Background

Current Position

Manager - Genomics Core Facility 

Background

I have been using genomic technologies in both research and commercial settings for over fifteen years and have extensive experience in the application of next-generation sequencing (NGS); working with clients in diagnostic, academic, government, and commercial sectors. I established (2016) and currently manage the Faculty of Medical Sciences 'Genomics Core Facility'; a NGS lab that specialises in single-cell and spatial transcriptomic applications. I have a research background in both cancer biology and mitochondrial genetics.

Qualifications

PhD, Cancer biology / nutrigenomics, Newcastle University, 2003.

BSc (Hons), Physiology, University of Sunderland, 1997 (Four-year sandwich degree including one-year industrial placement at the Jack Birch Unit for Molecular Carcinogenesis, University of York 1995-1996).

Previous Positions

Research Associate, Newcastle University, NIHR / BRC, 2012-2016

Senior Scientist, NewGene Limited, 2007-2012.

Research Associate, Newcastle University, Human Nutrition, 2002-2007.

Research Technician, University of York, Jack Birch Unit for Molecular Carcinogenesis, 1997-1999.

Esteem Indicators

Member of UK NEQAS Special Advisory Group for Next Generation Sequencing Quality Assessment 

Key Words

Genomics / Next-Generation sequencing / Single-cell / Transcriptomics / Spatial Gene Expression / DNA / RNA / ddPCR

