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The University of Southampton
Medicine
Phone:
(023) 8120 5246
Email:
jcs@soton.ac.uk

Professor Jonathan C Strefford BSc., PCCC, PhD

Professor of Cancer Genomics. Deputy Head of School – Research. Group Leader. Principle Investigator

Professor Jonathan C Strefford's photo

As a Professor of Cancer Genomics, and an Honorary NHS Clinical Scientist, my research is translational and spans genomic screening, diagnostic methods as well as molecular mechanisms. My focus is on the application of massively parallel sequencing approaches to dissect the human genome and its epigenetic regulation. We then exploit these findings to develop novel biomarkers that help predict the disease course in cancer patients.

My lab aims to develop precision medicine approaches through harnessing our understanding of the human genome. Through the application of DNA sequencing technologies we continue to unmask genetic defects in genome of cancer patients, DNA lesions that can be used to transform the management of cancer patients, through more accurate prognostication and the development of targeted treatments.

After two years NHS training in clinical cytogenetics, Jon started his postgraduate education with a Ph.D. in Cancer Genetics and Genetic Toxicology at the University of Wales, Swansea, with a successful placement at Glaxo Wellcome. In 2000, he started his postdoctoral careers, working with Professor Bryan Young at the Cancer Research UK Medical Oncology Laboratory at St Bartholomew’s Hospital, London. In 2002, he received a Lectureship from Queen Mary and Westfield College, University of London, prior to a move to the University of Southampton. In 2008, after four years working with Professor Christine Harrison, Jon was awarded a Personal Fellowship from Leukaemia and Lymphoma Research and a Senior Lectureship within the Faculty of Medicine.

His research focuses on the study of a number of mature B-cell neoplasm, in particular chronic lymphocytic leukaemia (CLL) and splenic marginal zone lymphoma (SMZL) and to a lesser extent follicular (FL) and diffuse large b-cell lymphoma (DLBCL).. The research projects coordinated by Professor Strefford runs from biomarker discover, using a plethora of genomics approaches, to biomarker validation employing large international patient cohorts, to functional analysis, employing in vitro and in vivo model systems.

To facilitate these research objectives, Professor Strefford has attracted more than £25 million in grant funding from national and international research agencies and charities. He has spoken at international meetings such as the American Society of Hematology, the International Workshop on CLL and the American Association for Cancer Research.

Professor Strefford has extensive experience as a consultant for commercial companies, facilitating the development of FISH, microarray and sequencing products. He also has strong links with the pharmaceutical industry and acts as a consultant and contract research provider for a series of large international clinical trials.


Dr Strefford’s Linkedin and ResearchGate profiles.

Cancer Genomics Group Facebook Page

Qualifications

Current appointments held

Previous appointments held

Research interests

Our research group is interested in the analysis of the genome and epigenome of mature B-cell tumours. Over three billion base-pairs of deoxyribonucleic acid (DNA), bound with accessory proteins in the form of chromatin, are super-coiled and packed into 23 autosomal and sex-determining chromosomes, constituting the human genome, the genetic blueprint for normal human development and cellular function.

A leukaemic cell, in addition to carrying this diploid genome that has been inherited from both parents, has also acquired a series of somatic genomic lesions, including base-pair mutations, chromosomal rearrangements and large-scale copy number alterations (CNAs). Epigenetic defects in the form of disordered DNA methylation, chromatin remodelling and dysregulation of small noncoding micro-ribonucleic acids (miRNAs) are also present.

The acquisition of these (epi)genomic defects can enable many of the hallmarks of leukaemogenesis, such as the promotion of proliferative signalling, the evasion of growth suppression and the resistance to apoptosis. Our work has involved the identification and characterisation of these defects, and these insights have helped us understand the leukaemic process, improving cancer diagnosis, accurate risk-adapted stratification and the development of targeted treatments for precision medicine.

