We provide bespoke sequencing and bioinformatic analysis to biomedical research scientists throughout Wales.

High-throughput (next generation) DNA and RNA sequencing is routinely utilised in modern genetic and biomedical research, for a range of applications.  Wales Gene Park offers a flexible, bespoke approach to support researchers access high-throughput sequencing technology and associated bioinformatic analysis for biomedical research in Wales.  We work with academic and non-academic colleagues, providing expert advice and support from project design through to tertiary analysis, to suit the needs of the research project.  We work to ensure access to these technologies is at a reasonable cost to encourage effective uptake of this fundamental technology.

 

NGS library preparation within the WGP laboratory

NGS laboratory in the Sir Geraint Evans Building

The WGP Genomic Facility laboratory is located within the Sir Geraint Evans Building, Heath Park site, and utilises access to NGS equipment within Cardiff University and the NHS All Wales Genomics Service (AWMGS). Through these flexible working arrangements, we are able to provide access to several NGS platforms:

  • Illumina MiSeq
  • Illumina NextSeq
  • Illumina NovaSeq

 

 

Our Team

NGS library preparation within the WGP laboratory

We are a team of experienced post-doctoral and technical staff with many years of sequencing experience between us. Working with the Wales Gene Park bioinformatics team, we have the necessary expertise to take a sequencing project from initial sample to final analysis and specialise in providing a bespoke resource for our many research colleagues.

  • Dr Karen Reed, Operations Manager
  • Ms Shelley Rundle, Research Manager
  • Dr Vikki Humphreys, Research Technician
  • Mr Rob Maddison, Research Technician

 

What we do

Illumina NovaSeq 6000 Next Generation Sequencer

We provide colleagues with a complete pipeline for genomic scale DNA and RNA Sequence analysis in medically important areas of genetic research such as cancer, inherited cardiovascular disease and neurological disorders that are priority health areas of the Welsh Government. Our team will support your project from initial design through to grant applications, lab work, data generation, primary, secondary and tertiary analysis. We work collaboratively and flexibly with researchers to support research key performance indicators.

We are passionate in championing the role of high-throughput sequencing in modern biomedical research, working closely with research colleagues and encouraging adoption through workshops and seminars.

 

 

Examples of work undertaken

Whole Exome Sequencing

Dr Laura Thomas (Swansea University)

Collaboration between The Inherited Tumour Syndrome Research Group (Cardiff University), Erasmus MC Rotterdam research team and AWMGS, used Wales Gene Park generated whole exome sequencing to identify new intronic mutations in 6 out of 133 patients with clinically diagnosed Tuberous sclerosis (TSC) or TSC-like symptoms who previously lacked molecular diagnosis.

Outcome: Inclusion of these mutations in a clinical screen of other TSC patients without known TSC1/2 mutation by the AWMGS identified two further individuals. These variants are now included in the standard diagnostic pipeline for TSC.

Dr Hannah West (Cardiff University, School of Medicine)

Wales Gene Park generated more than 100 whole exomes from the germline DNA of patients with clinically diagnosed colorectal polyposis who lacked a molecular diagnosis for their condition, as part of a “Genetic Mechanisms of Polyposis” project.

Outcome: This study underpinned the identification of genetic change in a known tumour suppressor gene in a previously unscreened location, highlighting the usefulness of expanding the diagnostic screen in patients with suspected polyposis Ref-1.

Prof Trevor Dale (Cardiff University, School of Biosciences)

Wales Gene Park undertook whole exome sequencing of 10 lines of patient derived colorectal cancer organoidsRef-2, allowing the mutational profile of these lines to be determined.

Outcome:  This is important for the interpretation of drug assay results.

 

RNA and single cell RNA Sequencing

Dr Ned Powell (Cardiff University, School of Medicine)

WGP generated mRNA sequencing from human papillomavirus positive (HPV+) and negative (HPV-) oropharyngeal squamous cell carcinoma (OPSCC) cell lines used to compare differences in sensitivity to radiotherapy treatments, dependant on HPV status.

