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 ncibbrb@nih.gov. 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).
This study investigated the effects of diagnosis on the concentration of cfDNA in plasma specimens and compared differences observed between quantification methods. Plasma was obtained from EDTA blood from 18 patients with malignant melanoma, 67 patients with prostate cancer, and 15 healthy individuals by centrifugation at 4˚C at 1600 x g for 10 min then at 16000 x g for 10 min. Plasma was aliquoted and stored at -80˚C until DNA extraction. DNA was extracted using the QIAamp circulating nucleic acid kit and stored at -20˚C. DNA was quantified using the Qubit dsDNA HS Assay Kit, the Qubit ssDNA Assay Kit, spectrophotometry, and real-time PCR amplification of a 67 bp region of APP.
| Technology Platform | Analyte | Spectrophotometry | DNA | Fluorometry | DNA | Real-time qPCR | DNA |
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A new Expert-Vetted Biospecimen Evidence-Based Practices document on nucleic acid extraction from FFPE tissue blocks is now available in the BRD's SOP library. Visit the publication announcing the release at https://www.ncbi.nlm.nih.gov/pubmed/29920119.
Don't miss BBRB's presentation on comparisons among SOPs from the BRD's SOP Library during this Wednesday's (5/23/18) morning session at the ISBER 2018 Annual Meeting.
Later, stop by and visit the ISBER Tool Bench at 3:30 pm (Wednesday, 5/23/18) to learn more about the BRD and how it may be of use to you.
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