Our laboratory works on a number of B-cell tumours, principally chronic lymphocytic leukaemia (CLL) and splenic marginal zone lymphoma (SMZL), and to a lesser extent follicular (FL) and diffuse large b-cell lymphoma (DLBCL). CLL is the most common form of leukaemia in Western populations, accounting for approximately one-third of all new diagnoses.  Clinically, the disease is highly heterogeneous, with patients surviving for decades with a benign disease requiring no treatment, while others exhibit a rapidly progressive disease despite aggressive therapy. SMZL is considered a low grade, indolent B-cell neoplasm with a median survival of approximately 10 years, but 70% of patients present with or develop progressive disease with a requirement for therapy, and 5–10% will undergo transformation to a large B-cell lymphoma. For both diseases, no biomarkers accurately predict the disease course, particularly in early stage disease. Furthermore, definitive diagnosis of SMZL can be challenging.

In CLL, we have identified, or help characterize many of the recurrently mutated genes emerging from recent high-throughput sequencing studies. We continue to be at the centre of large international collaborative studies, mapping the CLL genome and assessing the clinical importance of gene mutations. In SMZL, we published one of the seminal studies identifying KLF2 as a target of novel recurrent gene mutations. We currently lead a large international study investigating the importance of somatic mutations and DNA methylation changes in SMZL.



The research projects coordinated by Professor Strefford include:

  1. Biomarker Discovery: Using whole genome analysis for copy number changes and sequence mutations to screen clinically-informative leukaemia and lymphoma cohorts.
  2. Biomarker Validation: Using target molecular and NGS technologies to determine the clinical impact of genomic lesions on the patient survival and response to treatment, particularly in the clinical trials context.
  3. Functional Analysis: Using in vitro and in vivo model systems we assess the role of novel genetic lesions in the pathophysiology of B-cell neoplams.

Funding

  1. Cragg M, Beers SA, Johnson P, Davies A, Strefford JC (2013) Optimizing antibody treatment for patients with lymphoma. Leukaemia and Lymphoma Research Specialist Programme Grant (£1.3Million)
  2. Strefford JC, Steele A, Cragg M, Vorechovsky I (2012) Importance of SF3B1 mutations in the diagnosis, prognosis and biology of chronic lymphocytic leukaemia. Leukaemia and Lymphoma Research Project Grant (£230K)
  3. Strefford JC (2012) The importance of novel genetic lesions in patients with chronic lymphocytic leukaemia. Bournemouth Leukaemia Fund PhD Studentship (£100K)
  4. Strefford JC, Davies A (2012) FC Receptor analysis in the ROCHE GOYA Trial. ROCHE Pharmaceuticals Project Grant (£130K)
  5. Strefford JC, Collins A, Oscier DG (2012) The identification and characterization of novel genetic lesions associated with clinical outcome in patients with Splenic Marginal Zone Lymphoma. Leukaemia and Lymphoma Research Project Grant (£170K)
  6. Cross NC, Sahota S, Tapper W, Strefford JC (2012) Development and application of a bioinformatic pipeline to identify somatic mutations by exome sequencing. Leukaemia and Lymphoma Research Project Grant (£230K)
  7. Strefford JC, Davies A (2012) FC Receptor analysis in the ROCHE Gallium Trial. ROCHE Pharmaceuticals Project Grant (£130K)
  8. Glennie MJ, Williams T, Johnson PJ, Roghanian A, Strefford JC, Beers S, Reading I (2011) Improving the predictive capacity of in vitro cytokine release assays to reduce animal use and drug attrition. NC3R/SRBI - CRACK-IT (£500K)
  9. Strefford JC, Oscier DG, Packham GP (2011) The genetics and functional characterization of novel genetic lesions in patients with chronic lymphocytic leukaemia. Leukaemia and Lymphoma Research Project Grant (£200K)
  10. Strefford JC, Collins A, Oscier DG, Packham G (2011) The development of next generation sequencing for the analysis of B cell tumours: Understanding disease progression in patients with chronic lymphocytic leukaemia. Wessex Medical Research PhD studentship (£80K)
  11. Pepper C, Baird D, Oscier DG, Strefford JC (2011) Telomere length as a biomarker of genomic instability and predictor of response to treatment. Cancer Research UK - The Biomarkers and Imaging Discovery and Development Committee (£200K)
  12. Strefford JC, Collins A, Oscier DG (2011) The genetic analysis of patients with progressive CLL using next generation sequencing. Kay Kendell Leukaemia Fund Project Grant (£190K)

