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Last Updated: 05/15/2019

Biomarkers

Biomarker assays developed by the DCTD Clinical Pharmacodynamic Program for use by the scientific community, including National Clinical Laboratory Network (NCLN)-supported assays. Assay training and critical reagent support are available for the Validated Biomarker Assays shown below.

Validated Biomarker Assays: Overview

Validated assays, specimen handling procedures, and reagent sources for clinical pharmacodynamic studies with assay training and critical reagent support.

Method Target(s), Platform Description
Immunoassays Apoptosis Multiplex Immunoassay, Luminex Tumor biopsy fractionation method and assay kit use for the Apoptosis Multiplex Immunoassay Panels.
MET Immunoassays, ELISA Detection of Intact MET, Dual Phospho-Y1234/Y1235 MET, Phospho-Y1356 MET in needle tumor biopsies.
Poly(ADP-Ribose), ELISA Detection of PAR in needle tumor biopsies and PBMCs.
Immunofluorescence Assays γH2AX, pNBS1, and β-catenin Multiplex, IFA Detection of histone H2AX phosphorylated at Ser139 and NBS1 phosphorylated at Ser343 using β-Catenin tumor segmentation.

SOPs for Validated Biomarker Assays

Assay Tissue Specimen Collection Sample Preparation Assay(s) Data Analysis
Apoptosis Multiplex, Luminex tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP341401
Tumor Biopsy Lysate Fractionation for the Apoptosis Multiplex Immunoassay Panels
SOP341402
Procedure for Use of Bio-Rad Bio-Plex Pro RBM Apoptosis Panel Kits 1-3 for the Analysis of Clinical Tumor Biopsy Extracts and Reporting of Data
MET and pMET, ELISA tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP341201
Biopsy Specimen Processing for MET Immunoassay

SOP341203, Intact MET Immunoassay

SOP341206, Dual Phospho-Y1234/1235 MET Immunoassay

SOP341205, Phospho-Y1356 MET Immunoassay

SOP341208
MET Immunoassay Quality Control, Data Analysis, and Reporting
Poly(ADP-ribose), ELISA tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP340520
Biopsy Specimen Processing for PAR Immunoassay
SOP340505
Poly(ADP-ribose) (PAR) Immunoassay
SOP340530
PAR Immunoassay Quality Control, Data Analyses, and Reporting
PBMCs SOP340503
PBMC Specimen Collection, Preparation, and Freezing for Protein Extraction
SOP340506
PBMC Protein Extraction for PAR Immunoassay
SOP340505
Poly(ADP-ribose) (PAR) Immunoassay
SOP340530
PAR Immunoassay Quality Control, Data Analyses, and Reporting
γH2AX, pNBS1, and β-catenin Multiplex, IFA tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP340550
Tumor Frozen Needle Biopsy Preparation for Pharmacodynamic Immunofluorescence Assays Utilizing Murine Testis and/or Jejunum Control Tissues

SOP340543, γH2AX, pNBS1 IFA Staining with β-Catenin Segmentation for Tumor Biopsy Slides

SOP340544, Whole Slide Image Capture of Tumor Biopsy Slides for γH2AX, pNBS1 Immunofluorescence Assay with β-Catenin Segmentation

SOP340545
Image Extraction and Analysis of Tumor Biopsy Slides from γH2AX, pNBS1 IFA with β-Catenin Segmentation

Additional Published Biomarker Assays

Additional published biomarker assays developed by the DCTD Pharmacodynamic Biomarkers Program. Unlike the validated biomarker assays listed above, these additional published assays do not have a formal training program or qualified reagent supply; however, consultation may be requested.

Method Target(s), Platform Description
Circulating Tumor Cells Antibody Qualification and CTC Enumeration, CellSearch System Detection of PD biomarkers in CTCs using the CellSearch System.
Immunoassays γH2AX and Total H2AX, ELISA Detection of histone H2AX phosphorylated at Ser139 and Total H2AX in tumor biopsies and lysates of cultured cells or PBMCs.
Hypoxia Inducible Factor 1-alpha, ELISA Detection of HIF1-alpha in needle tumor biopsies.
Total Topoisomerase I, ELISA Detection of Top1 in needle tumor biopsies and PBMCs.
Immunofluorescence Assays γH2AX, Bond-Max Detection of histone H2AX phosphorylated at Ser139 in paraffin-embedded tumor biopsies using the Bond-Max System.

SOPs for Additional Published Biomarker Assays

Assay Tissue Specimen Collection Sample Preparation Assay(s) Data Analysis
CTC enumeration and γH2AX, CellSearch CTCs LHTP003.08.03
CellSave Tube: Human Blood Collection and Specimen Submission
LHTP003.8.1.1
γH2AX Immunofluorescence Assay Antibody Qualification and Laboratory Proficiency Testing
LHTP003.8.1
Immunofluorescence Assay for Circulating Tumor Cells Using the CellSearch System
HIF-1α, ELISA tumor SOP340902
HIF-1 alpha Immunoassay Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP340910
Biopsy Protein Extraction for the HIF-1 alpha Immunoassay
SOP340903
HIF-1alpha Immunoassay
SOP340904
HIF-1 alpha Immunoassay Quality Control, Data Analyses, and Reporting
Total Topoisomerase I, ELISA tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP340702
Biopsy Specimen Processing for TOP1 Immunoassay
SOP340701
Topoisomerase I Immunoassay
SOP340704
TOP1 Immunoassay Quality Control, Data Analyses, and Reporting
PBMCs SOP340503
PBMC Specimen Collection, Preparation, and Freezing for Protein Extraction
SOP340703
PBMC Protein Extraction for TOP1 Immunoassay
SOP340701
Topoisomerase I Immunoassay
SOP340704
TOP1 Immunoassay Quality Control, Data Analyses, and Reporting
γH2AX, pNBS1, and β-catenin Multiplex, Bond-Max tumor SOP340507
Tumor Frozen Needle Biopsy Specimen Collection and Handling
SOP340522
Tumor Frozen Needle Biopsy Preparation for the γH2AX IFA

SOP340523
γH2AX Immunofluorescence Assay for Tumor Biopsy Slides

SOP340533
Image Capture of Tumor Biopsy Slides from γH2AX Immunofluorescence Assay

SOP340534
Image and Data Analyses of Tumor Biopsy Slides from γH2AX Immunofluorescence Assay

Additional Resources

Please email any questions or comments to PDinfo@mail.nih.gov.