Miles C. Benton

Bioinformatics PhD and Genomic Scientist

Currently

Genomics and bioinformatics specialist with extensive experience in long-read sequencing, computational biology and the application of emerging genomic technologies. I have worked across experimental and computational genomics, from study design through to analysis, interpretation and population-scale implementation. My current role combines scientific leadership with commercial strategy, supporting complex customer and collaborative projects, engaging with senior researchers and key opinion leaders, and working across technical and commercial teams to identify where new technologies can have the greatest impact. I am particularly interested in translating genomic innovation into practical, responsible solutions that deliver meaningful benefit for researchers, communities and partners.

Professional Positions Held

2024-present Oxford Nanopore Technologies Associate Director | Commercial Applications (APAC)

2022-2024 Oxford Nanopore Technologies Senior Bioinformatician | Commercial Applications (APAC)

2019-2022 Genomics Aotearoa Bioinformatics Leadership Team (Health)

2018-2022 Institute of Environmental Science and Research (ESR) Senior Scientist, Bioinformatics / Data Science

2014-2018 Queensland University of Technology Postdoc Research Fellow, Bioinformatics

2013-2014 Institute of Environmental Science and Research (ESR) Honorary Senior Scientist (Bioinformatics)

2011-2021 Victoria University of Wellington Lecturer CLNR580 (Clinical Research Preparation)

2010-2020 Victoria University of Wellington Lecturer BMSC406 (Science and Ethics)

Education

2010-2014 Griffith University, Australia Bioinformatics PhD (supervisors: Lyn Griffiths, Rod Lea, Donia Macartney-Coxson and Geoff Chambers)
Thesis: “Identification of Susceptibility Genes for Metabolic Syndrome in the Isolated Population of Norfolk Island”

2007-2009 Victoria University of Wellington, NZ MSc Cell and Molecular Biology (HONS)
Thesis: “Mitochondrial Genome Variation and Metabolic Traits in a Maori Community”

2004-2007 Victoria University of Wellington, NZ BBMedSc Biomedical Science (Majors: Human Genetics, Molecular Pathology)

Technical skills

Distinctions and Memberships

Research Grants

2020 co-PI, ESR Pioneer Funding: Harnessing the disruptive nature of portable sequencing for community empowerment

2019 co-PI, ESR Pioneer Funding: Engineering, Robotics, Innovation, Coding and Automation code club pilot plus portable sequencers and remote sensors

2019 PI, ESR Strategic Science Investment Funding: Clinically Relevant Human Genomics at ESR

2019 PI, ESR Pioneer Funding: Growing ESRs genomics reputation – compiling and refining a eukaryotic reference genome

2015 PI. Wellington Medical Research Foundation: “Validation of Blood Cell Lineage Specific DNA methylation markers.”

Professional Memberships

2026-present Board member (Trustee) - Taranaki Conservation Genomics Trust

2021-2023

Chair of a committee of reviewers for the Health Research Council (HRC) of New Zealand

Panel member reviewing for the Health Research Council (HRC) of New Zealand

2020-present Certified Carpentries Instructor

Panel member reviewing for the Health Research Council (HRC) of New Zealand

2019-2021 Member Human Genomics Society of Australasia

2015-2023 Ad hoc reviewer, Nature Biotechnology, Clinical Epigenetics, PLoS One, BMC Medical Genetics, Gene

2015-2023 Reviewer National Health and Medical Research Council, Australia

2014-2021 Member Australasian Genomic Technologies Association (AGTA)

Honours and Distinctions

2021 Science New Zealand Awards - Early Career Researcher of the Year

2019 Mentor – Royal Society Powering Potential

2019 Data Carpentries Instructor

2017 QUT School of Biomedical Sciences Travel Grant

2016 QUT Carla Patterson Award – Best Paper, Early Career Researcher

2015 ESR Vision Best Paper Award (August 2015)

2014 Best Poster Presentation, Genemappers Conference 2014, Novotel Barossa Valley Resort, SA, Australia, 11th – 14th May 2014.

