Early Detection Research Network
Team Project

Breast Reference Set Application: Chris Li-FHCRC (2014)

Breast Ref Set App: Li (2014)
383
Feng, ZidingFred Hutchinson Cancer Research Center
m1   lactate m2   3HBA m3   N-AcetylGlycine m4   Proline m5   Glutamic Acid m6   Histidine m7   Arginine m8   Tyrosine Y   Combination m109   Choline
No design specified.
Metabolomics
Breast and Gynecologic Cancers Research Group

This application proposes to use Reference Set #1. We request access to serum samples collected at the time of breast biopsy from subjects with IC (n=30) or benign disease without atypia (n=30). Statistical power: With 30 BC cases and 30 normal controls, a 25% difference in mean metabolite levels can be detected between groups with 80% power and α=0.05, assuming coefficients of variation of 30%, consistent with our past studies. These sample sizes appear sufficient to enable detection of changes similar in magnitude to those previously reported in pre-clinical (BC recurrence) specimens (20).

Targeted LC-MS/MS: Electro-spray ionization (ESI) will be performed and MS acquisition will be performed in multiple reaction monitoring (MRM) mode following identical procedures used in past studies (21). An Agilent 6410 triple quad MS system equipped with an Agilent 1200 UPLC system will be utilized. Each MS acquisition for the serum samples (0.050 mL each) will target the 11-marker panel of metabolites, each of which has a 13C or D-labeled internal standard to provide for reliable quantitation of the absolute metabolite concentrations in blood. Appropriate separation conditions for positive and negative mode detection will be performed (21, 33). Data Analysis Plan: Welch’s t-tests will be performed to determine if observed differences in etabolite signal intensities between invasive cancer cases and benign disease without atypia controls reach statistical significance (p<0.05, corrected using the false discovery rate method). ROC curves will be generated for individual candidate markers to assess sensitivity and specificity at all possible marker cut-point levels.
Targeted LC-MS/MS: Electro-spray ionization (ESI) will be performed and MS acquisition will be performed in multiple reaction monitoring (MRM) mode following identical procedures used in past studies (21). An Agilent 6410 triple quad MS system equipped with an Agilent 1200 UPLC system will be utilized. Each MS acquisition for the serum samples (0.050 mL each) will target the 11-marker panel of metabolites, each of which has a 13C or D-labeled internal standard to provide for reliable quantitation of the absolute metabolite concentrations in blood. Appropriate separation conditions for positive and negative mode detection will be performed (21, 33).

There are currently no biomarkers annotated for this protocol.

No datasets are currently associated with this protocol.