{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001710","ANALYSIS_ID":"AN002785","VERSION":"1","CREATED_ON":"03-03-2022"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic signatures of NAFLD","PROJECT_SUMMARY":"Background and Aims: Nonalcoholic fatty liver disease (NAFLD) is a progressive liver disease that is strongly associated with type 2 diabetes. Accurate, non-invasive diagnostic tests to delineate the different stages: degree of steatosis, grade of nonalcoholic steatohepatitis (NASH) and stage fibrosis represent an unmet medical need. In our previous studies, we successfully identified specific serum molecular lipid signatures which associate with the amount of liver fat as well as with NASH. Here we report underlying associations between clinical data, lipidomic profiles, metabolic profiles and clinical outcomes, including downstream identification of potential biomarkers for various stages of the disease. Method: We leverage several statistical and machine-learning approaches to analyse clinical, lipidomic and metabolomic profiles of individuals from the European Horizon 2020 project: Elucidating Pathways of Steatohepatitis (EPoS). We interrogate data on patients representing the full spectrum of NAFLD/NASH derived from the EPoS European NAFLD Registry (n = 627). We condense the EPoS lipidomic data into lipid clusters and subsequently apply non-rejection-rate-pruned partial correlation network techniques to facilitate network analysis between the datasets of lipidomic, metabolomic and clinical data. For biomarker identification, a random forest ensemble classification approach was used to both search for valid disease biomarkers and to compare classification performance of lipids, metabolites and clinical factors in combination. Results: We found that steatosis and fibrosis grades were strongly associated with (1) an increase of triglycerides with low carbon number and double bond count as well as (2) a decrease of specific phospholipids, including lysophosphatidylcholines. In addition to the network topology as a result itself, we also present lipid clusters (LCs) of interest to the derived network of proposed interactions in our NAFLD data from the EPoS cohort, along with preliminary metabolite and lipid biomarkers to classify NAFLD fibrosis. Conclusions: Our findings suggest that dysregulation of lipid metabolism in progressive stages of NAFLD is reflected in circulation and may thus hold diagnostic value as well as offer new insights about NAFLD pathogenesis. Using this cohort as a proof-of-concept, we demonstrate current progress in tuning the accuracy random forest approaches with a view to predicting various subtypes of NAFLD patient using a minimal set of lipidomic and metabolic markers. For the first time, a detailed network-based picture emerges between lipids, polar metabolites and clinical variables. Lipidomic / metabolomic markers may provide an alternative method of NAFLD patient classification and risk stratification to guide therapy.","INSTITUTE":"Örebro University","LAST_NAME":"McGlinchey","FIRST_NAME":"Aidan","ADDRESS":"School of Medical Sciences, Örebro, Örebro, 70281, Sweden","EMAIL":"aidan.mcglinchey@oru.se","PHONE":"+46736485638","DOI":"http://dx.doi.org/10.21228/M85976"},

"STUDY":{"STUDY_TITLE":"Metabolic signatures of NAFLD - Lipidomics data (part 1 of 3)","STUDY_SUMMARY":"Serum samples were randomized and extracted using a modified version of the previously-published Folch procedure, as applied recently [20]. The maternal samples were analysed as one batch and the cord blood samples as a second batch. In short, 10 µL of 0.9% NaCl and, 120 µL of CHCl3: MeOH (2:1, v/v) containing the internal standards (c = 2.5 µg/mL) was added to 10 µL of each serum sample. The standard solution contained the following compounds: 1,2-diheptadecanoyl-sn-glycero-3-phosphoethanolamine (PE(17:0/17:0)), N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (SM(d18:1/17:0)), N-heptadecanoyl-D-erythro-sphingosine (Cer(d18:1/17:0)), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (PC(17:0/17:0)), 1-heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(17:0)) and 1-palmitoyl-d31-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/d31/18:1)), were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL, USA), and, triheptadecanoylglycerol (TG(17:0/17:0/17:0)) was purchased from Larodan AB (Solna, Sweden). The samples were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min). 