Richard Stewart Memorial Prize (2nd place best presentation), Wellington Health and Biomedical Research Society

2012 Inaugural Grasshopper prize for Scientific Innovation. Wellington Health and Biomedical Research Society annual students and early researchers meeting, Victoria University of Wellington, Wellington, New Zealand, 19th November 2012.

Best Student Presenter. 2nd Biomarker Discovery Conference, Shoal Bay Resort and Spa, NSW, Australia, 5th December 2012.

2010-2013 Griffith University Higher Degree Research Scholarship

2007-2010 ESR Masters Research Scholarship

Publication Metrics

Publications

2026

Imoto S, Yamamoto T, Nakamura Y et al. (2026) Diploid telomere-to-telomere assemblies reveal hierarchical satellite architectures and heritable MHC structural diversity in macaques. Pre Print

Meyjes-Brown JWI, Sutherland HG, Tran KN, Benton MC, Lea RA, Griffiths LR. (2026) An ACOT4 Multi-Nucleotide Variant Is Associated with Cardiovascular Risk in Norfolk Island and UK Biobank Cohorts. Genes 17(2)

2024

Hench J, Hultschig C, Brugger J, et al. (2024) EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics. acta neuropathol commun 12(51)

Bloomfield M, Hutton S, Velasco C, Burton M, Benton MC, Storey M, ESR Genomics Consortium. (2024) Oxford Nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians. Pathology 56(3)

Wong C, Tham CY, Yang L, Benton MC, Narang V, Denil S, Duan K, Yew YW, Lee B, Florez de Sessions P, Common JEA. (2024) Nanopore sequencing enables allelic phasing of FLG loss-of-function variants, intragenic copy number variation and methylation status in atopic dermatitis and ichthyosis vulgaris. Journal of Investigative Dermatology, Feb 7:S0022-202X(24)00097-6

Chin HL, Benton MC, Yang L, Poon KS, Tan KML, Jamuar SS, Foo R, Law HY, Goh DM, Chong SS, and de Sessions PF. (2024). Clinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling. Molecular Genetics & Genomic Medicine, 12, e2285.

2021

Tran NK, Lea RA, Holland S, Nguyen Q, Raghubar AM, Sutherland HG, Benton MC, Haupt LM, Blackburn NB, Curran JE, Blangero J, Mallett AJ, and Griffiths LR. (2021) Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. Scientific Reports Volume 11, Article number: 19425

Connell J, Benton MC, Lea RA, Sutherland H, Chaseling J, Haupt LM, Wright K, and Griffiths LR. (2021) Pedigree Derived Mutation Rate Across the Entire Mitochondrial Genome of the Norfolk Island Population. (Accepted at Scientific Reports) DOI: 10.21203/rs.3.rs-823709/v1

Cao TV, Lea RA, Sutherland HG, Benton MC, Pishva SR, Haupt LM, and Griffiths LR. (2021) A genome-wide methylation study of body fat traits in the Norfolk Island Isolate. Nutrition, Metabolism and Cardiovascular Diseases (Accepted, awaiting publication)

2020

Macartney-Coxson D, Cameron AM, Clapham J, and Benton MC. (2020) DNA methylation in blood-potential to provide new insights in immune cell biology. PLOS ONE 15(11): e0241367

Harvey NR, Voisin S, Lea RA, Yan X, MC Benton, Papadimitriou ID, Jacques M, Haupt LM, Ashton KJ, Eynon N, Griffiths and LR. Investigating the influence of mtDNA and nuclear encoded mitochondrial variants on high intensity interval training outcomes. (2020) Scientific Reports 10(1)

Dunn PJ, Maher BH, Albury CL, Stuart S, Sutherland HG, Maksemous N, Benton MC, Smith, RA, Haupt LM, and Griffiths LR. (2020) Tiered analysis of whole-exome sequencing for epilepsy diagnosis. Molecular Genetics and Genomics https://doi.org/10.1007/s00438-020-01657-x

Harvey NR, Voisin S, Lea RA, Yan X, MC Benton, Papadimitriou ID, Jacques M, Haupt LM, Ashton KJ, Eynon N, Griffiths and LR. (2020) Identification of novel mitochondrial and mitochondrial related genetic loci associated with exercise response in the Gene SMART study. biorxiv (DOI: https://doi.org/10.1101/2020.02.20.957340)

