The NIHR National Biosample Centre

Transcription

1 The NIHR National Biosample Centre Executive summary: There is limited biosample storage on site at the UHS Campus. NIHR has invested in the NIHR National Biosample Centre (BC) which is an off site storage solution that allows investigators to maintain full control of their professionally managed samples. UHS Infrastructure has a memorandum of understanding with the BC and can produce costings for sample storage at the point of application. Background & Facility - The NIHR National Biosample Centre.see page 2 for more detail The facility was established using a large capital grant from NIHR and is part of the NIHR national infrastructure to support clinical research. The facility is HTA-licensed, ISO 9001-certified service centre with its main site in Milton Keynes and a back-up site in Osney Mead, Oxford. The facilities can curate and house legacy collections as well as support currently active or planned studies...see page 3 for more detail of services Benefits to users: Studies can be started more quickly, at reduced cost (cost outlines for common requests see page 4 6, other bespoke activities can be added). NIHR-NBC staff can project manage the implementation and operation of the in-scope services in close collaboration with the researchers. Control of the samples is maintained by the PI (or their study access committee) under the existing arrangements for the study. UK Biocentre has no ownership or control over use of the samples. UK Biocentre will follow instructions from the research group in handling or distribution of samples and/or data. Researchers in Southampton/other organisations can arrange services individually with UK Biocentre. Alternatively a framework agreement is already in place with The Biosample centre with fixed prices for defined services see pages 4-6 below (other bespoke activities can be added). Page 1 of 6

2 Information for scientists on how to use this national resource 1. Background - The NIHR National Biosample Centre The NIHR-funded National Biosample Centre (NIHR-NBC) has been established in Milton Keynes and Oxford to provide a high quality, high capacity service for biomedical researchers engaged in studies that include the collection, processing, storage and analysis of biological samples from their volunteers and patients. The knowledge, skills and infrastructure developed from the recruitment and sample collection of 500,000 adults in the UK Biobank prospective cohort study ( have provided the foundations for the design and implementation of the NIHR-NBC. In 2011, staff at UK Biobank established UK Biocentre, a wholly owned subsidiary of UK Biobank, to make this expertise and infrastructure available to the wider biomedical community. The facility was established using a large capital grant from NIHR and is part of the NIHR national infrastructure to support clinical research. By building a centre of excellence with high capacity and high quality systems and infrastructure, existing studies can be done better or more cost-effectively, new studies can be done that were either previously unaffordable or not feasible and nationally important research collections can benefit from the highest standards of storage and processing. UK Biocentre has developed a core capacity at NIHR-NBC that will be valuable to a wide range of studies. It has implemented a highly-automated infrastructure and robust information and quality systems to provide a cost-effective, secure and responsive service. The extensive use of automation ensures speed and accuracy of processing, a robust and secure data trail and efficient archiving and retrieval of samples preventing mis-attribution of samples that can lead to false positives in cohort studies and mis-diagnosis in clinical settings. 2. The facility The NIHR-NBC consists of two sites: o The main site, located at Milton Keynes, is a 65,000sqft building that houses the processing and archiving automation and is equipped with emergency generators and fire suppression systems. All critical systems are alarmed and all sample archives have backup systems in the event of failure of the primary cooling. Profile-controlled entry to all areas and 24 hour monitoring of the site prevents unauthorised access to sample processing or archiving areas and IT infrastructure. o The second site, located at Osney Mead, Oxford is currently used as a back-up site and houses large, nitrogen-jacketed sample storage tanks that are remotely monitored. This site could readily be used as a main storage site for organisations (albeit there is no largescale automated archiving). Security and fire suppression systems are also in place at Osney Mead. Page 2 of 6