60 µL from the lower layer of each sample was then transferred to a glass vial with an insert and 60 µL of CHCl3: MeOH (2:1, v/v) was added to each sample. The samples were stored at -80 °C until analysis. Calibration curves using 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(16:0e/18:1(9Z))), 1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(18:0p/18:1(9Z))), 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:0)), 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:1)), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)), 1-(1Z-octadecenyl)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PC(18:0p/22:6)) and 1-stearoyl-2-linoleoyl-sn-glycerol (DG(18:0/18:2)), 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (LPE(18:1)), N-(9Z-octadecenoyl)-sphinganine (Cer(d18:0/18:1(9Z))), 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)) from Avanti Polar Lipids, 1-Palmitoyl-2-Hydroxy-sn-Glycero-3-Phosphatidylcholine (LPC(16:0)), 1,2,3 trihexadecanoalglycerol (TG(16:0/16:0/16:0)), 1,2,3-trioctadecanoylglycerol (TG(18:0/18:0/18:)) and 3β-hydroxy-5-cholestene-3-stearate (ChoE(18:0)), 3β-Hydroxy-5-cholestene-3-linoleate (ChoE(18:2)) from Larodan, were prepared to the following concentration levels: 100, 500, 1000, 1500, 2000 and 2500 ng/mL (in CHCl3:MeOH, 2:1, v/v) including 1250 ng/mL of each internal standard. The samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS). Briefly, the UHPLC system used in this work was a 1290 Infinity II system from Agilent Technologies (Santa Clara, CA, USA). The system was equipped with a multi sampler (maintained at 10 °C), a quaternary solvent manager and a column thermostat (maintained at 50 °C). Injection volume was 1 µL and the separations were performed on an ACQUITY UPLC® BEH C18 column (2.1 mm × 100 mm, particle size 1.7 µm) by Waters (Milford, MA, USA). The mass spectrometer coupled to the UHPLC was a 6545 QTOF from Agilent Technologies interfaced with a dual jet stream electrospray (Ddual ESI) ion source. All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively.","INSTITUTE":"Örebro University","LAST_NAME":"McGlinchey","FIRST_NAME":"Aidan","ADDRESS":"School of Medical Sciences, Örebro, Örebro, 70281, Sweden","EMAIL":"aidan.mcglinchey@oru.se","PHONE":"+46736485638","SUBMIT_DATE":"2021-02-10"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"1","Platelets.E10-9.per.L":"235","Liver.ALT":"173","Liver.AST":"248","AST.ALT.Ratio":"1.43352601156069","RAW_FILE_NAME":"170514sample402.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"278","Liver.ALT":"38","Liver.AST":"41","AST.ALT.Ratio":"1.07894736842105","RAW_FILE_NAME":"170514sample434.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"246","Liver.ALT":"22","Liver.AST":"27","AST.ALT.Ratio":"1.22727272727273","RAW_FILE_NAME":"170517sample544.mzdata.xml"}
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"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"1","T2DM":"NA","Kleiner.Steatosis":"1","Inflammation":"3"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"1c","NAS":"3","Platelets.E10-9.per.L":"283","Liver.ALT":"20","Liver.AST":"18","AST.ALT.Ratio":"0.9","RAW_FILE_NAME":"170507sample134.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"4","Platelets.E10-9.per.L":"200","Liver.ALT":"NA","Liver.AST":"NA","AST.ALT.Ratio":"NA","RAW_FILE_NAME":"170512sample327.mzdata.xml"}
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{
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"2","NAS":"4","Platelets.E10-9.per.L":"303","Liver.ALT":"28","Liver.AST":"25","AST.ALT.Ratio":"0.892857142857143","RAW_FILE_NAME":"170517sample506.mzdata.xml"}