PhD Supervision

Louise Carr – Current

Anna Takeuchi – Current

Sarah Frampton – Current

Lara Buermann – Current

Joe Taylor – Current

Jemma Longley – Current

Carolina Jaramillo – Current

Rachel Dobson – 2018

Stuart Blakemore – 2018

Kate Packwood – 2017

Jade Forster – 2016

Victoria Hammond – 2010

Helen Parker – 2008

Lisa Russell - 2007

 

Group Members (current)
Professor Jonathan Strefford – Professor in Cancer Molecular Genetics and Group Leader
Dr Helen Parker – Senior Postdoctoral Research Fellow
(CLL Genomics)
Dr Matthew Rose-Zerilli – Senior Postdoctoral Research Fellow
(CLL Genomics)
Dr Marina Parry – Postdoctoral Research Fellow (SMZL Genomics)
Dr Marta Larrayoz – Postdoctoral Research Fellow (Functional analysis of SF3B1)
Dr Chantal Hargreaves – Postdoctoral Research Fellow (FCGR Genetics)
Dr Chisako Iriyama – Visiting Clinician Scientist (Japan)
Mr Anton Parker – Visiting Scientist (Royal Bournemouth Hospital)
Miss Jade Forster – Graduate Student (CLL Genomics)
Mr Stuart Blakemore – Graduate Student (Functional analysis of SF3B1)

Group Members (past)
Mr Miqdad Rajibali – Welcome Trust PhD Student

Mr Lee Brown – Visiting Masters Student (Cranfield University)

Mr Alistair McIntosh – Visiting Undergraduate Project Student (Birmingham University)
Dr Qian An – Postdoctoral Fellow (now at Portsmouth University)

Research Projects

One of our principle interests is in the characterization of the CLL and SMZL genome, identifying recurrent chromosomal deletions and somatic mutations that can aid in more appropriate clinical management. We employ sophisticated sequencing approaches and comprehensive computational analysis to unravel the genomic landscape of CLL and SMZL tumour cells. We collaborated with other international opinion leaders to elucidate the biological and clinical importance of these DNA mutations. One of our key on-going projects focused on the importance of genomic complexity in CLL, based on the observation that patients exhibiting a high number of genomic lesions in their cancer cells, exhibit poor survival. We now lead national and international studies aimed at defining exactly what level of complexity is most clinically relevant, and how this measure can most accurately aid patient management.

Molecular mechanisms contributing to the survival of B-cell neoplasms.

In collaboration with Professor Graham Packham and Dr Francesco Forconi

This project focuses on understanding the impact of signalling via the B-cell receptor (BCR) and the microenvironment on the epigenome of CLL cells, particularly the dysregulation of miRNAs and DNA methylation, as well as chromatin remodelling. In vitro analysis of signalling has previously demonstrated that individual CLL samples vary in their ability to transmit signals via the cell surface BCR. Retained signalling is associated with the presence of poor prognostic markers and a poor clinical outcome. Thus, antigen signalling via the BCR, in the context of specific tissue microenvironments, is considered to play a key role in driving cell proliferation and survival, leading to disease progression. We employ state-of-the-art next generation sequencing approaches to identify epigenomic determinants of differential B-cell receptor responsiveness in tumour cells. These observations will have clinical utility, such that they will predict the aggressiveness of the disease or identify the most appropriate treatment.

(Epi)genomic analysis of the Fc gamma receptors (FcgR) in normal and malignant B-cells

In collaboration with Dr Jane Gibson and Professor Mark Cragg

Fc gamma receptors (FcgRs) are a protein family expressed by a variety of immune cells. Current evidence indicates that almost all monoclonal antibody therapies act by engaging FcgR in the host. The low-affinity FcgRs are encoded by a 200Kb gene cluster at 1p24, that is highly repetitive and difficult to study with traditional technologies. This project focuses on the application of long-read sequencing technologies to generate detailed sequencing maps of the FCGR in normal and malignant immune cells.

