Summary of study ST000389

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.

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Study IDST000389
Study TitleSerum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part II)
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 DetailGC-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

Select appropriate tab below to view additional metadata details:


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:SU000410
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
SA018224131007dlvsa37_1Current Female No Benign
SA018225131008dlvsa38_1Current Female No Benign
SA018226131007dlvsa28_1Current Female No Cancer
SA018227131008dlvsa40_1Current Female No Cancer
SA018228131008dlvsa10_1Current Female No Cancer
SA018229131009dlvsa27_1Current Female No Cancer
SA018230131007dlvsa24_1Current Female Yes Benign
SA018231131007dlvsa23_1Current Female Yes Benign
SA018232131007dlvsa27_1Current Female Yes Benign
SA018233131007dlvsa34_1Current Female Yes Benign
SA018234131007dlvsa35_1Current Female Yes Benign
SA018235131007dlvsa43_1Current Female Yes Benign
SA018236131007dlvsa18_1Current Female Yes Benign
SA018237131009dlvsa21_1Current Female Yes Cancer
SA018238131009dlvsa38_1Current Female Yes Cancer
SA018239131008dlvsa50_1Current Female Yes Cancer
SA018240131007dlvsa16_1Current Female Yes Cancer
SA018241131008dlvsa30_1Current Female Yes Cancer
SA018242131008dlvsa37_1Current Female Yes Cancer
SA018243131009dlvsa07_1Current Female Yes Cancer
SA018244131008dlvsa29_1Current Female Yes Cancer
SA018245131009dlvsa31_1Current Female Yes Cancer
SA018246131007dlvsa48_1Current Male No Benign
SA018247131008dlvsa32_1Current Male No Benign
SA018248131008dlvsa16_1Current Male No Cancer
SA018249131009dlvsa01_1Current Male No Cancer
SA018250131007dlvsa29_1Current Male Yes Benign
SA018251131007dlvsa17_1Current Male Yes Benign
SA018252131009dlvsa22_1Current Male Yes Cancer
SA018253131008dlvsa09_1Current Male Yes Cancer
SA018254131009dlvsa03_1Current Male Yes Cancer
SA018255131008dlvsa13_1Current Male Yes Cancer
SA018256131007dlvsa25_1Current Male Yes Cancer
SA018257131007dlvsa19_1Current Male Yes Cancer
SA018258131008dlvsa11_1Current Male Yes Cancer
SA018259131008dlvsa41_1Current Male Yes Cancer
SA018260131007dlvsa15_1Former Female No Benign
SA018261131008dlvsa21_1Former Female No Benign
SA018262131009dlvsa30_1Former Female No Benign
SA018263131009dlvsa23_1Former Female No Benign
SA018264131007dlvsa41_1Former Female No Benign
SA018265131007dlvsa31_1Former Female No Cancer
SA018266131007dlvsa39_1Former Female No Cancer
SA018267131009dlvsa15_1Former Female No Cancer
SA018268131007dlvsa30_1Former Female No Cancer
SA018269131008dlvsa45_1Former Female No Cancer
SA018270131008dlvsa22_1Former Female No Cancer
SA018271131007dlvsa36_1Former Female No Cancer
SA018272131009dlvsa06_1Former Female No Cancer
SA018273131009dlvsa05_1Former Female No Cancer
SA018274131009dlvsa24_1Former Female No Cancer
SA018275131009dlvsa17_1Former Female No Cancer
SA018276131007dlvsa33_1Former Female No Cancer
SA018277131008dlvsa17_1Former Female No Cancer
SA018278131009dlvsa19_1Former Female No Cancer
SA018279131007dlvsa32_1Former Female No Cancer
SA018280131007dlvsa50_1Former Female No Cancer
SA018281131007dlvsa40_1Former Female No Cancer
SA018282131008dlvsa14_1Former Female No Cancer
SA018283131009dlvsa29_1Former Female Yes Benign
SA018284131009dlvsa33_1Former Female Yes Benign
SA018285131009dlvsa36_1Former Female Yes Benign
SA018286131008dlvsa39_1Former Female Yes Benign
SA018287131009dlvsa11_1Former Female Yes Benign
SA018288131009dlvsa13_1Former Female Yes Benign
SA018289131009dlvsa20_1Former Female Yes Cancer
SA018290131008dlvsa02_1Former Female Yes Cancer
SA018291131008dlvsa19_1Former Female Yes Cancer
SA018292131008dlvsa28_1Former Female Yes Cancer
SA018293131009dlvsa16_1Former Female Yes Cancer
SA018294131007dlvsa22_1Former Female Yes Cancer
SA018295131008dlvsa05_1Former Female Yes Cancer
SA018296131009dlvsa28_1Former Female Yes Cancer
SA018297131009dlvsa26_1Former Female Yes Cancer
SA018298131008dlvsa01_1Former Female Yes Cancer
SA018299131009dlvsa32_1Former Female Yes Cancer
SA018300131007dlvsa38_1Former Male No Benign
SA018301131008dlvsa08_1Former Male No Benign
SA018302131007dlvsa20_1Former Male No Cancer
SA018303131008dlvsa36_1Former Male No Cancer
SA018304131008dlvsa42_1Former Male No Cancer
SA018305131008dlvsa47_1Former Male No Cancer
SA018306131008dlvsa06_1Former Male No Cancer
SA018307131009dlvsa35_1Former Male No Cancer
SA018308131008dlvsa46_1Former Male No Cancer
SA018309131007dlvsa42_1Former Male No Cancer
SA018310131008dlvsa20_1Former Male Yes Benign
SA018311131007dlvsa47_1Former Male Yes Benign
SA018312131008dlvsa27_1Former Male Yes Benign
SA018313131009dlvsa25_1Former Male Yes Benign
SA018314131007dlvsa26_1Former Male Yes Cancer
SA018315131009dlvsa39_1Former Male Yes Cancer
SA018316131008dlvsa44_1Former Male Yes Cancer
SA018317131008dlvsa49_1Former Male Yes Cancer
SA018318131009dlvsa14_1Former Male Yes Cancer
Showing results 1 to 95 of 95

Collection:

Collection ID:CO000404
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:TR000424
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:SP000417
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 AN000625
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus III GC
Column Restek Corporation Rtx-5Sil MS
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH000450
Instrument Name:Leco Pegasus III GC
Column Name:Restek Corporation Rtx-5Sil MS
Column Pressure:7.7 PSI
Column Temperature:50-330C
Flow Rate:1 ml/min
Injection Temperature:50 C ramped to 250 C by 12 C/s
Sample Injection:0.5 uL
Transferline Temperature:230C
Washing Buffer:Ethyl Acetate
Sample Loop Size:30 m length x 0.25 mm internal diameter
Randomization Order:Excel generated
Chromatography Type:GC

MS:

MS ID:MS000558
Analysis ID:AN000625
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250 C
Ionization:Pos
Ionization Energy:70 eV
Mass Accuracy:Nominal
Source Temperature:250 C
Scan Range Moverz:85-500 Da
Scanning Cycle:17 Hz
Scanning Range:85-500 Da
Skimmer Voltage:1850 V
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