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"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"1","T2DM":"NA","Kleiner.Steatosis":"3","Inflammation":"2"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"5","Platelets.E10-9.per.L":"204","Liver.ALT":"68","Liver.AST":"35","AST.ALT.Ratio":"0.514705882352941","RAW_FILE_NAME":"170515sample478.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"5","Platelets.E10-9.per.L":"261","Liver.ALT":"45","Liver.AST":"49","AST.ALT.Ratio":"1.08888888888889","RAW_FILE_NAME":"170518sample554.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"1c","NAS":"5","Platelets.E10-9.per.L":"247","Liver.ALT":"34","Liver.AST":"28","AST.ALT.Ratio":"0.823529411764706","RAW_FILE_NAME":"170515sample489.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"5","Platelets.E10-9.per.L":"279","Liver.ALT":"51","Liver.AST":"41","AST.ALT.Ratio":"0.803921568627451","RAW_FILE_NAME":"170513sample398.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"NA","NAS":"5","Platelets.E10-9.per.L":"288","Liver.ALT":"84","Liver.AST":"54","AST.ALT.Ratio":"0.642857142857143","RAW_FILE_NAME":"170504sample16.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"1","Platelets.E10-9.per.L":"205","Liver.ALT":"24","Liver.AST":"27","AST.ALT.Ratio":"1.125","RAW_FILE_NAME":"170513sample359.mzdata.xml"}
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"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"1a","NAS":"1","Platelets.E10-9.per.L":"NA","Liver.ALT":"48","Liver.AST":"53","AST.ALT.Ratio":"1.10416666666667","RAW_FILE_NAME":"0030_LC_20180718_sample_186.mzdata.xml"}
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},
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"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"1","T2DM":"N","Kleiner.Steatosis":"1","Inflammation":"1"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"228","Liver.ALT":"29","Liver.AST":"56","AST.ALT.Ratio":"1.93103448275862","RAW_FILE_NAME":"170514sample448.mzdata.xml"}
},
{
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"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"1","T2DM":"N","Kleiner.Steatosis":"1","Inflammation":"1"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"NA","Liver.ALT":"33","Liver.AST":"29","AST.ALT.Ratio":"0.878787878787879","RAW_FILE_NAME":"170517sample522.mzdata.xml"}
},
{
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"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"1","T2DM":"N","Kleiner.Steatosis":"1","Inflammation":"1"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"288","Liver.ALT":"159","Liver.AST":"75","AST.ALT.Ratio":"0.471698113207547","RAW_FILE_NAME":"170510sample224.mzdata.xml"}
},
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"Additional sample data":{"Ballooning":"1","Kleiner.Fibrosis":"-","NAS":"3","Platelets.E10-9.per.L":"183","Liver.ALT":"145","Liver.AST":"103","AST.ALT.Ratio":"0.710344827586207","RAW_FILE_NAME":"170515sample455.mzdata.xml"}
},
{
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"Sample ID":"1028969843",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"1"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"3","NAS":"5","Platelets.E10-9.per.L":"271","Liver.ALT":"144","Liver.AST":"63","AST.ALT.Ratio":"0.4375","RAW_FILE_NAME":"0030_LC_20180713_sample_113.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022385933",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"2"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"4","NAS":"6","Platelets.E10-9.per.L":"207","Liver.ALT":"33","Liver.AST":"34","AST.ALT.Ratio":"1.03030303030303","RAW_FILE_NAME":"170512sample340.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028939993",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"2"},
"Additional sample data":{"Ballooning":"1","Kleiner.Fibrosis":"-","NAS":"5","Platelets.E10-9.per.L":"123","Liver.ALT":"67","Liver.AST":"41","AST.ALT.Ratio":"0.611940298507463","RAW_FILE_NAME":"0030_LC_20180717_sample_168.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940027",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"2"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"3","NAS":"6","Platelets.E10-9.per.L":"303","Liver.ALT":"101","Liver.AST":"70","AST.ALT.Ratio":"0.693069306930693","RAW_FILE_NAME":"0030_LC_20180709_sample_25.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940033",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"2"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"3","NAS":"6","Platelets.E10-9.per.L":"342","Liver.ALT":"75","Liver.AST":"69","AST.ALT.Ratio":"0.92","RAW_FILE_NAME":"0030_LC_20180820_sample_219.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940045",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"2","Inflammation":"2"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"2","NAS":"6","Platelets.E10-9.per.L":"256","Liver.ALT":"92","Liver.AST":"91","AST.ALT.Ratio":"0.989130434782609","RAW_FILE_NAME":"0030_LC_20180713_sample_131.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028939968",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"1"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"2","NAS":"6","Platelets.E10-9.per.L":"257","Liver.ALT":"86","Liver.AST":"71","AST.ALT.Ratio":"0.825581395348837","RAW_FILE_NAME":"0030_LC_20180711_sample_99.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028939999",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"1"},