Macartney-Coxson D, Danielson K, Clapham J, Benton MC, Johnstone A, Jones A, Shaw O, Hagan RD, Hoffman EP, Hayes M, Harper J, Langston MA, and Stubbs RS. (2020) MicroRNA profiling in adipose before and after weight-loss highlights the role of miR-223-3p and the NLRP3 inflammasome. Obesity (epub 2020)

Osborne AJ, Pearson JF, Noble AJ, Gemmell NJ, Horwood LJ, Boden JM, Benton MC, Macartney-Coxson D, and Kennedy MA. (2020) Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort. Translational Psychiatry 10(1)

2019

Harvey NR, Albury CL, Stuart S, Benton MC, Ecccles DA, Connell J, Sutherland HG, Allcock RJ, Lea RA, Haupt LM, and Griffiths LR. (2019) Ion torrent high throughput mitochondrial genome sequencing (HTMGS). PLoS ONE 14(11):e0224847

Benton MC, Lea RA, Macartney-Coxson D, Sutherland HG, White NM, Kennedy DW, Mengersen K, Haupt LM, and Griffiths LR. (2019) Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate. Epigenetics and Chromatin 12(60)

Macartney-Coxson D, Cameron A, Clapham J, and Benton MC. (2019) DNA methylation in blood - potential to provide new insights in immune cell biology. PREPRINT (Version 1) available at Research Square [DOI: https://doi.org/10.21203/rs.2.13274/v1]

Benton MC, Smith RA, Haupt LM, Albury CL, Maksemous N, Lea RA, and Griffiths LR. (2019) Variant Call Format (VCF)-Diagnostic Annotation and Reporting Tool (VCF-DART) A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data. Journal of Molecular Diagnostics 21(6) [DOI: https://doi.org/10.1016/j.jmoldx.2019.07.001]

Kennedy DW, White NM, Benton MC, Lea RL and Mengersen K. (2019) Cell-type specific analysis of heterogeneous methylation signal using a Bayesian model-based approach. biorxiv (DOI: https://doi.org/10.1101/682070)

2018 Kennedy DW, White NM, Benton MC, Fox A, Scott R, Griffiths LR, Mengersen KL and Lea RA. (2018) Critical evaluation of linear regression models for cell-subtype specific methylation signal from mixed blood cell DNA. PLoS ONE (accepted 27th Nov 2018)

Maltby V, Lea RA, Graves M, Sanders K, Benton MC, Tajouri L, Scott R, and Lechner-Scott J. (2018) Genome-wide DNA methylation changes in CD19+ B cells from relapsing-remitting multiple sclerosis patients. Scientific Reports (published 27th November 2018)

Aquino EM, Benton MC, Haupt LM, Sutherland HG, Griffiths LR, and Lea RA. (2018) Current understanding of DNA methylation and age-related disease. OBM Genetics 2(2) [DOI:10.21926/obm.genet.1802016]

Bradshaw G, Lualhati RL, Albury CL, Maksemous N, Roos-Araujo D, Smith RA, Benton MC, Eccles DA, Lea RA, Sutherland HG, Haupt LM and Griffiths LR. (2018) Exome sequencing diagnoses X-linked moesin-associated immunodeficiency in a primary immunodeficiency case. Frontiers in Immunology 9

Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, and Griffiths LR. (2018) Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Frontiers in Genetics (accepted 16th Janurary)

Kho PF, Lea RA, Benton MC, Eccles DA, Haupt LM, Hewitt AW, Sherwin JC, Mackey DA, and Griffiths LR. (2018) Expression QTL analysis of glaucoma endophenotypes in the Norfolk Island isolate provides evidence that immune-related genes are associated with optic disc size. Journal of Human Genetics 63 [DOI:10.1038/s10038-017-0374-y]

2017 Matovinovic E, Kho PF, Lea RA, Benton MC, Eccles DA, Haupt LM, Hewitt AW, Sherwin JC, Mackey DA, and Griffiths LR. (2017) Genome-wide linkage and association analysis of primary open-angle glaucoma endophenotypes in the Norfolk Island isolate. Molecular Vision 23

