Laboratory Services (SDGS)

scientist

Laboratory Services supports the oncology and constitutional sections of Sheffield Diagnostic Genetics Service (SDGS) through a series of technical, administrative and IT teams.

We conduct cytogenetic and molecular laboratory techniques through robust processes alongside office based support and first pass analysis.

We also engage in research and development and run a clinical trials service.

The department is supported by an administrative team who are integral to the smooth running of the laboratory through booking on samples, invoicing and other administrative tasks.

Bioinformatics

Our Bioinformatics team supports the department’s clinical work, assists in service development, and is actively involved in multiple research projects. We can provide a range of bioinformatics services including:

  • Analysis of next generation sequencing data, statistical analysis of large data sets, data visualisation
  • Database and software development
  • Experimental design
  • Training
  • Data management, data sharing (including confidential data)

For further information contact Elizabeth Sollars at Elizabeth.Sollars@nhs.net 

Clinical trials

The Clinical Trials team provides contract research to clinical research organisations and university researchers. Studies undertaken range in size from tens to thousands of samples and can incorporate any of the technologies available in the laboratory.

The department offers a range of bespoke molecular and cytogenetic testing, with work undertaken to UKAS (ISO15189:2012) standards.

For further information contact Sara Morosini on 0114 271 7047 / email sara.morosini@nhs.net 

Cytogenetic services
This team has responsibility for the delivery of all aspects of laboratory processes and first line analysis for:

  • Karyotyping (Constitutional and Oncology including prenatal work) using CytoVision® (Leica Biosystems)
  • FISH analysis (Constitutional and Oncology including prenatal work)
  • Array CGH microarrays (BlueGnome platform) for whole genome work or targeted analysis
Genotyping technology
Within the Genotyping team the technological platforms used are:

  • 480 LightCycler coupled with COLD PCR for detection of low level mutations
  • COLD PCR coupled with the PyroMark Q96 platform for detection of low level mutations
  • Standard PCR coupled with the PyroMark Q96 platform for detection of known point mutations
  • 7500 Real time PCR platform for the monitoring and accurate quantitation of gene fusion events
  • Fluorescent tagged standard PCR and repeat primed PCR analysed on the 3730 DNA analyser for the accurate sizing of alleles and detections of large expansions
  • Fluorescent tagged PCR for gene dosage analysis determination using multiplex ligation-dependent probe amplification kits from MRC Holland
  • Standard PCR and multiplex PCR for the targeted amplification of specific genomic regions which are then further analysed on polyacrlyamide or agarose gels
Genotyping technology
Human embryonic stem cell lines

We have substantial experience with human embryonic stem cell lines in collaboration with Peter Andrews (Centre for Stem Cell Biology, University of Sheffield) and also karyotyping of fibroblast, tumour and mouse lines.

We would be happy to accept other cell types for analysis. We have a large range of Fluorescent in situ hybridisation (FISH) probes available, including Multi-Colour FISH, for characterising abnormal chromosomes and for chromosome mosaicism screens.

All analysis is performed by a UK Health Professionals Council Registered Clinical Cytogeneticist. Results will be reported within six weeks via email with representative karyotype images and interpretation.

For further information and costs please contact Duncan Baker on 0114 271 7019

Laboratory automation
The laboratory currently has a number of automated laboratory workstations which are utilised to increase efficiency, accuracy and eliminate human error.

Our post–PCR robotics system consists of several instruments including multi-channel and Span-8 Biomek NXp liquid handlers, Cytomat labware stacking systems, DNA Engine Tetrad thermal cycler, ALPS 300 plate sealers and VSpin plate centrifuge.

The system is fully automated via an ORCA robotic arm which moves labware between instruments. This system is currently primarily used to set up Sanger sequencing but is increasingly being used as part of the Next Generation Sequencing preparation workflow.

We also have a pre-PCR standalone Biomek FXp liquid handler which is used for preparation of Next Generation Sequencing libraries and will soon be used for PCR and microarray set up.

Laboratory informatics
Laboratory Informatics utilises StarLIMS a web-based Laboratory Information Management System (LIMS) as an enterprise class solution in order to provide a unified approach for the management of complex processes, regulatory compliance, data storage and reporting objectives.

Laboratory Informatics maintain, support and develop internal IT requirements based on cutting edge technologies such as Microsoft .Net and Microsoft SQL Server Technologies and support internal IT infrastructure requirements with respect to hardware and software implementations.

Next Generation Sequencing (NGS)

Our NGS facility currently has three NGS systems: an Illumina MiSeq and HiSeq 2500, and a Life Technologies Ion S5.

The HiSeq 2500 System is used to sequence multiplexed libraries prepared by the SureSelectXT target enrichment protocol, enabling the simultaneous sequencing of 96 samples covering custom designed gene panels. The Ion S5 and Ion Chef are used for the rapid preparation and sequencing of custom Ampliseq gene panels, with minimal hands-on time. The MiSeq is primarily used for sequencing research samples. All three  platforms are available for research projects alongside diagnostics, and we welcome discussions about how the laboratory can help support your research.

Download our Next Generation Sequencing document (V7) for details of current diagnostic NGS services, library preparation, data analysis and post analysis work flows. Previous versions of the NGS document are also available on request.

For more information on our NGS facility including NGS research services, please refer to our Next Generation Sequencing page.

PCR (polymerase chain reaction) set-up
Sanger Sequencing is performed on samples for full gene screens, predictive tests and familial cascade screening for a large number of genes across all of our clinical services.

Sequencing reactions of PCR products are prepared using BigDye® Terminator sequencing chemistry from Life Technologies on a robotic system supplied by Beckman Coulter.

Sequencing products are run on a 3730xl DNA Analyzer from Applied Biosystems®.

Research and Development

The Research and Development team provide liaison with external research groups to facilitate bespoke contract research and clinical trials work in the department.

They also co-ordinate research and development activity within SDGS and provide oversight of research governance for internal and external research activity. See the Clinical trials and Next Generation Sequencing sections above.

For further information contact Ann Dalton on 0114 271 7004 or Richard Kirk on 0114 305 3641

Sample management
Sheffield Diagnostic Genetic Service processes on average 26,000 samples per year.

All samples received are entered onto a Laboratory Information Management System (LIMS) database and individually barcoded. Processing of samples is barcode driven and electronically checked throughout all processes. Each process undertaken on a specific sample container is auditable.

Samples are processed by either producing cytogenetic preparations for analysis or DNA/RNA extraction from a variety of biological specimens. DNA extraction is routinely undertaken on the Perkin Elmer Chemagic 360 instrument or on Qiagen EZ1 robots.

Sequence checking 
SDGS provides checking of Sanger sequencing traces produced by the laboratory automation and PCR set up teams. All gene screens are independently checked by two analysts using two different sequence analysis packages, GAP4 (Staden) for first check and Mutation Surveyor for second check.

Last Updated on

You might also be interested in...

Sheffield Children’s NHS Foundation Trust
Sheffield Children's@SheffChildrens
We have lots of resources for young people, children and families on our website. Whether you're looking for exerc… https://t.co/T6HvEZjqSL
To protect our patients we are restricting visitors to one person per patient at Sheffield Children’s at all sites. Please help us to keep your family members safe.See more NHS guidance about COVID-19
+

By continuing to use the site, you agree to the use of cookies. more information

The cookie settings on this website are set to "allow cookies" to give you the best browsing experience possible. If you continue to use this website without changing your cookie settings or you click "Accept" below then you are consenting to this.

Close