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MB Sample ID: SA017745
| Local Sample ID: | 130731dlvsa20_1 |
| Subject ID: | SU000407 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000407 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 130731dlvsa20_1 | SA017745 | FL003959 | Plasma | Organ |
| 130731dlvsa20_1 | SA017745 | FL003959 | Healthy | Cancer status |
| 130731dlvsa20_1 | SA017745 | FL003959 | Former | Smoker |
| 130731dlvsa20_1 | SA017745 | FL003959 | F | Gender |
Collection:
| Collection ID: | CO000401 |
| Collection Summary: | Blood samples (serum and plasma) were collected from NSCLC adenocarcinoma and control subjects with patient consent using approved IRB protocols (LC001 for cancer cases and LC002 for control cases). |
| Collection Protocol Filename: | Cancer_Epidemiol_Biomarkers_Prev-2015-Fahrmann-1716-23.pdf |
| Sample Type: | Blood |
Treatment:
| Treatment ID: | TR000421 |
| Treatment Summary: | Subjects were recruited over a 4-year period (2010–2014) from the UC Davis Medical Center and Cancer Center Clinics. All subjects were diagnosed with NSCLC adenocarcinoma before specimen collection. The control population was heavily recruited from spouses and family members accompanying a lung cancer patient to their clinic to maintain as much of a similar environment and life styles, especially diet and smoking history, as possible. Cases were frequency matched with controls for gender, age, and smoking history. Only cases diagnosed with NSCLC adenocarcinoma were used in these studies. Fasting status was not controlled for as individuals were recruited upon their arrival to the clinic. The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. |
| Treatment Protocol Filename: | Cancer_Epidemiol_Biomarkers_Prev-2015-Fahrmann-1716-23.pdf |
Sample Preparation:
| Sampleprep ID: | SP000414 |
| 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 | AN000621 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco GC-TOF |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH000446 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Corporation Rtx-5Sil MS |
| Column Pressure: | 7.7 PSI (initial condition) |
| Column Temperature: | 50 - 330°C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50°C ramped to 250°C by 12°C/s |
| Sample Injection: | 0.5µl |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230°C |
| 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: | MS000554 |
| Analysis ID: | AN000621 |
| Instrument Name: | Leco GC-TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250°C |
| Ionization Energy: | 70eV |
| Mass Accuracy: | Nominal |
| Spray Voltage: | 250°C |
| Scan Range Moverz: | 85-500 |
| Scanning Cycle: | 17 Hz |
| Skimmer Voltage: | 1850 V |
