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Last Updated: 07/31/15

Biospecimen Pre-analytical Variables (BPV) Program

The BBRB Biospecimen Pre-analytical Variables (BPV) Program is designed to systematically investigate the effects of individual pre-analytical factors on the molecular profiles of biospecimens. The results of this study will be used to develop evidence-based protocols and best practices for optimal collection, processing, and storage of biospecimens. Moreover, accumulated data from these activities will be widely disseminated to the research community and strengthen the standards for human biobanking.

Highly annotated biospecimens are collected for the BPV program through a tightly regulated infrastructure. Patients are screened, consented, and enrolled in the BPV study at four Biospecimen Source Sites (BSSs): Boston Medical Center, Emory University, University of New Mexico, and University of Pittsburg Medical Center. The BSSs collect renal cell carcinoma, ovarian, fallopian tube, and primary peritoneal carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, and colorectal adenocarcinoma specimens along with matched blood samples and, when possible, adjacent "normal" tissue. Tumors are surgically removed and dissected into six blocks. One block is frozen for use in broad future research. A second block is formalin-fixed, paraffin embedded and an H&E slide is generated from this block. The H&E section is reviewed by a pathologist at the local BSS as well as by the Pathology Resource Center (PRC) for many parameters including confirmation of diagnosis and the requirement of at least 50% tumor cells by surface area and less than 20% necrosis present. The four remaining blocks are randomly assigned to an experimental protocol. Currently, the BPV program is collecting tumor and blood specimens to evaluate the effects of several pre-analytical factors on downstream molecular analysis results, including the effects of variations in:

  • cold ischemia time of FFPE tumor tissue
  • incubation time in formalin of FFPE tumor tissue
  • method of freezing tumor tissue
  • storage temperature of frozen tumor tissue
  • frozen storage temperature of plasma
Analytical Platforms
DNA RNA Protein Metabolite
DNA methylation RT-PCR and microarrays IHC Global metabolite profiling
CGH array hybridization RNA and miRNA sequencing Total protein analysis  
Whole Exome Sequencing miRNA profiling Phosphoprotein profiling  
  RNA in-situ detection    

The BSSs receive in person training on how to adhere to strict SOPs so that uniform collection and handling procedures occur across all sites. All of the BSSs use the same make and model processor for BPV FFPE tissues, which is completely dedicated to the BPV program. All BPV biospecimens are collected using kits provided by the Comprehensive Biospecimen Resource (CBR) and all specimens are shipped to one central location, the CBR, where they are inventoried and stored. The BSSs use a web-based interface (the Comprehensive Data Resource- CDR) to enter all the data regarding collection, processing, and handling of the biospecimens, clinical information related to the donor, and pathological evaluation of the tumor. Data quality managers review all data in the CDR and over 300 common data elements are collected for each case. BPV specimens are tracked via LIMS systems, specimen IDs, and unique barcodes.

Investigators interested in analyzing BPV specimens to evaluate how pre-analytical variables affect molecular profiles and specimen quality can view our collaborative announcement here.