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 two tiers: (1) SOPs, established protocols; and (2) Biospecimen Evidence-based Practices (BEBP), procedural guidelines developed using literature evidence. SOP-tiered documents are a product of the Source organization specified. SOPs shared by external organizations are done so only with their consent, and have not been vetted by BBRB. 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 Submit an 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 paper was to determine if chilling a breast mastectomy specimen at -80°C for 20 min prior to formalin fixation affects DNA quantity and purity; successful PCR amplification of differently sized β-actin amplicons; immunohistochemical staining of ER, PR, and HER-2; and histomorphology when compared to results obtained with case-matched, pre-surgical formalin-fixed, paraffin-embedded (FFPE) biopsy specimens. A total of 95 case-matched specimen pairs (pre-surgical FFPE biopsies, mastectomy specimens chilled to facilitate grossing and the production of 4 mm thick cross sections prior to formalin-fixation and paraffin embedding) were collected and analyzed for histomorphology by hematoxylin and eosin staining, and immunohistochemical staining of ER, PR, and HER2. Additional details on formalin fixation and paraffin embedded were not provided. Immunostaining was scored as the intensity and percentage of stained tumor nuclei. Specimens from six cases were used for DNA analysis. DNA was isolated from four 10 µm-thick FFPE sections per sample using the FFPE Plus LEV DNA purification kit and an automated extractor. DNA quantity and purity were assessed by spectrophotometry. DNA integrity was determined by PCR analysis of differentially sized β-actin amplicons (100-600 bp).
|Technology Platform||Analyte||Spectrophotometry||DNA||Immunohistochemistry||Protein||H-and-E microscopy||Morphology||PCR||DNA|
The top 5 most downloaded SOPs in the BRD in 2018 were supplied by:
GAPPS Repository: https://brd.nci.nih.gov/brd/sop/show/890
A new article from NCI's BPV Program is now available that reports deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles.
View the PubMed Abstract at https://www.ncbi.nlm.nih.gov/pubmed/31061401More...