Genomics Birmingham

Celina Whalley

Celina joined the Genomics Birmingham Team in 2018 with a career, in scientific service provision, spanning 20 years. This started after gaining an MSc in Medical Mycology from The University of Leeds that led to working for the NHS Leeds General Infirmary Medical Mycology Service. The focus on genomics began after a move to the Technology Facility at The University of York followed on by time at The Wellcome Trust Centre for Human Genetics at the University of Oxford. In 2016 she became a Research Associate in Professor Andrew Beggs’ group working on the Illumina microarray platform and helping the group form the Genomics Birmingham service as it is now. Her current role as Genomics Specialist is to continue to develop and oversee the genomics service alongside completing projects and provide training for staff and students. 

Email: C.M.Whalley@bham.ac.uk

Charlie Poxon

Charlie joined the Genomics Birmingham Service in February 2020. She was awarded a bachelor’s degree in Biology (BSc hons) and a master’s degree in Reproductive and Developmental Medicine (MSc) from the University of Sheffield. Charlie has recently gained professional accreditation with the Science Council so now holds her Registered Scientist (RSci) title. She runs the nucleic acid quality check service and completes a wide variety of library preparation projects, for Next Generation and long-read Sequencing.  Charlie also provides qPCR and Bioanalyser training for user access through the Technology Hub.  

Email: C.l.poxon@bham.ac.uk

Anetta Ptasinska

Anetta gained a PhD in molecular biology with a keen interest in haematological cancer genetics and epigenetics including haematological translational research and routine diagnostics. She has strong technical capabilities with molecular biological techniques and sequencing technologies. Anetta joined Prof. Andrew Beggs group in 2019 as a member of the University of Birmingham’s Genomics service provider, Genomics Birmingham and oversees the Single Cell Service within the lab using 10x Genomics Technology and validates cancer biomarkers using Next Generation Sequencing. Anetta is a competent article writer with a solid publication record.

Email: A.Ptasinska@bham.ac.uk

Research Facilities Manager

Dr Adriana Flores-Langarica

Email: A.FloresLangarica@bham.ac.uk 

Financial Assistant

James Batten

Email: J.Batten@bham.ac.uk 

Genomics Birmingham Academic Lead

Professor Andrew Beggs

Email: a.beggs@bham.ac.uk

We provide training and support for users to independently use all our available equipment available in Stratocore. Currently our training programmes are divided in two sections. Firstly, the CANVAS Module which can be completed at the user's pace and once that is completed we deliver an in person training session at the equipment. If you require training just request it in Stratocore. We deliver sessions regularly. 

For our bespoke services, please reach to us to discuss your project and how we can help you.

Equipment access via Stratocore

• ThermoFisher/Applied Biosystems QS5 384 and QS5 96-well plate qPCR platforms for qPCR and genotyping
• Fluidigm BioMark – high throughput qPCR and genotyping, and proteomics
• Thermofisher Qubit - nucleic acid quantification
• Agilent Bioanalyzer 
• CellRad – cell irradiator

Available on Request

• Nanodrop spectrophotometer
• Qubit fluorometer

Genomic services

• DNA/RNA/Next Generation Sequencing (NGS) library quality assessment
• Sequencing customer generated libraries on Illumina MiSeq, NextSeq NGS 500, NextSeq 2000 and NovaSeq 6000 platforms
• NGS library preparation covering a wide range of RNAseq/DNAseq applications including low input and FFPE sample input
• Epigenetic and genotyping micro-arrays using Illumina Bead Arrays and iScan Technology
• Single cell sequencing utilising the 10X Genomics Single Cell platform - RNA, 3’/5' transcript profiling, V(D)J, ATAC,  fixed cell and spatial transcriptomics
  

• Oxford Nanopore sequencing using the PromethION, GridION and Flongle platforms for long read RNA, DNA sequencing and methylation detection

• RT-PCR - ThermoFisher 384 and 96-well qPCR platforms. Training and support provided. Users can then access the equipment at their convenience by booking time via Stratocore
• Project planning, grant application quotes
• Sample processing advice

The University of Birmingham (UoB) is a founding signatory of ‘The Technician Commitment’. A sector wide, collaborative initiative that aims to ensure visibility, recognition, career development and sustainability for technical staff working in higher education and research, across all disciplines.

