The BioSpecimen Processing Lab (BSPL) provides a suite of biospecimen services to support clinical, translational, and basic life sciences research:
Biospecimen Acquisiton
Our team is specially trained in obtaining tissue and fluids in coordination with clinical procedures. We work with the clinical teams to develop procedures that permit research specimen collection while not impacting clinical sample evaluation.
Biopsy Collection - To ensure study requirements are communicated and high qualtity tissue is procured, a Research Associate attends biopsy procedures to receive tissue samples directly from the clinician and promptly preserve samples per study requirements.
Surgical Collection - Our team of Pathologists' Assistants are trained to perform complex tissue dissection in accordance with pathology departmental guidelines while prioritizing patient diagnostic safety. Specimens are retreived from surgical suites, rapidly dissected and fresh, frozen and fixed tissue procured per study requirements.
Available preparation methods:
Fresh tissue in media
Snap frozen, frozen in OCT, viable cryopreservation
Frozen tissue sectioning
Formalin-fixed tissue processed into FFPE blocks
Slide sectioning and staining
Biofluid Processing
Samples can be processed via one of our validated standard operating procedures, or according to specialized methods or sponsor requirements.
Separation of blood components
PBMC isolation and preservation
Whole blood stimulations
DNA Extraction from blood, tissue and saliva
RNA extraction from PAXGene tubes
Biospecimen Custodianship
The UCSF Biobank provides secure, round-the-clock monitored biospecimen storage and inventory mangement via a regulatory-complient online database.
Storage of blood, body fluids and tissue
Ambient, 4°C, -20°C -80°C, and liquid nitrogen sample storage
Controlled access, freezer alarms, back-up power and redundant temperature monitoring.
24/7 personnel coverage for off-hour freezer issues
Samples acquired and/or processed by the Biobank are 2D barcode labeled.
Inventory management through MBioLIMS, a web-based regulatory compliant database to track samples through collection, processing, storage and distribution.
BSP Lab Guidelines for Liquid Sample Processing:
Hours of operation (all campuses):
Monday through Friday, 8am – 4:30pm. Last samples must be received by 4:00pm.
Samples with same-day shipments must be received by 1:30pm to meet outbound shipping cutoffs.
Samples with complex processing, such as PBMCs, whole blood stimulations, must be received by 2:30pm.
If same-day shipment samples are received past the cut-off time, samples will be shipped the next business day. Ambient samples are generally more time sensitive and require same-day shipment.
If your protocol has samples that will be collected past the same-day processing cut off time, please consult with your PI and/or sponsor for next steps. We can store samples overnight at ambient and refrigerated (4C) temperatures for processing the next day, but only with PI and/or sponsor approval.
Scheduling sample drop-offs:
Schedule an appointment on our Outlook calendar by sending a calendar invite to biobank@ucsf.edu at least 24-hours in advance (last minute collections are subject to approval by on-site staff and are dependent on scheduled case volumes). Please include CC or study number, timepoint, and subject ID (SID) in the calendar invite title. Please attach the protocol/lab manual to the calendar invite. The duration of the calendar invite should be the expected times that the lab will receive samples.
Please notify us of sample delays or any changes to the calendar invite promptly via email/slack. Note: Samples should be dropped off promptly to the BSP labs following collection from the patient to ensure compliance with protocol requirements and to safeguard sample viability. Please do not drop off sample collections in batch if there are large delays between collections. Samples will no longer be picked up from clinical floors by the BSP team.
Label all blood tube samples and cryovials with SIDs prior to drop off.
You are welcome to bring all shipping supplies and kits to the lab in advance. Please label all kits, shippers, and airway bills (AWBs) with the study or protocol number, SID, visit, and collection date.
Provide sponsor requisitions (if applicable) and complete all required fields prior to drop off: e.g. DOB, Patient ID, Site #, Visit date.
Management
Aras Mattis, MD PhD - Director (aras.mattis@ucsf.edu)
Kirsten Mowry, PA (ASCP)cm - BioSpecimen Processing Lab Manager (kirsten.mowry@ucsf.edu)
Ron Honrada - BioSpecimen Processing Lab Manager (ronald.honrada@ucsf.edu)
Transfer of unprocessed blood or body fluids into storage tubes (cryovials etc). No other processing.
Inquire
Biopsy Collection
A biobank technician attends biopsy procedure and coordinates with research staff and clinical staff to collect specified type and quantiy of material required for study. Tissue is collected and preserved in the procedure room to ensure viability.
Inquire
Blood Processing
Centrifugation of blood collection tubes to isolate serum, plasma or buffy coat. Pooled blood tubes are treated as a single specimen; each additional tube type or special processing step is subject to additional fee.
Inquire
Body Fluid Processing
Centrifuge, wash and pellet up to 1 L fluid. Isolate pellet and process to frozen or FFPE block.
Inquire
PBMC Processing
Isolation of PBMC by one of the Biobank Laboratory standard protocols.
SepMate Isolation Method (Ficoll)
CPT Tube Processing
Inquire
RNA or DNA Extraction
The Biobank & Processing Core extracts DNA from formalin-fixed paraffin embedded (FFPE) tissue, frozen tissue blood and body fluids. Our protocols utilize commercially available kits and methods have been further optimized in house. DNA & RNA quantitation via Nanodrop. Sample preparation, specialty kits, small runs and custom methods are subject to additional fees.
