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 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).
Featured Paper
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The purpose of this study was to compare results of RNAseq analysis of FFPE breast tumor specimens obtained using 3’capture (Lexogen, Lexogen’s QuantSeq 3’ Kit), exome-capture (RNAaccess, TruSeq RNA exome Kit), and ribodepletion (Smarter, SMARTer Stranded Total RNA-seq Kit v3-Pico; Solovation, Ovation SoLo Kit; Sequoia, SEQuoia Complete Stranded RNA Kit) approaches to gene expression results obtained using NanoString in tumor-matched FFPE specimens and RNAseq results from case-matched frozen tumor specimens using polyA enrichment (TruSeq, TruSeq polyA enrichment kit). Twenty tumor-matched FFPE and frozen breast tumor specimens were used for all comparisons, with the exception of the RNAaccess method that used 12 specimens. RNA was isolated from frozen specimens with the RNeasy Mini Kit and from FFPE specimens with the ALLPrep FFPE Tissue Kit. The amount of RNA isolated from FFPE specimens used as input depended upon the library sequencing kit and assay used: Nanostring (150 ng), Truseq (400 ng), RNAaccess (400 ng), Lexogen (50, 150, 400 ng), Sequoia (2, 26 ng), Solovation (2, 5 ng), Smarter (2, 8 ng). Samples were analyzed by Illumina short-read sequencing at a depth of 10 million single-end reads (Lexogen) or 20 million paired-end reads (all other kits).
Biospecimens
- Tissue - Breast
Platform:
Technology Platform Analyte DNA sequencing RNA
News and Announcements
April 24, 2024: Biobanking for Precision Medicine Seminar
Join us for a Biobanking for Precision Medicine Seminar by Dr. Muhammed Murtaza, M.B.B.S., Ph.D., entitled "Preanalytical Considerations for Analysis of Circulating Tumor DNA"
Date: Wednesday, April 24, 2024, 1:00 p.m.–2:30 p.m. ET
Location: Virtual, WebEx Registration
Participants must register using the WebEx link prior to the meeting.
Most Popular SOPs in March 2024
The most popular SOPs downloaded from the BRD's SOP Library in March 2024, were the CDC's SOP on the Collection and Transport of Clinical Specimens and the UCHC Tissue Repository's SOP on Tissue Processing.
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