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 email@example.com. 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 compared the cellularity and tumor content of 100 matched FNA and CNB specimens and investigated the effects of neoplasm type (adenocarcinoma, squamous cell carcinoma, poorly differentiated carcinoma, or neuroendocrine carcinoma/small cell carcinoma) and location. Two to three FNA specimens were obtained using 20-25 gauge (G) needles under computed tomography (CT) or ultrasound guidance with a 17-19 G guide needle. Three to four cores were obtained using the guide needle with a 16-20 G needle. The FNA was obtained first for most tumors but the CNB was obtained first for subcentimeter tumors. FNA specimens were smeared and Diff-Quik and Papanicolaou stained. CNB slides were prepared and H&E stained. Cellularity was described as high for >5000 cells per FNA slide or >2000 cells per CNB slide, moderate for 1000-5000 cells per FNA slide or 300-2000 cells per CNB slide and low for <1000 cells per FNA slide or <300 cells per CNB slide. Tumor fraction was determined independently by two cytopathologists and then reviewed together in cases with >10% discordance.
|Technology Platform||Analyte||Light microscopy||Morphology||H-and-E microscopy||Morphology|
This study compared the tumor content, DNA yield, and NGS sequencing coverage of 100 matched FNA and CNB specimens. Matched image-guided CNB and FNA specimens from 17 adenocarcinomas, four carcinomas not specified, two squamous cell carcinomas, and one melanoma. Two to three FNA specimens were obtained using 20-25 G needles under computed tomography (CT) or ultrasound guidance with a 17-19 G guide needle. Three to four cores were obtained using the guide needle with a 16-20 G needle. The FNA was obtained first for most tumors but the CNB was obtained first for subcentimeter tumors. FNA specimens were smeared and Diff-Quik and Papanicolaou stained. CNB slides were prepared and H&E stained. Tumor fraction was determined independently by two cytopathologists and then reviewed together in cases with >10% discordance. DNA was extracted from tumor-enriched areas of smears and FFPE sections using PicoPure. DNA was quantified using Qubit. NGS was conducted on an Ion Torrent using the Ampliseq Cancer panel primers.
|Technology Platform||Analyte||Fluorometry||DNA||Light microscopy||Morphology||H-and-E microscopy||Morphology||Next generation sequencing||DNA|
The newest edition of the ISBER Best Practices was released on January 31, 2018. View the document at http://www.isber.org/?page=BPR.
The top 5 most downloaded SOPs in the BRD in 2017 were supplied by:
GAPPS Repository: https://brd.nci.nih.gov/brd/sop/show/890
UCHC Tissue Repository: https://brd.nci.nih.gov/brd/sop/show/841More...