3 3. Summary of services The NIHR-NBC has been established as an HTA-licensed, ISO 9001-certified service centre with its main site in Milton Keynes and a back-up site in Osney Mead, Oxford. The facilities can curate and house legacy collections as well as support currently active or planned studies. NIHR-NBC has been designed to offer a menu of activities: Advisory services Provision of advice on sample collection, shipping and storage. Interfacing of LIMS systems with researchers databases. Supply of sample collection consumables, leveraging NIHR-NBC s bulk discounts. Provision of courier service with a national provider. Sample receipt Receipt and secure logging of samples from national collection centres either as fresh sample for processing or pre-processed samples for immediate archiving. Sample processing Manual processing for complex protocols (e.g., lymphoprep, manual handling of Cerebro- Spinal Fluid). Fully automated processing and aliquotting of blood, urine, saliva, solid tissue up to 2,000 primary samples per day. Sample archiving Capacity to store all types of common consumables in manual or automated systems. Capacity to store 18 million 1.2ml cryovials in fully automated -80 o C archives (storage capacity for larger consumables is reduced in a roughly linear fashion). Capacity to store 2 million 1.2ml cryovials in fully automated -20 o C archives. Very large and scalable capacity to store samples in NIHR-NBC manual -80 o C freezers. Unlimited capacity to store room temperature samples (e.g. dried blood spots, Formalin Fixed Paraffin Embedded [FFPE] sections). 2,000m 2 of low cost storage space for researchers to locate their own freezers. Capacity to store 5 million 1.2ml cryotubes at -196 o C at a secure off-site back up facility. Capacity for researchers to connect a further 85 nitrogen-jacketed tanks to liquid nitrogen infrastructure. Sample processing Capacity to extract DNA from up to 1,000 samples per day includes buffy coat, whole blood, solid tissue, saliva, FFPE sections. Capacity to extract whole cell RNA from up to 650 whole blood, buffy coat or solid tissue samples per day. Sample dispatch and shipping High throughput, accurate picking of samples with the option for randomisation of output plates. Dispatch against researchers instructions and follow up to ensure receipt of samples Project services Full project management of project and operational phases of the study. Quality, health and safety and financial management and reporting for the in-scope processes Page 3 of 6

4 4. Benefits to the user The NIHR-NBC will be a major enabler to the successful completion of biomedical studies. Once the study protocol has been developed and ethics approval obtained, researchers can begin recruitment without waiting for the prolonged process of establishing the necessary infrastructure, IT systems and staff resources. Researchers can access a complete service or discrete elements. They can discuss and develop this part of their study with experts from the centre. Studies can be started more quickly, at reduced cost and risk. NIHR-NBC staff can project manage the implementation and operation of the in-scope services in close collaboration with the researchers. Control of the samples is maintained by the PI (or their access committee) under the existing arrangements for the study. UK Biocentre has no ownership or control over use of the samples. UK Biocentre will follow instructions from the research group in handling or distribution of samples and/or data. Researchers in the organisation can arrange services individually with UK Biocentre. Alternatively, a framework services agreement can be put in place with the broader organisation with fixed prices for defined services see appendix 2 (other bespoke activities can be added). 5. Cost of services Pricing at NIHR-NBC has been developed to facilitate biomedical research as cost-effectively and flexibly as possible. This pricing is provided for information purposes only and any resultant work will be subject to UK Biocentre s Terms and Conditions. Please find pricing below. Item Service/ Product Description Pricing Ex. VAT Pricing Inc. VAT 1 Sample collection packs Provision of sample collection packs containing blood (and other sample types) tubes, sample collection form and replicate adhesive barcodes. Courier service from sites to the NIHR National Biosample Centre. 2 Courier service to UK Biocentre 3 Sample receipt Receipt of samples at the NIHR National Biosample Centre and logging of sample information into LIMS. Sample receipt is charged per sample. This is our std rate but is dependent on volumes and sample/ labware type. On average this rate can be reduced for larger volume shipments. 4 Sample processing Processing of primary tubes into aliquots for storage. Primary sample tube volume range is from 1-10ml. Service will be charged based on the total number of aliquots produced per sample. a) 1 aliquot 1.98 b) 2 aliquots 2.45 c) 3 aliquots 2.93 d) 4 aliquots 3.41 e) 5 aliquots * 0.16* *These rates assume barcoded samples. If samples need manual storage (handwritten labels) then per hour rate may be required for sample storage a) 1 aliquot 2.38 b) 2 aliquots 2.94 c) 3 aliquots 3.52 d) 4 aliquots 4.10 e) 5 aliquots PBMC isolation PBMC recovery from blood samples. Recovery is performed using a lymphoprep procedure and includes a cell count and cell viability measure. Price per sample Page 4 of 6

