Genomics Birmingham

Genomics Specialist 

Matthew Newbould, MBiol

Matt studied biological sciences at Durham University as an integrated master’s degree, with an emphasis on ecology, evolution, and genetics. He completed his master’s project on population genomics of a deep-sea amphipod and was awarded an MBiol in 2019. Matt then worked at an Oxford University-based high-throughput sequencing and genomics service provider, supporting researchers from Oxford and around the world with their next-generation sequencing projects. Matt joined Genomics Birmingham in 2023 focussing on single-cell technology.
Email: m.r.newbould@bham.ac.uk

Genomics Specialist 

Kate Carruthers, MBiomed

Kate studied Biomedical Science at Cardiff University and was awarded an integrated masters degree in 2019. Her masters project focussed on investigating the effects of external influences on gene expression in the development of osteoarthritis. Kate then worked in the West Midlands Regional Genetics Laboratories, processing clinical samples for genetic analysis by performing next generation sequencing techniques. Kate joined the Genomics Birmingham team in 2023 to use and expand her skills in NGS technologies.
Email: k.l.carruthers@bham.ac.uk

Senior Research Technician

Cristina Escribano-Gonzalez, BSc (Hons), MSc

Cristina was awarded a BSc and MSc in Biotechnology from Polytechnic University of Valencia, Spain, in 2014. She worked in the Microbiology team at Eurofins Group, Wolverhampton, before joining the Tennant lab at University of Birmingham in 2016. At UoB she investigated changes in the bone marrow stroma with the development of multiple myeloma using molecular techniques and isotope tracing, while providing support to the lab and visiting students. She joined the Genomics Birmingham Team 2023 to further expand her skill set. 
Email: c.escribano@bham.ac.uk

Senior Research Technician

Faileigh Harriott 

Faileigh completed a Level 5 apprenticeship in 2021 as part of her role in the Medical School teaching laboratories. She supported all laboratory practical sessions for Biomedical Science and Pharmacy. In 2021 she joined the Open University part time to complete her Bsc Biology degree, whilst continuing to work in the teaching laboratories and taking on a responsibility to mentor new apprentices joining the team. She joined the Genomics Birmingham team in 2023 as part of her aim to develop her career on the area while completing further studies.
Email: f.i.harriott@bham.ac.uk

Senior Research Technician

Kamila Orzechowska, BSc (Hons), MSc

Kamila has a BSc in Biological and Chemical Sciences in 2021 from Coventry University and an MSc in Molecular Biotechnology in 2022 from University of Birmingham. She was awarded “The Olly Beswetherick Prize in Molecular Biotechnology” for the best research project during her MSc. While working at ALS Environmental she gained experience in water samples microbial analysis. She joined the Beggs Group in February 2023 and recently she has joined the Genomics Birmingham Team. 
Email: k.orzechowska@bham.ac.uk

Senior Research Technician

Ross Worledge, BSc (Hons), MRes

Ross studied Biomedical Science at Aston University. This included NIHR placements in 2020/21, based at Wolverhampton University, researching Crohn’s disease and IBD and at the Wellcome Trust Birmingham Clinical Research Facility working predominantly on processing samples for COVID-19 vaccine trials. Ross also obtained a MRes at Aston, where he researched the effect of vesicles on the immune system and the regulation of inflammation. He joined the Genomics Birmingham team to expand his skillset and ability.
Email: r.m.worledge@bham.ac.uk

Facility Manager

Dr Samantha Tull

Email: s.p.tull@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 RT-PCR systems
• CellRad – cell irradiator

Both require training to prior use, request via Stratocore.

Genomic services

• DNA/RNA quantification and fragment length assessment using the Qubit Fluorometer and Tapestation
• Next generation sequencing on Illumina MiSeq, NextSeq 500, NextSeq 2000 and NovaSeq 6000
• Library prep and next generation sequencing on the Ion Torrent Genexus Integrated Sequencer
• NGS library preparation covering a wide range of RNAseq/DNAseq applications including low input and FFPE samples
• Single cell technologies including 3’/5' transcript profiling, V(D)J, ATAC, fixed cell, and spatial transcriptomics
• Olink target 48 and 96 proteomic analysis using the Fluidigm Biomark
• Oxford Nanopore sequencing using the PromethION, GridION and Flongle platforms for long read RNA/DNA sequencing and methylation detection
• Project planning and writing 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

Facility Manager

Dr Samantha Tull

Email: s.p.tull@bham.ac.uk

Genomics Birmingham Academic Lead

Professor Andrew Beggs

Email: a.beggs@bham.ac.uk