Welcome to the newest version of the Biospecimen Research Database (BRD), which accommodates Standard Operating Procedures (SOP). We encourage your contributions to our new SOP library!
The BRD is a free and publicly accessible database that contains peer-reviewed primary and review articles as well as SOPs in the field of human Biospecimen Science.
Each literature curation has been created by a Ph.D.-level scientist to capture the following: (1) relevant parameters that include the biospecimen investigated (type and location, patient diagnosis), preservation method, analyte(s) of interest and technology platform(s) used for analysis; (2) the pre-analytical factors investigated, including those relating to pre-acquisition, acquisition, preservation, processing, storage, and analysis; and (3) an original summary of relevant results. Browse literature curations or submit specific queries using the Advanced Search page with keyword search for specific biomakers or genes, PubMed ID, or pre-analytical factor values (anticoagulant, fixative, reagent, etc).
SOPs are organized in a hierarchy system consisting of three tiers: (1) SOPs, established protocols; (2) Biospecimen Evidence-based Practices (BEBP), procedural guidelines developed using literature evidence; and (3) Expert-vetted, evidence-based guidelines vetted by a panel of experts in the field. SOP documents are searchable by keyword, or by curated fields (source organization, tier, applicable biospecimens, and topic) on the Search SOPs page. Related SOP documents are assembled in Compendiums, which are viewable on the SOP Compendiums page. You can also create your own Compendium and download SOPs together rather than individually.
We encourage you to submit SOPs from your lab or institution for inclusion in the BRD by clicking on the Suggest a New SOP tab or at email@example.com. Individuals and organizations that suggest articles for inclusion in the BRD will receive acknowledgement on the paper's curation page. Articles may be submitted by clicking on the Suggest a New Paper tab or via the email above. Feedback is also welcome.
The BRD is an initiative of the NCI Biorepositories and Biospecimen Research Branch (BBRB).
The purpose of this study was to determine the effects of preservation method (snap frozen, PAXgene fixation, or formalin fixation) on morphological preservation and protein analyses using a variety of malignant, nonmalignant, and non-neoplastic tissue specimens. Protein was extracted from PFPE and snap frozen specimens by the QProteome FFPE Tissue Kit with protocol modifications and from FFPE specimens using the same kit's manufacturer suggested protocol.
|Technology Platform||Analyte||Immunohistochemistry||Protein||Western blot||Protein||H-and-E microscopy||Morphology|
The purpose of this study was to determine the effects of preservation method (snap frozen, PAXgene fixation, or formalin fixation) on RNA and microRNA (miRNA) analysis using a variety of malignant and nonmalignant tissue specimens. mRNA was extracted from 10-20 sections each of an unspecified number of specimens using the PAXgene Tissue RNA Kit for PFPE specimens, the RNeasy FFPE Kit for FFPE specimens, and the Invitrogen TRIzol procedure for snap frozen specimens. miRNA was extracted from three colon cancer specimens using PAXgene Tissue miRNA Kit for PFPE tissue, Recover All Total Nucleic Acid Isolation Kit for FFPE tissue, and the miRNeasy Mini Kit using TissueLyser II system for snap frozen specimens.
|Technology Platform||Analyte||Spectrophotometry||RNA||Bioanalyzer||RNA||Real-time qRT-PCR||RNA|
The purpose of this study was to determine the effects of preservation method (snap frozen, PAXgene fixation, or formalin fixation) on DNA analysis using five colorectal cancer tissue specimens. DNA extraction was performed using PAXgene Tissue DNA Kit for PFPE tissue, QIAamp DNA FFPE Tissue Kit for FFPE tissue, and QIAamp DNA Mini Kit with TissueLyser II system for snap frozen specimens.
|Technology Platform||Analyte||Spectrophotometry||DNA||Electrophoresis||DNA||PCR||DNA||DNA sequencing||DNA|
The review appears in Cancer Research's OnlineFirst section, and both summarizes the challenges associated with molecular analysis of FFPE biospecimens as well as highlights analytical techniques and parameters that result in strong concordance with a fresh or frozen cohort.
A new review summarizing the effects of FFPE processing factors on nucleic acid, protein, and morphological endpoints appears in the November 2014 issue of Arch Pathol Lab Med. The review was drafted using references housed in the BRD.More...