Biospecimen Processing and Biorepository Publications

Biospecimen Processing and Biorepository Shared Resource Grant Descriptions

Short Grant Description

The Biospecimen Processing and Biorepository (BPB) shared resource has 10 well trained and experienced staff who provide a range of standardized and centralized services for processing and storing biospecimens. We process blood, urine, buccal, stool and other biospecimens; isolate DNA and/or RNA from the samples; store cells, nucleic acids and other samples in liquid nitrogen tanks, -80-degree freezers. We operate and manage the data entry and biorepository data bases. We host and operate several large Biorepositories as well as repositories for individual studies. We provide service for sample retrieval and shipment. We offer dedicated laboratory support for large size, long-term, population-based studies.
 

Long Grant Description 

The Biospecimen Processing and Biorepository (BPB) shared resource provides interconnected and stream-lined services of Biospecimen processing and storage. These services are carried out by 10 well trained staff and following standard procedures.

Biospecimen processing - The BPB-SR provides services of processing biospecimen originated from blood, urine, buccal swabs, stool swabs, BAL fluids. We have standard operating procedures (SOP) in the lab for most of the sample types we process. We use and can adapt new SOPs according to individual study’s specific needs.

DNA extraction - The BPB-SR provides DNA extraction using various salting out techniques. We can extract from whole blood, peripheral mononuclear cells, B-lymphoblastoid cells, bone marrow, tissues (frozen and formalin-fixed paraffin-embedded), buccal brushes, swabs and organelles. The extraction procedure varies by sample type, allowing us to obtain the highest quality and the largest yield possible. We use Picogreen or Qubit to measure the DNA quantity, and we assess the OD A260/A280 via Nanodrop to measure the quantity and quality. Analysis using Agilent’s TapeStation can provide additional quality metrics. DNA can be prepared to a specific concentration as required and stored.

RNA extraction - The BPB-SR provides RNA extraction from a wide variety of starting materials, including Paxgene, tissues, cells, blood (buffy coats), serum/plasma, FFPE, globin mRNA depletion and bone marrow. We provide the A260/A280 ratio and concentration for RNA isolation and determine quality using Agilent’s TapeStations. We also offer microdissection service on FFPE samples.

Biorepository - The BPB-SR provides Biorepository services for internal and external investigators. We operate and manage various repositories of PBMC, plasma, serum and other biospecimens. The Biorepositories are invaluable shared resources for Fred Hutch researchers and outside investigators. Besides many Biorepositories for many individual investigators, we host two large Biorepositories.

The International Histocompatibility Work Group (IHWG) Cell and DNA Bank - Established in 1999 to support research projects of IHWG workshops, the Cell and DNA Bank contains a large inventory of reference material studied in 10th, 12th and 13th Workshops.  The B-cell lines and DNA reference panels available from the repository provide an extensive array of HLA and HLA-related sequence polymorphisms for the study of the human MHC.

Our repository of HLA reference standards comprises more than 1,000 B-lymphoblastoid cell lines derived from past IHWG workshops. Find more information about the IHWG collection, including ordering instructions, on the Fred Hutch IHWG website. https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html

Hematopoietic Cell Therapy Research Cell and DNA Bank (HCT-RCB) - The HCT-RCB is a centralized repository of biospecimens established and maintained to support research projects within the Fred Hutch Hematopoietic Cell Transplantation Program. Specimens include peripheral blood and bone marrow mononuclear cells, B-lymphoblastoid cell lines immortalized in-house, and DNA. Samples are only available for distribution internally to Fred Hutch investigators and members of the Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium.

Transformation of B-Cell Lines - The BPB-SR provides immortalization of B-lymphoblastoid cells using Epstein-Barr virus. We use cyclosporine A in this process to inhibit T-cell populations, and we proliferate lines in culture without the use of antibiotics. We generally cryopreserve the cells in short- or long-term storage in concentrations of 5 to 7 million in a 10% DMSO freezing solution.

Biospecimen ordering and shipping service - The BPB-SR provides biospecimen ordering and shipping services. We follow each study and Biorepository’s protocol in ordering, specimen retrieval and shipping.

Mycoplasma testing - The BPB-SR offers Mycoplasma testing services. The test currently is done using the MycoProbe kit from D&D solution.  It captures and detects the 16S ribosomal RNA of the most common strains of Mycoplasma. It is a high-throughput screening assay. Fresh or frozen cell pellets or cell culture supernatants can be submitted for analysis. We are currently exploring additional testing methods using a PCR based kit and a rapid test kit.