Jones A, Danielson KM, Benton MC, Ziegler O, Shah R, Stubbs RS, Das S, and Macartney-Coxson D. (2017) miRNA signatures of insulin resistance in obesity. Obesity 25(10) [DOI: 10.1002/oby.21950]

White NM, Benton MC, Kennedy D, Fox A, Griffiths LR, Lea RA, and Mengersen KL. (2017) Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm. PLoS One 12(9)

Maltby V, Lea RA, Sanders K, White NM, Benton MC, Scott R, and Lechner-Scott J. (2017) Differential Methylation at MHC in CD4+ T cells is associated with multiple sclerosis independently of HLA-DRB1. Clinical Epigenetics 9(71)

Macartney-Coxson D, Benton MC, Blick R, Stubbs RS, Hagan RD, and Langston MA. (2017) Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals. Clinical Epigenetics 9(48)

Benton MC, Sutherland HG, Macartney-Coxson D, Haupt LM, Lea RA, and Griffiths LR. (2017) Methylome-wide association study of whole blood DNA in the Norfolk Island isolate identifies robust loci associated with age. Aging 9(3)

Stuart S, Benton MC, Eccles D, Sutherland H, Haupt LM, Lea RA and Griffiths LR. (2017) Gene-Centric Analysis Implicates Nuclear Encoded Mitochondrial Protein Gene Variants in Migraine Susceptibility. Molecular Genetics & Genomic Medicine

2016 Sanders KA, Benton MC, Lea RA, Maltby VE, Agland S, Griffin N, Scott RJ, Tajouri L and Lechner-Scott J. (2016) Next-generation sequencing reveals broad down-regulation of microRNAs in secondary progressive multiple sclerosis CD4+ T-cells. Clinical Epigenetics 8(87)

2015 Fernando S, Speicher DJ, Bakr MM, Benton MC, Lea RA, Scuffham PA and Johnson NW. (2015) A Protocol for assessing maternal, environmental and epigenetic risk factors for dental caries in children. BMC Oral Health 15(167)

Benton MC, Lea RA, Macartney-Coxson D, Carless MA, Bellis C, Hanna M, Eccles D, Chambers GK, Curran JE, Blangero J and Griffiths LR. (2015) Serum bilirubin concentration is modified by UGT1A1 Haplotypes and Influences Risk of Type-2 Diabetes in the Norfolk Island Genetic Isolate. BMC Genetics 16(1)

Maltby VE, Graves MC, Lea RA, Benton MC, Sanders KA, Tajouri L, Scott RJ and Lechner-Scott J. (2015) Genome-wide DNA methylation profiling of CD8+ T cells shows a distinct epigenetic signature to CD4+ T cells in Multiple Sclerosis patients. Clinical Epigenetics 7(118)

Benton MC, Lea RA, Macartney-Coxson D, Carless MA, Göring HH, Bellis C, Hanna M, Eccles D, Chambers GK, Curran JE, Harper JL, Blangero J and Griffiths LR. (2015) A phenomic scan of the Norfolk Island genetic isolate identifies a major pleiotropic effect locus associated with renal disorder markers. PLoS Genetics 11(10)

Benton MC, Stuart S, Bellis C, Macartney-Coxson D, Eccles D, Curran JE, Chambers G, Blangero J, Lea RA and Griffiths LR. (2015) ‘Mutiny on the Bounty’: The Genetic History of Norfolk Island reveals extreme gender biased admixture. Investigative Genetics 6(11)

Rodriguez-Acevedo AJ, Ferreira MA, Benton MC, Carless MA, Göring HH, Curran JE, Blangero J, Lea RA and Griffiths LR. (2015) Common Polygenic Variation Contributes to Risk of Migraine in the Norfolk Island Population. Human Genetics (published online July 29th)

Bosch P, Benton MC, Macartney-Coxson D and Kivell B. (2015) mRNA and microRNA analysis reveals modulation of biochemical pathways related to addiction in the ventral tegmental area of methamphetamine self-administering rats. BMC Neuroscience 16(1)

