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MB Sample ID: SA018171
| Local Sample ID: | LungNodule_25 |
| 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 |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| LungNodule_25 | SA018171 | FL004944 | Former | Smoking Status |
| LungNodule_25 | SA018171 | FL004944 | Female | Gender |
| LungNodule_25 | SA018171 | FL004944 | No | Emphysema/COPD |
| LungNodule_25 | SA018171 | FL004944 | Cancer | Group |
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: | 100% water; 4 mM acetic acid; 6 mM ammonium acetate |
| Solvent B: | 90% acetonitrile/10% water; 4 mM acetic acid; 6 mM 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 |
| Analysis Protocol File: | LungNodule_HILIC_Pos_101_AcqMethodReport.pdf |
