA230738VT_181110_M338_205case
SA230739VT_181130_M338_043case
SA230740VT_181211_M338_074case
SA230741VT_181211_M338_073case
SA230742VT_181110_M338_206case
SA230743VT_181031_M338_097case
SA230744VT_181031_M338_098case
SA230745VT_181116_M338_230case
SA230746VT_181122_M338_212case
SA230747VT_181103_M338_056case
SA230748VT_181103_M338_055case
SA230749VT_181202_M338_230case
SA230750VT_181109_M338_049case
SA230751VT_181109_M338_050case
SA230752VT_181208_M338_127case
SA230753VT_181022_M338_097case
SA230754VT_181116_M338_164case
SA230755VT_181116_M338_229case
SA230756VT_181202_M338_229case
SA230757VT_181028_M338_014case
SA230758VT_181212_M338_164case
SA230759VT_181212_M338_217case
SA230760VT_181212_M338_163case
SA230761VT_181203_M338_241case
SA230762VT_181203_M338_242case
SA230763VT_181212_M338_218case
SA230764VT_181203_M338_086case
SA230765VT_181028_M338_013case
SA230766VT_181028_M338_158case
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Collection:

Collection ID:CO002412
Collection Summary:The Autism Genetic Resource Exchange (AGRE) Consortium has the collection of WGS, biospecimen and phenotype data of families containing at least one individual diagnosed with Autism Spectrum Disorder (ASD) by the Autism Diagnostic Interview-Revised (ADI-R) and the Autism Diagnostic Observation Schedule (ADOS). For identifying ASD patients, we used AGRE’s “derived affected status” information marked with “Autism”, “Not Quite Autism (NQA)“, or “ASD”. Patients with known genetic causes of ASD (e.g., Fragile X, Trisomy 21, 15q deletion, and 22q duplication) or syndromes with overlapping ASD-features (e.g., Sotos syndrome) were excluded. We used plasma samples from individuals with both WGS and detailed phenotype information were available.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002431
Treatment Summary:Plasma samples in 50μL aliquot were mixed with acetonitrile containing 14 stable isotope internal standards at a 2:1 ratio to precipitate proteins. Samples were then equilibrated on ice for 30 minutes and centrifuged for 10 minutes at 13,400 rpm at 4°C. The supernatant was transferred to autosampler vials and kept in a refrigerated autosampler until analysis. Each extract was analyzed in triplicate using a dual column chromatography scheme that includes hydrophilic interaction liquid chromatography (HILIC; XBridge BEH Amide XP HILIC column; Waters, Waltham, MA, 50x2.1mm, 2.5μm) and reversed phase liquid chromatography (RPLC; C18 column; Higgins Analytical, Mountain View, CA, 50x2.1mm, 2.6 μm).

Sample Preparation:

Sampleprep ID:SP002425
Sampleprep Summary:Samples are prepared for metabolomics analysis using established methods (Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80°C and thawed on ice. Each cryotube is then vortexed briefly to ensure homogeneity, and 50 μL transferred to a clean microfuge tube. Immediately after, the plasma is treated with 100 μL of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 μL of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, plasma is then equilibrated for 30 min on ice, upon which precipitated proteins are removed by centrifuge (16.1 ×g at 4°C for 10 min). The resulting supernatant (100 μL) is removed, added to a low volume autosampler vial and maintained at 4°C until analysis (<22 h).
Sampleprep Protocol Filename:EmoryUniversity_HRM_sample_preparation_082016_01.pdf

Combined analysis:

Analysis ID AN003806 AN003807
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP HILIC (50 x 2.1mm,2.5um) Product #186006089; Thermo Accucore HILIC guard with holder,Product # 17526-012105 Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002816
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10- port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 μL of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods Filename:EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP HILIC (50 x 2.1mm,2.5um) Product #186006089; Thermo Accucore HILIC guard with holder,Product # 17526-012105
Column Temperature:60
Solvent A:100% water
Solvent B:100% acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH002817
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6- port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods Filename:EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name:Dionex UltiMate 3000
Column Name:Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
Column Temperature:60
Solvent A:100% water
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS003548
Analysis ID:AN003806
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:No comment
Ion Mode:POSITIVE
Acquisition Parameters File:EmoryUniversity_HRM_DataAnalysis-MS_092017_v1.pdf
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
  
MS ID:MS003549
Analysis ID:AN003807
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:No comment
Ion Mode:NEGATIVE
Acquisition Parameters File:EmoryUniversity_HRM_DataAnalysis-MS_092017_v1.pdf
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
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