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

Validating quantitative PCR assays for cfDNA detection without DNA extraction in exercising SLE patients.

Author(s): Neuberger EWI, Brahmer A, Ehlert T, Kluge K, Philippi KFA, Boedecker SC, Weinmann-Menke J, Simon P

Publication: Sci Rep, 2021, Vol. 11, Page 13581

PubMed

1 study(s)

The purpose of this study was to investigate the effects of blood collection time relative to exercise, blood centrifugation delays, speed and temperature, plasma storage and freeze-thaw cycling, and cfDNA extraction method on the yield and/or fragmentation of cfDNA from capillary and venous blood. Venous and capillary blood were collected from 28 patients with systemic lupus erythematosus before, immediately following and 90 min after a stepwise exercise test. During the exercise test the speed and elevation of the treadmill increased every 3 min until the participants stopped voluntarily. Unless otherwise specified, plasma was collected from venous blood by immediate dual-centrifugation at 2500 x g for 15 min and from capillary blood by centrifugation at 600 x g for 10 min after an unspecified delay at 4°C. Unless otherwise specified cfDNA copy number was evaluated by direct real-time PCR amplification of 90m and 222 bp fragments of L1PA2 from plasma diluted 1:10 in DNase/RNase-Free H2O. To test the effects of delayed centrifugation matched capillary and venous blood specimens from 3 patients were stored at room temperature for 0, 60 min, 90 and 180 min before plasma separation. To evaluate the stability of cfDNA in diluted plasma, 20 plasma specimens diluted 1:10 were analyzed again after storage for >2 months at -20°C. To evaluate the effects of centrifugation speed, matched blood from three subjects was centrifuged at 600 x g and 2500 x g at 4°C and room temperature. To evaluate the effects of cfDNA isolation, cfDNA was isolated from four aliquots of the same thawed plasma sample using QIAamp Circulating Nucleic Acid kit, NucleoSnap plasma cfDNA kit and the QIAamp DNA Blood Mini kit and levels and fragmentation were compared to direct amplification from matched plasma.
Biospecimens
- Fluid - Plasma
- Fluid - Blood
Platform:

Technology Platform Analyte

Real-time qPCR DNA