The UoB has invested and supports the Technology Hub facilities not only with equipment but also specialist staff. The staff are a key element of our offering since they not only ensure that all equipment is looked after and performing to specification, but they also have a significant experience, and the input and advice is very valuable to our users. 

In line with this, the Technology Hub Facilities request that all users of the facilities to recognize its contribution to manuscripts in one of the following ways:   

The authors would like to acknowledge the (Facility) at the UoB for support of (technology used) experiments. The authors would like to acknowledge (specialist name).

In some instances, the specialist may make substantial contributions to the conception / design of the work or the acquisition, analysis, or interpretation of data for a manuscript. In this case, it is expected that this is appropriately recognized through co-authorship on any publications resulting from the work. Criteria for inclusion of a specialist as an author on a publication. Where the specialist has either: 

• Performed experiments or analysis, the data from which is included in the manuscript.
• Produced customized analysis workflows or scripts for the work.
• Significantly contributed to the design, conception, or interpretation of the experiments.

1 - Goel, A., Ward, D.G., Noyvert, B. et al. Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes. Genome Med 14, 59 (2022). https://doi.org/10.1186/s13073-022-01056-4

2 - Kidd, S. P., Burns, D., Armson, B., Beggs, A. D., Howson, E. L., Williams, A., ... & Fowler, V. L. (2022). RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals. medRxiv, 2021-06.

3 - Sirinukunwattana K, Domingo E, Richman SD On behalf of S:CORT consortium, et al. Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using  deep learning. Gut 2021;70:544-554.

4 - Ptasinska, A., Whalley, C., Bosworth, A., Poxon, C., Bryer, C., Machin, N., ... & Beggs, A. D. (2021). Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clinical microbiology and infection, 27(9), 1348-eKidd

5 - Dependence on Myb expression is attenuated in myeloid leukaemia with N-terminal CEBPA mutations. Giacomo Volpe, Pierre Cauchy, David S Walton, Carl Ward, Daniel Blakemore, Rachael Bayley, Mary L Clarke, Luisa Schmidt, Claus Nerlov, Paloma Garcia, Stephanie Dumon, Florian Grebien, Jon Frampton. Life Science Alliance. Published Online: 15 March, 2019. http://doi.org/10.26508/lsa.201800207

6 - Genomic and transcriptomic characterisation of undifferentiated pleomorphic sarcoma of bone. Naser M Ali,  Stefania Niada,  Anna T Brini,  Mark R Morris,  Sathishkumar Kurusamy,  Abdullah Alholle,  David Huen,  Cristina R Antonescu,  Franck Tirode,  Vaiyapuri Sumathi,  Farida Latif. Journal of Pathology. 2019;247:166–176 https://doi.org/10.1002/path.5176

7 - Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma.  Benjamin Edginton-White, Pierre Cauchy, Salam A. Assi, Sylvia Hartmann, Arthur G. Riggs, Stephan Mathas, Peter N. Cockerill, Constanze Bonifer. Lymphoma. Published online 13 December 2018. https://www.nature.com/articles/s41375-018-0311-x

8 - The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification. Jane Gilmour, Salam A. Assi, Laura Noailles, Monika Lichtinger, Nadine Obier & Constanze Bonifer. Nature. 2018 July. https://doi.org/10.1038/s41598-018-28506-7

9 - C/EBPα overrides epigenetic reprogramming by oncogenic transcription factors in acute myeloid leukemia. Loke J, Chin PS, Keane P, Pickin A, Assi SA, Ptasinska A, Imperato MR, Cockerill PN, Bonifer C. Blood Adv. 2018 Feb 13;2(3):271-284. https://doi.org/10.1182/bloodadvances.2017012781

All general enquiries to Genomics Birmingham should be directed to:

Telephone: +44 (0)121 415 8783
Email: mds-sequencing@contacts.bham.ac.uk

techhubfinance@contacts.bham.ac.uk

Research Facilities Manager

Dr Adriana Flores-Langarica

Email: A.FloresLangarica@bham.ac.uk 

Genomics Birmingham Academic Lead

Professor Andrew Beggs

Email: a.beggs@bham.ac.uk