Summary of study ST000388

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 PR000304. The data can be accessed directly via it's Project DOI: 10.21228/M8RC8J This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000388
Study TitleSerum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part I)
Study SummaryRecent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-04-26
Publicationsdoi: 10.3233/CBM-160602.
Raw Data AvailableYes
Raw Data File Type(s).bin, .xsd, .xml
Analysis Type DetailLC-MS
Release Date2016-05-01
Release Version2
Release CommentsUpdated study design factors
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8RC8J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000304
Project DOI:doi: 10.21228/M8RC8J
Project Title:Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer.
Project Summary:Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154
Publications:doi: 10.3233/CBM-160602.

Subject:

Subject ID:SU000409
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:53-81
Gender:Male/Female
Human Smoking Status:Former/Current
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Smoking Status Gender Emphysema/COPD Group
SA018129LungNodule_23Current Female No Benign
SA018130LungNodule_74Current Female No Benign
SA018131LungNodule_14Current Female No Cancer
SA018132LungNodule_76Current Female No Cancer
SA018133LungNodule_46Current Female No Cancer
SA018134LungNodule_113Current Female No Cancer
SA018135LungNodule_10Current Female Yes Benign
SA018136LungNodule_9Current Female Yes Benign
SA018137LungNodule_13Current Female Yes Benign
SA018138LungNodule_20Current Female Yes Benign
SA018139LungNodule_21Current Female Yes Benign
SA018140LungNodule_29Current Female Yes Benign
SA018141LungNodule_4Current Female Yes Benign
SA018142LungNodule_107Current Female Yes Cancer
SA018143LungNodule_124Current Female Yes Cancer
SA018144LungNodule_86Current Female Yes Cancer
SA018145LungNodule_2Current Female Yes Cancer
SA018146LungNodule_66Current Female Yes Cancer
SA018147LungNodule_73Current Female Yes Cancer
SA018148LungNodule_93Current Female Yes Cancer
SA018149LungNodule_65Current Female Yes Cancer
SA018150LungNodule_117Current Female Yes Cancer
SA018151LungNodule_34Current Male No Benign
SA018152LungNodule_68Current Male No Benign
SA018153LungNodule_52Current Male No Cancer
SA018154LungNodule_87Current Male No Cancer
SA018155LungNodule_15Current Male Yes Benign
SA018156LungNodule_3Current Male Yes Benign
SA018157LungNodule_108Current Male Yes Cancer
SA018158LungNodule_45Current Male Yes Cancer
SA018159LungNodule_89Current Male Yes Cancer
SA018160LungNodule_49Current Male Yes Cancer
SA018161LungNodule_11Current Male Yes Cancer
SA018162LungNodule_5Current Male Yes Cancer
SA018163LungNodule_47Current Male Yes Cancer
SA018164LungNodule_77Current Male Yes Cancer
SA018165LungNodule_1Former Female No Benign
SA018166LungNodule_57Former Female No Benign
SA018167LungNodule_116Former Female No Benign
SA018168LungNodule_109_2Former Female No Benign
SA018169LungNodule_27Former Female No Benign
SA018170LungNodule_17Former Female No Cancer
SA018171LungNodule_25Former Female No Cancer
SA018172LungNodule_101Former Female No Cancer
SA018173LungNodule_16Former Female No Cancer
SA018174LungNodule_81Former Female No Cancer
SA018175LungNodule_58Former Female No Cancer
SA018176LungNodule_22Former Female No Cancer
SA018177LungNodule_92Former Female No Cancer
SA018178LungNodule_91Former Female No Cancer
SA018179LungNodule_110Former Female No Cancer
SA018180LungNodule_103Former Female No Cancer
SA018181LungNodule_19Former Female No Cancer
SA018182LungNodule_53Former Female No Cancer
SA018183LungNodule_105Former Female No Cancer
SA018184LungNodule_18Former Female No Cancer
SA018185LungNodule_36Former Female No Cancer
SA018186LungNodule_26Former Female No Cancer
SA018187LungNodule_50Former Female No Cancer
SA018188LungNodule_115Former Female Yes Benign
SA018189LungNodule_119Former Female Yes Benign
SA018190LungNodule_122Former Female Yes Benign
SA018191LungNodule_75Former Female Yes Benign
SA018192LungNodule_97Former Female Yes Benign
SA018193LungNodule_99Former Female Yes Benign
SA018194LungNodule_106Former Female Yes Cancer
SA018195LungNodule_38Former Female Yes Cancer
SA018196LungNodule_55Former Female Yes Cancer
SA018197LungNodule_64Former Female Yes Cancer
SA018198LungNodule_102Former Female Yes Cancer
SA018199LungNodule_8Former Female Yes Cancer
SA018200LungNodule_41Former Female Yes Cancer
SA018201LungNodule_114Former Female Yes Cancer
SA018202LungNodule_112Former Female Yes Cancer
SA018203LungNodule_37Former Female Yes Cancer
SA018204LungNodule_118Former Female Yes Cancer
SA018205LungNodule_24Former Male No Benign
SA018206LungNodule_44Former Male No Benign
SA018207LungNodule_6Former Male No Cancer
SA018208LungNodule_72Former Male No Cancer
SA018209LungNodule_78Former Male No Cancer
SA018210LungNodule_83Former Male No Cancer
SA018211LungNodule_42Former Male No Cancer
SA018212LungNodule_121Former Male No Cancer
SA018213LungNodule_82Former Male No Cancer
SA018214LungNodule_28Former Male No Cancer
SA018215LungNodule_56Former Male Yes Benign
SA018216LungNodule_33Former Male Yes Benign
SA018217LungNodule_63Former Male Yes Benign
SA018218LungNodule_111Former Male Yes Benign
SA018219LungNodule_12Former Male Yes Cancer
SA018220LungNodule_125Former Male Yes Cancer
SA018221LungNodule_80Former Male Yes Cancer
SA018222LungNodule_85Former Male Yes Cancer
SA018223LungNodule_100Former Male Yes Cancer
Showing results 1 to 95 of 95

