Wellcome Sanger Institute

Sample Management

Scientific Operations

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.

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    [introduction] => 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: <a href="mailto:sample-management@sanger.ac.uk">sample-management@sanger.ac.uk</a>
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                            [post_content] => <p>The Vertebrate Genomes Project (VGP) at the Sanger Institute aims to provide reference quality assemblies for hundreds of fish, rodents and caecilians to contribute to the Tree of Life Sequencing effort. The current pilot focusses on cyprinids, cichliforms, notothenioid and anabantoid fishes, as well as select rodents and caecilians.</p><p></p>
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                            [post_title] => 25 Genomes for 25 Years
                            [post_excerpt] => The project's primary goal was to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute'&nbsp;<span title="... s wider 25th Anniversary celebrations. This project was a pathfinder for long-read sequencing projects to demonstrate the Institute&rsquo;s capabilities and provided reference genomes for the global scientific community.">...</span>
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                            [post_title] => Human Cell Atlas
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                    [content] => <h5>Services:</h5>
<p>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.</p>
<p>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.</p>
<h5>QC:</h5>
<p>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.</p>
<h5>Fluidigm genotyping:</h5>
<p>Currently Sample Management offer two types of Fluidigm chips capable of testing using three sets of assays as part of the standard human QC.</p>
<ul>
<li>192.24 chip which utilises the 22 QC plex SNPs and 2 gender SNPs</li>
<li>96.96 DDD project chip which utilises 57 SNPs of which 22 are QC plex SNPs and 3 are gender SNPs</li>
<li>96.96 CGP project chip which utilises 95 SNPS of which 22 are QC plex SNPs and 3 are gender SNPs</li>
</ul>
<h5>Normalisation and Formatting:</h5>
<p>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.</p>
<h5>Extraction platforms:</h5>
<p>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.</p>
<p>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.</p>
<p>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.</p>
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    [page_url] => https://www.sanger.ac.uk/group/sample-management/
    [page_title] => Sample Management
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    [post_url] => https://www.sanger.ac.uk/group/sample-management/
    [post_title] => Sample Management
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    [created_at] => 2015-10-15 11:14:03
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    [custom_credit] => Wellcome Sanger Institute
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Our people

Group lead

Core team

Photo of Mr Ian Still

Mr Ian Still

Advanced Research Assistant

Photo of Theresa Feltwell

Theresa Feltwell

Advance Research Assistant

Photo of Maria Coppola

Maria Coppola

Research Assistant

Photo of Leanne Morrow

Leanne Morrow

Advanced Research Assistant

Photo of Adrian Clarke

Adrian Clarke

Research Assistant