Joshi PK, … Benton MC, Lea RA, Griffiths LR, … and Wislon JF. (2015) Directional dominance on stature and cognition in diverse human populations. Nature 523(7561)

Benton MC, Johnstone A, Eccles D, Harmon B, Hayes MT, Lea RA, Griffiths LR, Hoffman E, Stubbs RS and Macartney-Coxson D. (2015) An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight-loss. Genome Biology 16(1)

2014 Aya-Bonilla C, Camilleri E, Benton MC, Haupt LM, Marlton P, Lea RA, Gandhi MK and Griffiths LR. (2014) Fine mapping of the 15q21 region implicate TP53BP1 and B2M in the lymphomagenesis of Follicular and Diffuse Large B-Cell lymphomas. Carcinogenesis & Mutagenesis 5(6)

Gunawardhana LP, Gibson PG, Simpson JL, Benton MC, Lea RA and Baines, KJ. (2014) Characteristic DNA methylation profiles in peripheral blood monocytes are associated with inflammatory phenotypes of asthma. Epigenetics 9(9)

2013 Benton MC, Lea RA, Macartney-Coxson D, Carless MA, Göring HH, Bellis C, Hanna M, Eccles D, Chambers GK, Curran JE, Harper JL, Blangero J and Griffiths LR. (2013) Mapping eQTLs in the Norfolk Island Genetic Isolate Identifies Candidate Genes for CVD-risk Traits. American Journal of Human Genetics 93(6): 1087-99

Graves M, Benton MC, Lea R, Boyle M, Tajouri L, Macartney-Coxson D, Scott R and Lechner-Scott J. (2013) Methylation differences at the HLA-DRB1 locus in CD4+ T-Cells are associated with multiple sclerosis. Multiple Sclerosis 20(8):1033-1041

Aya-Bonilla C, Green MR, Camilleri E, Benton MC, Keane C, Marlton P, Lea RA, Gandhi MK and Griffiths LR. (2013) High resolution loss of heterozygosity screening implicates PTPRJ as a potential tumor suppressor gene that affects susceptibility to non-Hodgkin’s lymphoma. Genes, Chromosomes and Cancer 52(5):467-79

Rodriguez-Acevedo AJ, Maher BH, Lea RA, Benton MC, and Griffiths LR. (2013) Association of oestrogen-receptor gene (ESR1) polymorphisms with migraine in the large Norfolk Island pedigree. Cephalalgia 33(14):1139-1147

Stuart S, Maher BH, Sutherland H, Benton MC, Rodriguez A, Lea RA, Haupt LM and Griffiths LR. (2013) Genetic Variation in Cytokine-Related Genes and Migraine Susceptibility. Twin Res Hum Genet 20:1-8

2012 Benton MC, Macartney-Coxson D, Eccles DA, Griffiths LR, Chambers GK and Lea, RA. (2012) Complete Mitochondrial Genome Sequencing Reveals Novel Haplotypes in a Polynesian Population. PLoS ONE 7(4): e35026

Maher BH, Lea RA, Benton MC, Cox HC, Bellis C, Carless M, Dyer TD, Curran J, Charlesworth JC, Buring JE, Kurth T, Chasman DI, Ridker PM, Schürks M, Blangero J and Griffiths LR. (2012) An X Chromosome Association Scan of the Norfolk Island Genetic Isolate Provides Evidence for a Novel Migraine Susceptibility Locus at Xq12. PLoS ONE 7(5): e37903

Other dissemination

Media

Radio New Zealand - Miles Benton: diagnosing serious illnesses cheaper and faster. An interview that I did with Kim Hill on Radio NZ’s Saturday Morning show. link

ESR Media Release - ESR scientists showcase benefits of collaboration for rapid-DNA sequencing. Another article highlighting the work we are doing in the Nanopore space to make the technology more affordable and accessible. link

New Zealand Herald - The genius of genomics: The revolution that helped NZ quash Covid-19. A NZ Herald article that contains a section on the Nanopore portable bed-side sequencing projects that we have underway. link

References

Available on request.