Genomics Birmingham

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Genomics Birmingham is a resource centre providing a range of genomic services, along with a Technology Suite for researcher access. We seek to establish excellence as a routine and seamless part of research provision, as well as keeping up to date with technological developments.

Genomics Birmingham Team

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 

Genomics Birmingham Academic Lead

Professor Andrew Beggs

Email: a.beggs@bham.ac.uk

Why work with us?

Genomics Birmingham comprises a specialist team using the latest genomic technologies to support genomic, transcriptomic and epigenetic based research. The service was founded in 2016 and resides within the Institute of Cancer and Genomic Sciences. It is housed over three purpose-built laboratories in a fully equipped facility largely funded through the University of Birmingham and the MRC. We provide a trusted service supporting experimental design, as well as sample processing. Projects are focused towards University of Birmingham researchers, but we welcome collaboration with external academics and commercial businesses.

Who do we work with?

Genomics Birmingham is available to the following groups:

  • Current staff and students
  • Prospective staff and students
  • Academics both internal and external
  • Industry professionals
For all enquiries to Genomics Birmingham please use the contact details at the bottom of this page.

Resources and Services

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Genomic services

  • DNA/RNA/Next Generation Sequencing (NGS) library quality assessment
  • Sequencing customer generated libraries on the Illumina MiSeq, NextSeq NGS and NovaSeq 6000 platforms
  • NGS library preparation covering a wide range of RNAseq/DNAseq applications including low input and FFPE sample methods
  • Epigenetic and genotyping micro-arrays using Illumina Bead Arrays and iScan Technology
  • Single cell sequencing utilising the 10X Genomics Single Cell platform - DNA, 3’ transcript profiling, V(D)J, ATAC and exome sequencing
  • Oxford Nanopore sequencing using the PromethION, GridION and Flongle platforms for long read sequencing, RNA and DNA projects

  • 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

Equipment access via the Technology Hub

  • ThermoFisher/Applied Biosystems 7500 and 7900HT qPCR platforms
  • ThermoFisher/Applied Biosystems QS5 384 and QS5 96-well plate qPCR platforms
  • Fluidigm BioMark
  • Thermofisher Qubit - nucleic acid quantification
  • Agilent Bioanalyzer 

Publications

1 - 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

2 - 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

3 - 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

4 - 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

5 - 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

6 - Whole Genome Methylation Analysis of Nondysplastic Barrett Esophagus that Progresses to Invasive Cancer. Mark P. Dilworth, Tom Nieto, Jo D. Stockton, Celina M. Whalley, Louise Tee, Jonathan D. James, Fergus Noble, Tim J. Underwood, Michael T. Hallissey, Rahul Hejmadi, Nigel Trudgill, Olga Tucker, Andrew D. Beggs. Annals of Surgery. 2018. January. https://doi.org/10.1097/SLA.0000000000002658

Contact us

All general enquiries to Genomics Birmingham should be directed to:

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