Laboratory Services (SDGS)

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)

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.

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)
• SNP Array microarrays (BlueFuse Multi software) for whole genome work or targeted analysis

Within the Genotyping team the technological platforms used are:

• 480 LightCycler coupled with COLD PCR for detection of low level 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
• ddPCR (Biorad) for detection of low level mutations and copy number variants (CNVs).

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.

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 NX^p 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 FX^p liquid handler which is used for preparation of Next Generation Sequencing libraries and will soon be used for PCR set up.

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.

Our NGS facility currently has three NGS systems: an Illumina MiSeq and HiSeq 2500, and the ThermoFisher Scientific Ion GeneStudio S5 Prime System.

The HiSeq 2500 System is used to sequence multiplexed libraries prepared by the SureSelect^XT target enrichment protocol, enabling the simultaneous sequencing of 96 samples covering custom designed gene panels. The S5 prime and Ion Chef are used for the rapid preparation and NGS sequencing of custom and ready-made 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 most recent Next Generation Sequencing document 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.

For research users, we offer a complete sequencing service including library preparation, sequencing, and bioinformatics, or we can provide standalone sequencing of user-prepared libraries. We can make a wide variety of RNA and DNA libraries, and should be able to accommodate most library preparation requests, including:

• Whole genome
• RNA-Seq
• Capture enrichment e.g. whole exome, custom gene panels
• Amplicon e.g. 16S metagenomics, custom gene panels

Note that we can prepare capture or amplicon libraries for custom panels designed around your genes of interest, which can be very cost-effective compared to e.g. whole exome sequencing. Capture libraries for exomes or gene panels can also be prepared and sequenced to diagnostic standards.

Please contact us if you require a quote.

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®.

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.

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 advanced or Maxwell RS C16 extraction robotics.

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 Mutation Surveyor software.