Outcome: This study showed the HPV+ OPSCC cell lines showed greater variation in sensitivity to ionizing irradiation (IR) and tended to be more sensitive than HPV‑ OPSCC cell lines Ref-3.

Dr Neil Rodrigues (Cardiff University, European Cancer Stem Cell Research Institute)

The data from RNA-Seq libraries generated by Wales Gene Park for this project aiming to understand the mechanisms that cause leukemic stem cells to give rise to acute myeloid leukaemia (AML) helped identify these changes in cell renewal, cell death and myeloid differentiation perturbations Ref-4 of specific target genes in a cell subset.

Outcome: Identification of subset of leukemic stem cells specific GATA2 target genes that have the capacity to cause AML

Dr Francesca Keefe (Cardiff University, School of Medicine)

WGP supported the single cell sequencing, which characterised a distinct subtype of brain cells known as inhibitory interneurons, which have important roles to play keeping brain activity in check.

Outcome: Improved understanding of the biology of brain cells will help determine the causes of some neuropathologies, including schizophrenia, autism and epilepsies.

 

Projects using other applications for NGS sequencing

Simon Reed (Cardiff University, School of Medicine)

ChIP Seq on yeast samples subjected to induced DNA damaged.

Prof Duncan Baird (Cardiff University, School of Medicine)

Examination of telomere fusion fragments using NGS.

Dr Gareth Griffith (Aberystwyth University)

Metabarcoding and Genome sequencing for work using probiotic bacteria and fungi, for research into fungal diseases.

Dr Hywel Williams (Cardiff University, School of Biosciences)

Sequencing for Hi-C analysis associated with a programme of work looking into Autism Spectrum Disorder (ASD).

Dr Matt Hitchings (Swansea University Medical School)

“Wales Gene Park has provided a high throughput sequencing resource required for us to sequence and compare the genomes of thousands of bacteria at a time, or extreme numbers of microbial communities, so that we can elucidate and monitor the effects the microbial world has on human health and agriculture.”

 

How we help

We provide colleagues with a complete pipeline for genomic scale DNA and RNA Sequence analysis. Our team will support your project from initial design through to grant applications, lab work, data generation, primary, secondary and tertiary analysis. We work collaboratively and flexibly with researchers to support research key performance indicators.

Our funding policy

Wales Gene Park is funded by Welsh Government through Health and Care Research Wales as an infrastructure support group. As such, we work collaboratively with partners to meet the requirements of each project and deliver mutually beneficial outputs.

Contact us

We are located within the Sir Geraint Evans Building, on the Cardiff University Heath Campus.

For enquiries, please contact Wales Gene Park Operations Manager, Dr Karen Reed (ReedKR@Cardiff.ac.uk)

 

 

References Provided:

-1: Short E, et al.  APC Transcription Studies and Molecular Diagnosis of Familial Adenomatous Polyposis. European Journal of Human Genetics. 2020 Jan;28(1):118-121 (IF 3.650) DOI: doi.org/10.1038/s41431-019-0486-2

-2: Badder et al. 3D imaging of colorectal cancer organoids identifies responses to Tankyrase inhibitors. PLOS ONE 2020 Aug 18 doi.org/10.1371/journal.pone.0235319.

-3: Holzhauser et al Sensitivity of human papillomavirus‑positive and ‑negative oropharyngeal cancer cell lines to ionizing irradiation Oncol Rep. 2020 Oct;44(4):1717-1726 DOI: 10.3892/or.2020.7709

-4: Menendez-Gonzalez et al Gata2 as a Crucial Regulator of Stem Cells in Adult Hematopoiesis and Acute Myeloid Leukemia 2019 Stem Cell reports VOLUME 13, ISSUE 2, P291-306, AUGUST 13, 201:https://doi.org/10.1016/j.stemcr.2019.07.005