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MB Sample ID: SA089363
| Local Sample ID: | CA209025-1-961_baseline |
| Subject ID: | SU001305 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001305 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CA209025-1-961_baseline | SA089363 | FL013016 | baseline | Time point |
| CA209025-1-961_baseline | SA089363 | FL013016 | 1 | OS_Censor (1 means the time is a censoring time and 0 means a failure time in OS) |
| CA209025-1-961_baseline | SA089363 | FL013016 | INTERMEDIATE | CRF_MSKCC_Risk_Group |
| CA209025-1-961_baseline | SA089363 | FL013016 | NIVOLUMAB | Treatment |
| CA209025-1-961_baseline | SA089363 | FL013016 | FALSE | Prior antiangiogenic regimens (≥2) |
Collection:
| Collection ID: | CO001299 |
| Collection Summary: | Serum was collected at the specified time-points by centrifugation at 4000g for 4 minutes at 25°C within 2 hours of collection. Samples were frozen immediately and stored at or below -20°C for up to two months followed by storage at -80°C. |
| Sample Type: | Blood (serum) |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001320 |
| Treatment Summary: | CA209025 (CheckMate 025, NCT01668784) was a phase 3 study of nivolumab in comparison with everolimus for treatment of advanced renal cell carcinoma (RCC). The study was stratified according to region (United States or Canada, Western Europe, and the rest of the world), Memorial Sloan Kettering Cancer Center (MSKCC) prognostic risk group, and the number of previous antiangiogenic therapy regimens (one or two) for advanced renal cell carcinoma. The MSKCC prognostic risk is based on the presence of zero (favorable risk), one (intermediate risk), or two or three (poor risk) of the following prognostic factors: anemia, hypercalcemia, and poor performance status. Nivolumab was administered at a dose of 3 mg per kilogram of body weight as a 60-minute intravenous infusion every 2 weeks and everolimus was administered orally as a daily dose of 10 mg. |
| Treatment Protocol ID: | NCT01668784 |
Sample Preparation:
| Sampleprep ID: | SP001313 |
| Sampleprep Summary: | Serum samples (10 µL) were extracted using 90 µL of 74.9:24.9:0.2 (v/v/v) acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (0.2 ng/µL valine-d8, Isotec; 0.2 ng/µL phenylalanine-d8, Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9000g, 4ºC) and the supernatants were transferred to autosampler vials with de-activated inserts (Waters). |
Combined analysis:
| Analysis ID | AN002055 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2.1mm) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | Log10(Peak Area) |
Chromatography:
| Chromatography ID: | CH001494 |
| Chromatography Summary: | Extracts (10 µL) were injected onto a 150 x 2.1 mm Atlantis HILIC column (Waters). The column was eluted isocratically at a flow rate of 250 µL/min with 5% mobile phase A (10 mM ammonium formate and 0.1% formic acid in water) for 1 minute followed by a linear gradient to 40% mobile phase B (acetonitrile with 0.1% formic acid) over 10 minutes |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2.1mm) |
| Column Temperature: | 30 |
| Flow Rate: | 250 µL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001907 |
| Analysis ID: | AN002055 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | High resolution, accurate mass data were acquired using a system comprised of a Shimadzu Nexera X2 U-HPLC (Shimadzu Corp.; Marlborough, MA) coupled to a Q Exactive hybrid quadrupole orbitrap mass spectrometer (Thermo Fisher Scientific; Waltham, MA). MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 70-800 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 40, sweep gas 2, spray voltage 3.5 kV, capillary temperature 350°C, S-lens RF 40, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 250 ms. Raw data were processed using TraceFinder software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). The identities of 202 profiled metabolites were confirmed using reference standards. |
| Ion Mode: | POSITIVE |