5 6a 6b Automated DNA extraction from whole blood, saliva and buffy coat Automated DNA extraction from whole blood and buffy coat DNA extraction from 1-6ml whole blood/ buffy coat. For fresh whole blood samples greater than 6ml in volume we would recommend performing a buffy coat recovery first with subsequent extraction from buffy coat (EDTA sample processing charge to apply if required). Subsequent storage will be charged based on the number of stock DNA samples produced. DNA extraction from: a) 200ul buffy coat, per sample b) 400ul whole blood, per sample a) 1 ml Blood 7.00 b) 4 ml Blood c) 6 ml Blood d) 1ml Buffy coat e) Saliva (Oragene) a) 4.60 b) 4.00 a) 1 ml Blood 8.40 b) 4 ml Blood c) 6 ml Blood d) 1ml Buffy coat e) Saliva (Oragene) a) 5.52 b) DNA quantification - absorbance DNA is quantified using a Trinean Dropsense absorbance system. Price per sample. 8 DNA normalisation DNA will be normalised to the required concentration as requested by the researcher. Two standard formats are provided for: a) PCR plate, per plate b) FluidX 2D barcoded 1ml tubes, per 96 DNA can be normalised to other labware types on request, a quotation will be provided for bespoke requests. Plate seal to be specified and is not included in the price. 9 Sample reformatting Samples can be reformatted from the standard FluidX 1ml 2D barcoded format to two standard formats: a) PCR plate, per plate. b) FluidX 1ml 2D barcoded tubes, per 96. a) b) a) b) a) b) a) b) Automated sample storage 1ml tubes 11 Manual sample storage, -80 C, per shelf 12 Manual sample storage, -80 C, entire freezer 13 Manual freezer management Samples can be reformatted to other labware types on request, a quotation will be provided for bespoke requests. Plate seal to be specified and is not included in the price. Storage of 1ml samples at -80 C or -20 C in automated archives. Storage is charged per sample per annum. This price includes all subsequent retrieval tasks i.e. no retrieval charge is incurred to access or pick samples. Storage of samples in UK Biocentre provided manual -80 C freezers. Price per shelf per annum. Rental of UK Biocentre provided manual - 80C freezer per annum , , , , Relocation of manual freezers to the NIHR National Biosample Centre: 1) Freezer management is charged 1) 2, ) 3, Page 5 of 6

6 14 Manual sample storage, liquid nitrogen, 1ml tubes 15 Manual sample storage, liquid nitrogen, 2ml tubes 16 Liquid nitrogen tank management 17 Sample retrieval Automated freezers 18 Sample retrieval Manual freezers (- 80 C and liquid nitrogen) per freezer per annum. Shipping is not included. Several additional options are available: a) Connection to UK Biocentre CO2 cylinder, per freezer. b) Connection to temperature monitoring system only, per freezer. c) Connection to temperature monitoring system and CO2 cylinder (freezer supplied with CO2 backup systems already installed), per freezer. d) UK Biocentre supplied CO2 backup systems and connection to CO2 cylinder, per freezer. e) UK Biocentre supplied CO2 backup systems, connection to CO2 cylinder and installation of temperature monitoring systems, per freezer. f) Annual subscription to online temperature monitoring system (from year 2 onwards where item (b) is selected). Storage of 1ml samples in manual liquid nitrogen tanks. Price per 96 way SBS rack per annum. Storage of 2ml samples in manual liquid nitrogen tanks. Price per 10x10 box per annum. Relocation of liquid nitrogen tanks to UK Biocentre. Price per tank. Shipping is not included. Retrieval of samples from -80 C automated archives at the NIHR National Biosample Centre. Price per sample. Retrieval of samples from -80 C and liquid nitrogen manual freezers. Price per hour, minimum charge of one hour. 19 Project management Project management is provided in line with the demands and scale of the project, per day. 20 Sample shipping Shipping of samples stored at UK Biocentre to Client, or the Client specified destination. Price dependent on shipping conditions, size of shipment and destination. a) b) c) d) 1, e) 2, f) a) b) c) d) 2, e) 2, f) , , No charge No charge per hour per hour To be specified per shipment. Please contact Dr Kristian Spreckley if you require any further information. Kristian.spreckley@ukbiocentre.com Telephone: To be specified per shipment. R&D, or the CRF team, can work with the Biosample Centre team to provide a formal accurate costing for any grant application Page 6 of 6