"Additional sample data":{"Ballooning":"1","Kleiner.Fibrosis":"3","NAS":"5","Platelets.E10-9.per.L":"211","Liver.ALT":"132","Liver.AST":"58","AST.ALT.Ratio":"0.439393939393939","RAW_FILE_NAME":"0030_LC_20180820_sample_201.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940037",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"1"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"2","NAS":"6","Platelets.E10-9.per.L":"167","Liver.ALT":"52","Liver.AST":"38","AST.ALT.Ratio":"0.730769230769231","RAW_FILE_NAME":"0030_LC_20180825_sample_232.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028969833",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"1"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"2","NAS":"6","Platelets.E10-9.per.L":"211","Liver.ALT":"140","Liver.AST":"52","AST.ALT.Ratio":"0.371428571428571","RAW_FILE_NAME":"0030_LC_20180825_sample_234.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028969874",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"1"},
"Additional sample data":{"Ballooning":"1","Kleiner.Fibrosis":"3","NAS":"5","Platelets.E10-9.per.L":"178","Liver.ALT":"41","Liver.AST":"37","AST.ALT.Ratio":"0.902439024390244","RAW_FILE_NAME":"0030_LC_20180709_sample_15.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940011",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"2"},
"Additional sample data":{"Ballooning":"2","Kleiner.Fibrosis":"3","NAS":"7","Platelets.E10-9.per.L":"237","Liver.ALT":"210","Liver.AST":"175","AST.ALT.Ratio":"0.833333333333333","RAW_FILE_NAME":"0030_LC_20180711_sample_58.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940230",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"3","Inflammation":"2"},
"Additional sample data":{"Ballooning":"1","Kleiner.Fibrosis":"-","NAS":"6","Platelets.E10-9.per.L":"NA","Liver.ALT":"NA","Liver.AST":"140","AST.ALT.Ratio":"NA","RAW_FILE_NAME":"0030_LC_20180711_sample_52.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028940155",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"-","Inflammation":"1"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"1","Platelets.E10-9.per.L":"170","Liver.ALT":"25","Liver.AST":"19","AST.ALT.Ratio":"0.76","RAW_FILE_NAME":"0030_LC_20180716_sample_135.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022384017",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"82","Liver.ALT":"26","Liver.AST":"52","AST.ALT.Ratio":"2","RAW_FILE_NAME":"170513sample384.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022384080",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"79","Liver.ALT":"48","Liver.AST":"57","AST.ALT.Ratio":"1.1875","RAW_FILE_NAME":"170510sample236.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022385857",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"184","Liver.ALT":"76","Liver.AST":"103","AST.ALT.Ratio":"1.35526315789474","RAW_FILE_NAME":"170519sample635.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022385867",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"139","Liver.ALT":"18","Liver.AST":"26","AST.ALT.Ratio":"1.44444444444444","RAW_FILE_NAME":"170519sample649.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022386191",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"151","Liver.ALT":"46","Liver.AST":"26","AST.ALT.Ratio":"0.565217391304348","RAW_FILE_NAME":"170520sample677.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022386897",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"NA","T2DM":"Y","Kleiner.Steatosis":"NA","Inflammation":"NA"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"NA","NAS":"NA","Platelets.E10-9.per.L":"267","Liver.ALT":"32","Liver.AST":"32","AST.ALT.Ratio":"1","RAW_FILE_NAME":"170504sample09.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1026694057",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"-","T2DM":"N","Kleiner.Steatosis":"-","Inflammation":"-"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"-","Platelets.E10-9.per.L":"NA","Liver.ALT":"27","Liver.AST":"21","AST.ALT.Ratio":"0.777777777777778","RAW_FILE_NAME":"0030_LC_20180710_sample_48.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028937993",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"-","T2DM":"N","Kleiner.Steatosis":"-","Inflammation":"-"},
