Sample Management
Sanger Institute, Genome Research LimitedOur Research and Approach
Sample management undertake DNA and RNA extraction from biological materials, provide automated QC and normalisation to the DNA pipelines teams, an archiving service to internal and external customers, management of the sites cryostores and irreplacable biological resources (IBRs). Contact: sample-management@sanger.ac.uk
Services:
We currently register and process approximately 25-30,000 samples a month through the team; this includes extracted and pre-extracted DNA and RNA. Samples will be processed using a laboratory information management system (LIMs) which provides unique Sanger IDs per sample as well as per container. Containers are also electronically stored using this ID in our growing freezer farm.
Samples are requested to be supplied in specific labware types as well as differing concentration/volume/total amounts depending on the destination pipeline team. This ensures that there is sufficient sample for QC and for successful downstream processing. The accepted labware types and requirements are available in our submission guidelines.
QC:
For DNA and RNA we use various processes to determine sample volume, sample concentration, RNA integrity number and a SNP genotyping assay in order to Quality Check samples in Sample management.
Fluidigm genotyping:
Currently Sample Management offer two types of Fluidigm chips capable of testing using three sets of assays as part of the standard human QC.
- 192.24 chip which utilises the 22 QC plex SNPs and 2 gender SNPs
- 96.96 DDD project chip which utilises 57 SNPs of which 22 are QC plex SNPs and 3 are gender SNPs
- 96.96 CGP project chip which utilises 95 SNPS of which 22 are QC plex SNPs and 3 are gender SNPs
Normalisation and Formatting:
Post QC Sample Management can normalise DNA/RNA samples in terms of concentration and volume using automated liquid handlers. Samples can also be re-arrayed according to their unique identifiers and downstream specifications.
Extraction platforms:
Currently within Sample Management we have several automated extraction platforms capable of isolating DNA and/or RNA from differing input materials and labware types. These automated platforms include the Qiagen QIAcube and QIAsymphony. We also have semi-automated processes and can carry out more bespoke extractions if required.
Sample Management can extract from various fresh or frozen sample types including: Cell pellets, Tissue, Blood, Buffy Coat, Saliva, virus/pathogens, dried blood spots and saliva on FTA cards. Samples can be sent in pre-lysed or lysed in house on request.
We have a containment level 2 lab within our current facility allowing us to receive hazard group one and two biological agents
For any queries, please contact Sample Management for an extraction project proposal form or our submission guidelines.
People
Clarke, Adrian
Adrian Clarke
Coppola, Maria
Maria Coppola
Morrow, Leanne
Leanne Morrow
Still, Ian
Mr Ian Still
Key Projects, Collaborations, Tools & Data
25 Genomes for 25 Years
The project's primary goal is to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute's wider 25th Anniversary celebrations. This project will be a pathfinder for future long-read sequencing projects to demonstrate the Institute’s capabilities and will provide reference genomes for the global scientific community.Human Cell Atlas
The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease.UK Biobank Whole Genome Sequencing project
UK Biobank is a health resource with unparalleled research opportunities. UK Biobank data will enable the scientific community to understand, diagnose, treat and prevent life-changing diseases– including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia. UK Biobank is following the health and well-being of 500,000 volunteer participants and provides anonymised health information to approved researchers in the UK and overseas, from academia and industry.Vertebrate Genomes Project
The Vertebrate Genomes Project (VGP) at the Sanger Institute aims to provide reference quality assemblies for hundreds of fish, rodents and caecilians as part of the Tree of Life Sequencing effort. The current pilot focusses on cyprinids, cichliforms, notothenioid and anabantoid fishes, as well as select rodents and caecilians.
Partners and Funders
Internal Partners
Bespoke Sequencing
The remit of the Bespoke team within DNA Pipelines Operations is to process samples that cannot be handled within the standard pipeline provided by the high throughput teams. This might be due to insufficient DNA, poor sample performance within standard processes or a requirement for a novel library type.Genotyping, Index Sequence Capture (ISC) and Single-cell sequencing
The Genotyping, Index Sequence Capture (ISC) & Single-cell Sequencing team within DNA Pipelines Operations is a high throughput Illumina® library creation team specialising in producing libraries quickly and at scale from extracted material and single cells.High-Throughput DNA Sequencing
The High Throughput DNA sequencing team within DNA Pipelines Operations is a highly automated hig