The Biospecimen Research Database

Welcome to the Biospecimen Research Database (BRD)!

Article Curations on COVID-19 and SARS-CoV-2

SOPs on COVID-19 and SARS-CoV-2

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 emailing us 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

Frozen section histopathology and preanalytical factors affecting nucleic acid integrity in biobanked fresh-frozen human cancer tissues.

Author(s): Kim S, Kang J, Kim B, Kwak Y, Lee HS

Publication: J Pathol Transl Med, 2025, Vol. , Page

PubMed

1 study(s)

This study investigated the effects of cold ischemia and frozen storage duration on DNA and RNA integrity by comparing unmatched colon adenocarcinoma (COAD), hepatocellular carcinoma (HCC), and renal cell carcinoma (RCC) specimens obtained after cold ischemia times ranging from <30 min to >120 min or frozen storage for 1-10 years. The authors also investigated potential correlations between DNA/RNA integrity and histopathologic parameters (tumor cell percentage, presence of normal tissue, extent of inflammatory cell infiltration, extent of stromal fibrosis, percentage necrosis or percentage extracellular mucin pool). A total of 105 tissue specimens were obtained during surgical resection from patients with colon adenocarcinoma (COAD), hepatocellular carcinoma (HCC), or renal cell carcinoma (RCC). The COAD specimens that were stored frozen for 1 year were collected immediately upon resection prior to pathology processing, but those stored for 3 years were collected pre-gross examination and were not washed, and those stored for >3 years were collected post-gross examination and after washing with water. All HCC specimens and partial nephrectomy specimens were collected in the operating room and delivered to the bank. RCC specimens collected during radical nephrectomy were collected during (specimens stored ≤ 5 years) or before (specimens stored >5 years) gross examination. Tissue specimen storage at 4°C prior to freezing (cold ischemia time) was ≤30 minutes (17 specimens), 31 to ≤60 minutes (18 specimens), 61 to ≤120 minutes (37 specimens), or >120 minutes (33 specimens). Specimens were then cut into 0.5 cm³ fragments and frozen by immersion in isopentane (temperature not specified) and stored in liquid nitrogen. Specimens were stored for 1 year (27 specimens), 3 years (25 specimens), 5 years (26 specimens) and 10 years (27 specimens). After storage, each specimen was divided into two parts, and half was refrozen in optimal cutting temperature compound (OCT); RNA and DNA were extracted from the remaining half using the PureLink RNA Mini Kit and the QIAamp DSP DNA Mini Kit, respectively. RNA and DNA integrity were evaluated using Genomic ScreenTape Kits and an Agilent Tapestation 4200 instrument. Sections (4 µm) were cut from OCT-embedded tissue and were H&E stained. Pathologists graded the sections based on tumor cell percentage (0 if 0%, 1 if 1-30%, 2 if 31-60% and 3 if >60%), the presence of normal tissue (0 for no and 1 for yes), inflammatory cell infiltration (0 for no, 1 if scanty, 2 if moderate and 3 if marked), stromal fibrosis (0 for no, 1 if scanty, 2 if moderate and 3 if marked), percentage necrosis (0 if absent, 1 if <10%, 2 if 10-50% and 3 if >50%), and percentage extracellular mucin pool (0 if absent, 1 if <10%, 2 if 10-50% and 3 if >50%).