Frozen Tissue: Genotyping and other DNA analyses using PCR or next-generation sequencing (NGS) require a suitable amount of high-quality genomic DNA as starting material. The most common bottleneck to obtaining high-quality DNA is tissue lysis. Fibrous or other hard-to-lyse tissues require lengthy and tedious protocols that often result in low yields of low-quality DNA. The QIAamp Fast DNA Tissue Kit overcomes this bottleneck by providing innovative disruption tubes that significantly improve yield and shorten the overall time to result.
Blood & Body Fluids: Fresh and frozen whole blood with common anticoagulants, such as citrate, EDTA, and heparin, may be processed. The QIAamp DNA Blood Mini Kit processes sample sizes of up to 200 µl. The typical yield from 200 µl healthy whole blood is 4–12 µg, with an elution volume of 50–200 µl. QIAamp DNA Blood technology yields genomic, mitochondrial, or viral DNA from blood and related body fluids ready to use in PCR and blotting procedures.
Fresh and frozen whole blood or buffy coat
Plasma or serum
Bone marrow
Lymphocytes
Platelets
Body fluids
Formalin Fixed Paraffin Embedded Tissue*: Artificial C>T mutations caused by cytosine deamination are critical in next-generation sequencing (NGS). These artifacts are caused by formalin fixation and aging, and result in sequencing errors. The GeneRead FFPE purification procedure also includes enzymatic removal of these artifacts, while ensuring high yields and purity, making it especially suitable for NGS applications.
PAXgene Blood DNA*: Purification of up to 500 µg genomic DNA from fresh or frozen whole blood collected. Used in conjunction with PAXgene DNA blood collection tubes.
PAXgene Blood RNA*: Purification of intracellular RNA from whole blood for applications in molecular diagnostic testing, such as real-time RT-PCR analysis of specific transcripts. Used in conjunction with PAXGene RNA blood collection tubes.
* Subject to specialty kit surcharge
Inquire
Tissue Preparation Sets
Tissue preparation* service sets:
Snap frozen in cryovials (5 vials)
OCT Embedded and frozen in molds (2 molds)
Viable freeze with cell preservation media (2 vials)
RNAlater treated and frozen (2 vials)
Fresh tissue in culture media (1 tube)
*All reagents and supplies are provided by Biobank.
Inquire
Urine Processing
Centrifugation of urine with aliquoting of supernate and cell pellet isolation. Up to 100mL and 10 aliquots.
A biobank technician attends biopsy procedure and coordinates with research staff and clinical staff to collect specified type and quantiy of material required for study. Tissue is collected and preserved in the procedure room to ensure viability.
Centrifugation of blood collection tubes to isolate serum, plasma or buffy coat. Pooled blood tubes are treated as a single specimen; each additional tube type or special processing step is subject to additional fee.
Inquire
PBMC Processing
Isolation of PBMC by one of the Biobank Laboratory standard protocols.
SepMate Isolation Method (Ficoll)
CPT Tube Processing
Inquire
Aliquoting Only
Transfer of unprocessed blood or body fluids into storage tubes (cryovials etc). No other processing.
Inquire
Urine Processing
Centrifugation of urine with aliquoting of supernate and cell pellet isolation. Up to 100mL and 10 aliquots.
Inquire
Body Fluid Processing
Centrifuge, wash and pellet up to 1 L fluid. Isolate pellet and process to frozen or FFPE block.
Inquire
RNA or DNA Extraction
The Biobank & Processing Core extracts DNA from formalin-fixed paraffin embedded (FFPE) tissue, frozen tissue blood and body fluids. Our protocols utilize commercially available kits and methods have been further optimized in house. DNA & RNA quantitation via Nanodrop. Sample preparation, specialty kits, small runs and custom methods are subject to additional fees.
Frozen Tissue: Genotyping and other DNA analyses using PCR or next-generation sequencing (NGS) require a suitable amount of high-quality genomic DNA as starting material. The most common bottleneck to obtaining high-quality DNA is tissue lysis. Fibrous or other hard-to-lyse tissues require lengthy and tedious protocols that often result in low yields of low-quality DNA. The QIAamp Fast DNA Tissue Kit overcomes this bottleneck by providing innovative disruption tubes that significantly improve yield and shorten the overall time to result.
Blood & Body Fluids: Fresh and frozen whole blood with common anticoagulants, such as citrate, EDTA, and heparin, may be processed. The QIAamp DNA Blood Mini Kit processes sample sizes of up to 200 µl. The typical yield from 200 µl healthy whole blood is 4–12 µg, with an elution volume of 50–200 µl. QIAamp DNA Blood technology yields genomic, mitochondrial, or viral DNA from blood and related body fluids ready to use in PCR and blotting procedures.
Fresh and frozen whole blood or buffy coat
Plasma or serum
Bone marrow
Lymphocytes
Platelets
Body fluids
Formalin Fixed Paraffin Embedded Tissue*: Artificial C>T mutations caused by cytosine deamination are critical in next-generation sequencing (NGS). These artifacts are caused by formalin fixation and aging, and result in sequencing errors. The GeneRead FFPE purification procedure also includes enzymatic removal of these artifacts, while ensuring high yields and purity, making it especially suitable for NGS applications.
PAXgene Blood DNA*: Purification of up to 500 µg genomic DNA from fresh or frozen whole blood collected. Used in conjunction with PAXgene DNA blood collection tubes.
PAXgene Blood RNA*: Purification of intracellular RNA from whole blood for applications in molecular diagnostic testing, such as real-time RT-PCR analysis of specific transcripts. Used in conjunction with PAXGene RNA blood collection tubes.