"Additional sample data":{"Ballooning":"NA","Kleiner.Fibrosis":"-","NAS":"NA","Platelets.E10-9.per.L":"NA","Liver.ALT":"26","Liver.AST":"27","AST.ALT.Ratio":"1.03846153846154","RAW_FILE_NAME":"0030_LC_20180709_sample_21.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1028939944",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"-","T2DM":"N","Kleiner.Steatosis":"-","Inflammation":"-"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"-","Platelets.E10-9.per.L":"187","Liver.ALT":"29","Liver.AST":"26","AST.ALT.Ratio":"0.896551724137931","RAW_FILE_NAME":"0030_LC_20180713_sample_108.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1026694049",
"Factors":{"Data type":"Serum lipidomics","NAFLD.Category":"-","T2DM":"Y","Kleiner.Steatosis":"-","Inflammation":"-"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"-","Platelets.E10-9.per.L":"NA","Liver.ALT":"18","Liver.AST":"20","AST.ALT.Ratio":"1.11111111111111","RAW_FILE_NAME":"0030_LC_20180718_sample_182.mzdata.xml"}
},
{
"Subject ID":"-",
"Sample ID":"1022385827",
"Factors":{"Data type":"Serum lipidomics","Sex":"NA","NAFLD.Category":"1","T2DM":"NA","Kleiner.Steatosis":"1","Inflammation":"1"},
"Additional sample data":{"Ballooning":"-","Kleiner.Fibrosis":"-","NAS":"2","Platelets.E10-9.per.L":"NA","Liver.ALT":"35","Liver.AST":"22","AST.ALT.Ratio":"0.628571428571429","RAW_FILE_NAME":"170510sample232.mzdata.xml"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Serum samples were randomized and extracted using a modified version of the previously-published Folch procedure, as applied recently. The maternal samples were analysed as one batch and the cord blood samples as a second batch. In short, 10 µL of 0.9% NaCl and, 120 µL of CHCl3: MeOH (2:1, v/v) containing the internal standards (c = 2.5 µg/mL) was added to 10 µL of each serum sample. The standard solution contained the following compounds: 1,2-diheptadecanoyl-sn-glycero-3-phosphoethanolamine (PE(17:0/17:0)), N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (SM(d18:1/17:0)), N-heptadecanoyl-D-erythro-sphingosine (Cer(d18:1/17:0)), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (PC(17:0/17:0)), 1-heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(17:0)) and 1-palmitoyl-d31-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/d31/18:1)), were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL, USA), and, triheptadecanoylglycerol (TG(17:0/17:0/17:0)) was purchased from Larodan AB (Solna, Sweden). The samples were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min). 60 µL from the lower layer of each sample was then transferred to a glass vial with an insert and 60 µL of CHCl3: MeOH (2:1, v/v) was added to each sample. The samples were stored at -80 °C until analysis. Calibration curves using 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(16:0e/18:1(9Z))), 1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(18:0p/18:1(9Z))), 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:0)), 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:1)), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)), 1-(1Z-octadecenyl)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PC(18:0p/22:6)) and 1-stearoyl-2-linoleoyl-sn-glycerol (DG(18:0/18:2)), 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (LPE(18:1)), N-(9Z-octadecenoyl)-sphinganine (Cer(d18:0/18:1(9Z))), 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)) from Avanti Polar Lipids, 1-Palmitoyl-2-Hydroxy-sn-Glycero-3-Phosphatidylcholine (LPC(16:0)), 1,2,3 trihexadecanoalglycerol (TG(16:0/16:0/16:0)), 1,2,3-trioctadecanoylglycerol (TG(18:0/18:0/18:)) and 3β-hydroxy-5-cholestene-3-stearate (ChoE(18:0)), 3β-Hydroxy-5-cholestene-3-linoleate (ChoE(18:2)) from Larodan, were prepared to the following concentration levels: 100, 500, 1000, 1500, 2000 and 2500 ng/mL (in CHCl3:MeOH, 2:1, v/v) including 1250 ng/mL of each internal standard. The samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS). Briefly, the UHPLC system used in this work was a 1290 Infinity II system from Agilent Technologies (Santa Clara, CA, USA). The system was equipped with a multi sampler (maintained at 10 °C), a quaternary solvent manager and a column thermostat (maintained at 50 °C). Injection volume was 1 µL and the separations were performed on an ACQUITY UPLC® BEH C18 column (2.1 mm × 100 mm, particle size 1.7 µm) by Waters (Milford, MA, USA). The mass spectrometer coupled to the UHPLC was a 6545 QTOF from Agilent Technologies interfaced with a dual jet stream electrospray (Ddual ESI) ion source. All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively. Mass spectrometry data processing was performed using the open source software package MZmine 2.18. The following steps were applied in this processing: (i) Crop filtering with a m/z range of 350 – 1200 m/z and an RT range of 2.0 to 12 minutes, (ii) Mass detection with a noise level of 750, (iii) Chromatogram builder with a minimum time span of 0.08 min, minimum height of 1000 and a m/z tolerance of 0.006 m/z or 10.0 ppm, (iv) Chromatogram deconvolution using the local minimum search algorithm with a 70% chromatographic threshold, 0.05 min minimum RT range, 5% minimum relative height, 1200 minimum absolute height, a minimum ration of peak top/edge of 1.2 and a peak duration range of 0.08 - 5.0, (v), Isotopic peak grouper with a m/z tolerance of 5.0 ppm, RT tolerance of 0.05 min, maximum charge of 2 and with the most intense isotope set as the representative isotope, (vi) Peak filter with minimum 12 data points, a FWHM between 0.0 and 0.2, tailing factor between 0.45 and 2.22 and asymmetry factor between 0.40 and 2.50, (vii) Join aligner with a m/z tolerance of 0.009 or 10.0 ppm and a weight for of 2, a RT tolerance of 0.1 min and a weight of 1 and with no requirement of charge state or ID and no comparison of isotope pattern, (viii) Peak list row filter with a minimum of 10% of the samples (ix) Gap filling using the same RT and m/z range gap filler algorithm with an m/z tolerance of 0.009 m/z or 11.0 ppm, (x) Identification of lipids using a custom database search with an m/z tolerance of 0.009 m/z or 10.0 ppm and a RT tolerance of 0.1 min, and (xi) Normalization using internal standards PE(17:0/17:0), SM(d18:1/17:0), Cer(d18:1/17:0), LPC(17:0), TG(17:0/17:0/17:0) and PC(16:0/d30/18:1)) for identified lipids and closest ISTD for the unknown lipids followed by calculation of the concentrations based on lipid-class concentration curves.","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment applied."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Serum samples were randomized and extracted using a modified version of the previously-published Folch procedure, as applied recently. The maternal samples were analysed as one batch and the cord blood samples as a second batch. In short, 10 µL of 0.9% NaCl and, 120 µL of CHCl3: MeOH (2:1, v/v) containing the internal standards (c = 2.5 µg/mL) was added to 10 µL of each serum sample. The standard solution contained the following compounds: 1,2-diheptadecanoyl-sn-glycero-3-phosphoethanolamine (PE(17:0/17:0)), N-heptadecanoyl-D-erythro-sphingosylphosphorylcholine (SM(d18:1/17:0)), N-heptadecanoyl-D-erythro-sphingosine (Cer(d18:1/17:0)), 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine (PC(17:0/17:0)), 1-heptadecanoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(17:0)) and 1-palmitoyl-d31-2-oleoyl-sn-glycero-3-phosphocholine (PC(16:0/d31/18:1)), were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL, USA), and, triheptadecanoylglycerol (TG(17:0/17:0/17:0)) was purchased from Larodan AB (Solna, Sweden). The samples were vortex mixed and incubated on ice for 30 min after which they were centrifuged (9400 × g, 3 min). 60 µL from the lower layer of each sample was then transferred to a glass vial with an insert and 60 µL of CHCl3: MeOH (2:1, v/v) was added to each sample. The samples were stored at -80 °C until analysis. Calibration curves using 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(16:0e/18:1(9Z))), 1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (PC(18:0p/18:1(9Z))), 1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:0)), 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC(18:1)), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)), 1-(1Z-octadecenyl)-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PC(18:0p/22:6)) and 1-stearoyl-2-linoleoyl-sn-glycerol (DG(18:0/18:2)), 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (LPE(18:1)), N-(9Z-octadecenoyl)-sphinganine (Cer(d18:0/18:1(9Z))), 1-hexadecyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (PE(16:0/18:1)) from Avanti Polar Lipids, 1-Palmitoyl-2-Hydroxy-sn-Glycero-3-Phosphatidylcholine (LPC(16:0)), 1,2,3 trihexadecanoalglycerol (TG(16:0/16:0/16:0)), 1,2,3-trioctadecanoylglycerol (TG(18:0/18:0/18:)) and 3β-hydroxy-5-cholestene-3-stearate (ChoE(18:0)), 3β-Hydroxy-5-cholestene-3-linoleate (ChoE(18:2)) from Larodan, were prepared to the following concentration levels: 100, 500, 1000, 1500, 2000 and 2500 ng/mL (in CHCl3:MeOH, 2:1, v/v) including 1250 ng/mL of each internal standard. The samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS). Briefly, the UHPLC system used in this work was a 1290 Infinity II system from Agilent Technologies (Santa Clara, CA, USA). The system was equipped with a multi sampler (maintained at 10 °C), a quaternary solvent manager and a column thermostat (maintained at 50 °C). Injection volume was 1 µL and the separations were performed on an ACQUITY UPLC® BEH C18 column (2.1 mm × 100 mm, particle size 1.7 µm) by Waters (Milford, MA, USA). The mass spectrometer coupled to the UHPLC was a 6545 QTOF from Agilent Technologies interfaced with a dual jet stream electrospray (Ddual ESI) ion source. All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively. Mass spectrometry data processing was performed using the open source software package MZmine 2.18. The following steps were applied in this processing: (i) Crop filtering with a m/z range of 350 – 1200 m/z and an RT range of 2.0 to 12 minutes, (ii) Mass detection with a noise level of 750, (iii) Chromatogram builder with a minimum time span of 0.08 min, minimum height of 1000 and a m/z tolerance of 0.006 m/z or 10.0 ppm, (iv) Chromatogram deconvolution using the local minimum search algorithm with a 70% chromatographic threshold, 0.05 min minimum RT range, 5% minimum relative height, 1200 minimum absolute height, a minimum ration of peak top/edge of 1.2 and a peak duration range of 0.08 - 5.0, (v), Isotopic peak grouper with a m/z tolerance of 5.0 ppm, RT tolerance of 0.05 min, maximum charge of 2 and with the most intense isotope set as the representative isotope, (vi) Peak filter with minimum 12 data points, a FWHM between 0.0 and 0.2, tailing factor between 0.45 and 2.22 and asymmetry factor between 0.40 and 2.50, (vii) Join aligner with a m/z tolerance of 0.009 or 10.0 ppm and a weight for of 2, a RT tolerance of 0.1 min and a weight of 1 and with no requirement of charge state or ID and no comparison of isotope pattern, (viii) Peak list row filter with a minimum of 10% of the samples (ix) Gap filling using the same RT and m/z range gap filler algorithm with an m/z tolerance of 0.009 m/z or 11.0 ppm, (x) Identification of lipids using a custom database search with an m/z tolerance of 0.009 m/z or 10.0 ppm and a RT tolerance of 0.1 min, and (xi) Normalization using internal standards PE(17:0/17:0), SM(d18:1/17:0), Cer(d18:1/17:0), LPC(17:0), TG(17:0/17:0/17:0) and PC(16:0/d30/18:1)) for identified lipids and closest ISTD for the unknown lipids followed by calculation of the concentrations based on lipid-class concentration curves.","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"All analyses were performed in positive ion mode and MassHunter B.06.01 (Agilent Technologies) was used for all data acquisition. Quality control was performed throughout the dataset by including blanks, pure standard samples, extracted standard samples and control serum samples, including in-house serum and a pooled QC with an aliquot of each sample was collected and pooled and used as quality control sample. Relative standard deviations (% RSDs) for identified lipids in the control serum samples (n = 13) and in the pooled serum samples (n = 54) were on average 22.4% and 17.5%, respectively. Regarding data processing, and missing values (likely below limit of detection) were imputed as half of the minimum observed value for that feature. Values were then log2-transformed and subsequently autoscaled (scaled to mean and unit variance).","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"log2-transformed autoscaled values",

"Data":[{"Metabolite":"CE(16:0) + 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}