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 firstname.lastname@example.org. 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 explored the potential influence of a change in workflow on an observed difference between mRNA signatures and progression-free survival rates that were in two specimen cohorts. Specifically, the potential influence of a change in unbuffered formalin and paraffin manufacturers and the duration of FFPE block storage were also investigated. Tumor specimens from 208 breast cancer patients were fixed in 10% unbuffered formalin overnight, dehydrated in alcohol (70%, 90% and 4 changes of 100%), cleared with three changes of xylene, and paraffin embedded at 60°C. Specimens were collected from 2005-2010 and a change in paraffin and unbuffered formalin manufacturers occurred in 2009. The authors note that a change in humidity during block storage also occurred in 2009, but further details were not provided. Specimens were divided into two sets: set 1 (117 specimens) and set 2 (66 specimens); each specimen set included specimens collected before and after the change in workflow. RNA was extracted from two 10 µm thick sections using the RNeasy FFPE kit and quantified using a NanoDrop Spectrophotometer. RNA was reverse transcribed using QuantiNova Reverse Transcription Kit and levels of 21 mRNAs were quantified by real-time PCR.
|Technology Platform||Analyte||Spectrophotometry||RNA||Real-time qRT-PCR||RNA|
New Contributing SOP Sources Include:
The top 5 most downloaded SOPs from the BRD are:More...