Publications

• Payne BAI, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF. Universal heteroplasmy of human mitochondrial DNA. Human Molecular Genetics 2012, 22(2), 384-390.
• Borras S, Bromley D, Scully P, Coxhead JM, Spiden S, Short J, Robinson J, Huntley D, Curtis A, Taylor R. 'Noonan Spectrum Test' - comprehensive screening for RASopathies. In: European Human Genetics Conference 2012. 2012, Nürnberg, Germany: Nature Publishing Group.
• Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PL, Clayton J, Rowe W, Coxhead J, Irving J, Elliott DJ, Hall AG, Santibanez-Koref M, Jackson MS. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Research 2011, 21(11), 1788-1799.
• Frey A, Coxhead J, Curtis A. Solid Phase Sequence Capture vs PCR Targeted Enrichment of Muscular Dystrophy genes for Next Generation Sequencing. In: British Human Genetics Conference 2010. 2010, Warwick, RI: BMJ Publishing Group.
• Leaver M, Dominguez-Cuevas P, Coxhead JM, Daniel RA, Errington J. Life without a wall or division machine in Bacillus subtilis. Nature 2009, 457(7231), 849-853.
• Stanley L, Coxhead J, Burn J, Curtis A. Early experiences in amplicon sequencing using the Roche GS-FLX massively parallel DNA sequencer and its application within a diagnostic laboratory. In: British Human Genetics Conference 2008. 2008, University of York, UK: Journal of Medical Genetics: BMJ Group.
• Tzoulis C, Tran GT, Coxhead J, Bertelsen B, Lilleng PK, Balafkan N, Payne B, Miletic H, Chinnery PF, Bindoff LA. Molecular Pathogenesis of Polymerase Gamma-Related Neurodegeneration. Annals of Neurology 2014, 76(1), 66-81.
• Pfeffer G, Gorman GS, Griffin H, Kurzawa-Akanbi M, Blakely EL, Wilson I, Sitarz K, Moore D, Murphy JL, Alston CL, Pyle A, Coxhead J, Payne B, Gorrie GH, Longman C, Hadjivassiliou M, McConville J, Dick D, Imam I, Hilton D, Norwood F, Baker MR, Jaiser SR, Yu-Wai-Man P, Farrell M, McCarthy A, Lynch T, McFarland R, Schaefer AM, Turnbull DM, Horvath R, Taylor RW, Chinnery PF. Mutations in the SPG7 gene cause chronic progressive external ophthalmoplegia through disordered mitochondrial DNA maintenance. Brain 2014, 137(5), 1323-1336.
• Łastowska M, Al-Afghani H, Al-Balool HH, Sheth H, Mercer E, Coxhead JM, Redfern CPF, Peters H, Burt AD, Santibanez-Koref M, Bacon CM, Chesler L, Rust AG, Adams DJ, Williamson D, Clifford SC, Jackson MS. Identification of a neuronal transcription factor network involved in medulloblastoma development. Acta Neuropathologica Communications 2013, 1, 35.
• Pyle A, Hudson G, Wilson IJ, Coxhead J, Smertenko T, Herbert M, Santibanez-Koref M, Chinnery PF. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Evidence of Paternal Transmission in Humans. PLoS Genetics 2015, 11(5), e1005040.
• Collin J, Zerti D, Queen R, SantoFerreira T, Bauer R, Coxhead J, Hussain R, Steel D, Mellough C, Ader M, Sernagor E, Armstrong L, Lako M. CRX Expression in Pluripotent Stem Cell‐Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones. Stem Cells (Durham) 2019, 37(5), 609-622.
• Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M. Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina. Stem Cells (Durham) 2019, 37(5), 593-598.
• Duncan CJA, Dinnigan E, Theobald R, Grainger A, Skelton AJ, Hussain R, Willet JDP, Swan DJ, Coxhead J, Thomas MF, Thomas J, Zamvar V, Slatter MA, Cant AJ, Engelhardt KR, Hambleton S. Early-onset autoimmune disease due to a heterozygous loss-of-function mutation in TNFAIP3 (A20). Annals of the Rheumatic Diseases 2018, 77(5), 783-786.
• Keogh MJ, Wei W, Aryaman J, Walker L, van den Ameele J, Coxhead J, Wilson I, Bashton M, Beck J, West J, Chen R, Haudenschild C, Bartha G, Luo S, Morris CM, Jones NS, Attems J, Chinnery PF. High prevalence of focal and multi-focal somatic genetic variants in the human brain. Nature Communications 2018, 9(1), 4257.
• Floros VI, Pyle A, Dietmann S, Wei W, Tang WWC, Irie N, Payne B, Capalbo A, Noli L, Coxhead J, Hudson G, Crosier M, Strahl H, Khalaf Y, Saitou M, Ilic D, Surani MA, Chinnery PF. Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos. Nature Cell Biology 2018, 20, 144-151.
• Keogh MJ, Wei W, Wilson I, Coxhead J, Ryan S, Rollinson S, Griffin H, Kurzawa-Akanbi M, Santibariez-Koref M, Talbot K, Turner MR, McKenzie CA, Troakes C, Attems J, Smith C, Al Sarraj S, Morris CM, Ansorge O, Pickering-Brown S, Ironside JW, Chinnery PF. Genetic compendium of 1511 human brains available through the UK Medical Research Council Brain Banks Network Resource. Genome Reseach 2017, 27(1), 165-173.
• Wei W, Keogh MJ, Wilson I, Coxhead J, Ryan S, Rollinson S, Griffin H, Kurzawa-Akanbi M, Santibanez-Koref M, Talbot K, Turner MR, McKenzie CA, Troakes C, Attems J, Smith C, Al Sarraj S, Morris CM, Ansorge O, Pickering-Brown S, Ironside JW, Chinnery PF. Mitochondrial DNA point mutations and relative copy number in 1363 disease and control human brains. Acta Neuropathologica Communications 2017, 5, 17.
• Lindsay SJ, Xu YB, Lisgo SN, Harkin LF, Copp AJ, Gerrelli D, Clowry GJ, Talbot A, Keogh MJ, Coxhead J, Santibanez-Koref M, Chinnery PF. HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. Frontiers in Neuroanatomy 2016, 10, 86.
• Coxhead J, Kurzawa-Akanbi M, Hussain R, Pyle A, Chinnery P, Hudson G. Somatic mtDNA variation is an important component of Parkinson's disease. Neurobiology of Aging 2016, 38, 217.e1-217.e6.
• Payne BAI, Gardner K, Coxhead J, Chinnery PF. Deep Resequencing of Mitochondrial DNA. In: Mitochondrial Medicine. Springer New York, 2015, pp.59-66.
• Collin J, Queen R, Zerti D, Dorgau B, Georgiou M, Djidrovski I, Hussain R, Coxhead JM, Joseph A, Rooney P, Lisgo S, Figueiredo FC, Armstrong L, Lako M. Co-expression of SARS-CoV-2 entry genes in the superficial adult human conjunctival, limbal and corneal epithelium suggests an additional route of entry via the ocular surface. The Ocular Surface 2020, 19, 190-200.
• Davies HR, Hodgson K, Schwalbe E, Coxhead J, Sinclair N, Zou X, Cockell S, Husain A, Nik-Zainal S, Rajan N. Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nature Communications 2019, 10, 4717.
• Lowes H, Robertson F, Pyle A, Hussain R, Coxhead J, Yarnall AJ, Burn D, Payne BAI, Santibanez-Koref M, Hudson G. The Human Coronavirus Receptor ANPEP (CD13) Is Overexpressed in Parkinson's Disease. Movement Disorders 2020, 35(12), 2134-2136.