Collection:

Collection ID:CO000403
Collection Summary:Blood samples were collected from all patients enrolled in the protocol before diagnosis (>6 months prior to surgery, pre-diagnostic). Additional blood samples were collected from some of the lung cancer patients, at-diagnosis (at diagnosis) and post-treatment (after surgery). All but one patient had their “at-diagnosis” sample collected before surgery, usually within days prior to surgery, likely on their pre-operation visit. Surgery was usually performed within 1–3 months of diagnosis. Diagnosis was made by biopsy and/or surgery with all tissue diagnoses confirmed by pathology.
Sample Type:Blood
Blood Serum Or Plasma:Serum

Treatment:

Treatment ID:TR000423
Treatment Summary:The NYU Lung Cancer Biomarker Center performs low-dose CT-scan screening for high-risk smokers as part of the National Cancer Institute’s Early Detection Research Network Program (EDRN). Lung cancer cases for this study were confirmed by pathology (Table 1). Patients with benign nodules were those with stable nodules or ground glass opacity (GGO) over at least two year period with annual CT scans performed. Post-diagnosis samples were collected at least one month post-surgery. Selection of cases was performed by NYU and the blinded serum samples were sent to University of California, Davis Medical Center (UCDMC) for analysis. None of the study subjects had previous cancer or chemotherapy. All subjects had blood drawn by EDRN protocol, performed spirometry according to ATS guidelines,and answered questionnaires with smoking and occupational history.

Sample Preparation:

Sampleprep ID:SP000416
Sampleprep Summary:1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30μl of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450μL portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450μL aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 μL 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization.
Sampleprep Protocol Filename:SOP_blood-GCTOF-11082012.pdf

Combined analysis:

Analysis ID AN000624
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 6530
Column Waters Acquity BEH HILIC (150 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530A QTOF
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH000449
Methods Filename:CH_LungNodule_HILIC_Pos_101_AcqMethodReport
Instrument Name:Agilent 6530
Column Name:Waters Acquity BEH HILIC (150 x 2.1mm, 1.7um)
Column Pressure:1200 bar
Column Temperature:45 C
Flow Gradient:100%B to 45% B
Flow Rate:0.4 mL/min
Solvent A:H2O + 4mM Acetic Acid + 6 mM Ammonium Acetate
Solvent B:9:1 Acetonitrile: H2O + 4mM Acetic Acid + 6mM Ammonium Acetate
Analytical Time:20 min
Randomization Order:Excel generated
Chromatography Type:HILIC

MS:

MS ID:MS000557
Analysis ID:AN000624
Instrument Name:Agilent 6530A QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3000 V
Dry Gas Flow:8 L/min
Dry Gas Temp:350 C
Fragment Voltage:125 V
Nebulizer:35 psig
Octpole Voltage:750 V
Scanning Cycle:2 Hz
Scanning Range:57-1400
Skimmer Voltage:65 V
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