The Biospecimen Research Database

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).

Featured Paper

Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues.

Author(s): Groelz D, Viertler C, Pabst D, Dettmann N, Zatloukal K

Publication: PLoS One, 2018, Vol. 13, Page e0203608

PubMed

1 study(s)

The purpose of this study was to explore the potential effects of long-term FFPE and PFPE block storage duration and temperature on RNA yield, integrity, and suitability for qRT-PCR analysis. Tissue from eight different cases were used and included malignant liver and non-malignant stomach, liver, and duodenum tissues. Non-malignant and malignant specimens were not compared experimentally, nor were were the different tissue types. Each tissue specimen was aliquoted and snap-frozen in liquid nitrogen-cooled methyl butane or fixed in neutral buffered formalin or PAXgene Tissue Fixative for 3 (aliquots from 5 cases), 24 (aliquots from 7 cases), 72, 96, or 120 h (aliquots from 1 case each) at room temperature. Notably, the different fixation timepoints were designed to mirror the variability observed in clinical settings but fixation duration was not investigated experimentally. Fixed specimens were dehydrated through a grade series of ethanol then isopropanol, cleared in xylene, and impregnated in low-melting paraffin. FFPE and PFPE blocks were stored in the dark at ambient or 4°C. RNA was extracted from 10-20 (5 µm-thick) sections of FFPE blocks with Qiagen's RNeasy FFPE Kit, of PFPE blocks with PreAnalytiX's PAXgene Tissue RNA Kit, and from 20-70 mg of snap-frozen specimens with Invitrogen's TRIzol protocol. RNA concentration was determined by spectrophotometer and integrity was assessed by RNA integrity number (RIN) using a bioanalyzer. RNA was reverse-transcribed using the High-Capacity cDNA Reverse Transcription Kit and analyzed by qRT-PCR using Power SYBR Green PCR Master Mix for different sized amplicons of GAPDH (71, 153, 200, 277, 323 bp).