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 biospecimens@mail.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).
The purpose of this study was to assess the potential effects introduced by delay to fixation (DTF) on immunohistochemical staining of cancer biomarkers in prospectively collected FFPE tumor specimens under the National Cancer Institute's Pre-analytical Variable (BPV) program. Tumors from 111 kidney, 29 colon, 28 ovarian, and 8 lung resections were collected at four medical institutions using a common set of standard operating procedures (SOPs). Each surgical resection was dissected to yield tumor segments of approximately equivalent size (0.33 cm x 0.5 cm) which were stored for 1 h (control), 2 h, 3 h, or 12 h in a humidified chamber at room temperature before fixation. Tumor segments were then fixed in 10% neutral buffered formalin (NBF) at room temperature for 10-12 h before paraffin-embedding. Depending on the tissue, between 5 and 13 biomarkers were examined in FFPE sections (5 µm) by immunohistochemistry. Positive immunostaining was quantified using Aperio software after calibration using slides manually scored by a pathologist. H-score was calculated by multiplying the percentage of positively stained cells/nuclei by the intensity of the stain (0-3). Statistical analysis included the mean and percent difference in H-scores for experimental (2, 3, 12 h DTF) specimens relative to corresponding 1 h DTF controls. H-score data collected from BPV tumor specimens was used to calculate the estimated probability of a change in intensity score (0-3) for each DTF timepoint relative to the 1 h DTF control. Statistical significance was set to p<0.05. A subset of specimens stored as FFPE blocks were re-evaluated one year post-collection.
Technology Platform | Analyte | Immunohistochemistry | Protein |
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The purpose of this study was to assess the potential effects associated with time in fixative (TIF) on immunohistochemical staining of cancer biomarkers in prospectively collected FFPE kidney tumor specimens under the National Cancer Institute's Pre-analytical Variable (BPV) program. Tumors from 60 kidney resections were collected at four medical institutions using a common set of standard operating procedures (SOPs). Each surgical resection was dissected to yield tumor segments of approximately equivalent size (0.33 cm x 0.5 cm) that included a quality control for histopathology, a snap-frozen control, and four experimental tumor segments. After a DTF of 1 h, experimental segments were placed in 10% NBF at room temperature for 6, 12 (control), 23, or 72 h. A total of 13 biomarkers were examined in FFPE sections (5 µm) by immunohistochemistry. Positive immunostaining was quantified using Aperio software after calibration using slides manually scored by a pathologist. H-score was calculated by multiplying the percentage of positively stained cells/nuclei by the intensity of the stain (0-3). Statistical analysis included the mean and percent difference in H-scores of experimental (6, 23, 72 h TIF) specimens relative to corresponding 12 h TIF controls. H-score data collected from BPV tumor specimens was used to calculate the estimated probability of a change in intensity score for each TIF timepoint relative to the 12 h TIF control. Statistical significance was set to p<0.05. A subset of specimens stored as FFPE blocks were re-evaluated one year post-collection for RCC1 immunostaining.
Technology Platform | Analyte | Immunohistochemistry | Protein |
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Effects of delay-to-fixation and time-in-fixative on IHC staining of cancer biomarkers
A compendium of SOPs related to the collection and testing for the novel 2019 coronavirus (SARS-CoV2, COVID-19) is available: https://brd.nci.nih.gov/brd/sop-compendium/show/1361.
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