Research group

Cancer Sciences

Affiliate research group

Cancer Sciences Research group

Postgraduate student supervision

2011 Miqdad Rajabaki, MPhil
2010 Victoria Hammond, PhD
2008 Helen Parker, PhD

2007 Lisa Russell, PhD

2005 Timothy Lane, MD

Current

Jade Forster, PhD (2011-2015)
Stuart Blakemore, PhD (2012-2016)

Faculty of Medicine

Member – Faculty Website Strategy Committee
Member – Faculty IT Strategy Group
Member - Postdoctoral Association Committee

Member - Postdoctoral Mentoring Working Group

Member - Divisional Laboratory Committee

National and International Responsibilities

Editorial Board Member – Cancer Genomics and Proteomics

Editorial Board Member – Journal of Hematology
Editorial Board Member – Journal of Carcinogenesis and Mutagenesis

Editorial Board Member – The Open Access Journal of Science
Editorial Board Member – Open Journal of Genomics
Editorial Board Member – Archives of Medical Research



Member – Association of Clinical Cytogenetics

Member – British Society of Human Genetics

Member – British Society of Haematology

Member – American Association for Cancer Research

Member – American Society of Hematology

Member – European Research Initiative on CLL (ERIC)

Co-Chairperson - UK CLL Scientific Workshop
Co-Chairperson – ERIC Novel mutations Project
Executive Member - UK CLL Forum
Member - UK CLL Biobank Research Governence Committee
Member - UK CLL Trials Committee
Member – UK Childhood Leukaemia Research Group



Manuscripts review including - Annals of Clinical Biochemistry, Anticancer Research, Archives of Medical Research, Blood, BioEssays, Bioinformatics, Biotechniques, BMC Gastroenterology, BMC Medical Genomics, BMC Research Notes, British Journal of Cancer, British Journal of Haematology, Cancer Genomics and Proteomics, Cancer Genetics and Cytogenetics, Cancer Therapy, Cancer Therapy and Molecular Biology, Critical Reviews in Oncogenesis, Cytogenetics and Genome Research, Genes Chromosome and Cancer, Heamatologica, Hematological Oncology, Human Molecular Genetics, Journal of Carcinogenesis and Mutagenesis, Journal of Medical Genetics, Journal of Pathology, Laboratory Medicine, Leukemia, Leukemia and Lymphoma, Leukemia Research, Molecular Cytogenetics, Molecular Genetics, Oncogene.

Grant review for - Leukaemia and Lymphoma Research, Medical Research Council (Project grants and Clinical Research Training Fellowship awards), the Kay Kendell Leukaemia Fund (Project grants and Clinical Research Training Fellowship awards), Cancer Research UK, the Association for International Cancer Research (AICR) and CHILDREN with LEUKAEMIA.

Current Group Members (research focus)

Professor Jonathan Strefford – Professor in Cancer Molecular Genetics and Group Leader

Dr Helen Parker – Senior Postdoctoral Research Fellow
(CLL Genomics)

Dr Dean Bryant – Senior Postdoctoral Fellow (Bioinformatics)

Dr Jaya Thomas – Senior Bioinformatician

Mrs Lara Buermann – Graduate Student (Chromatin modelling)

Miss Carolina Jaramillo – Graduate Student (Lymphoma Genomics)

Miss Sarah Frampton – Graduate Student (long-read sequencing)

Miss Anna Takeuchi – Graduate Student (Hydroxymethylation analysis)

Miss Louise Carr – Graduate Student (CLL Genomics)

Past Group Members (current affiliation)

Dr Harindra Amarasinghe – Postdoctoral Fellow (University of Oxford)

Dr Tomasz Wojdacz – Postdoctoral Fellow (Pomeranian Medical University)

Dr Matthew Rose-Zerilli – Postdoctoral Research Fellow (Group Leader in Cancer Sciences)

Dr Linsey Smith – Postdoctoral Fellow (University of Southampton)

Dr Marina Parry – Postdoctoral Research Fellow (University College London)

Dr Stuart Blakemore – Graduate Student (Uniklinik Köln)

Dr Marta Larrayoz – Postdoctoral Research Fellow (Cima Universided de Navarra)

Dr Jade Forster – Graduate Student (University of Southampton)

Dr Chantal Hargreaves – Postdoctoral Research Fellow (University of Oxford)

Dr Chisako Iriyama – Visiting Clinician Scientist (Nagoya University Graduate School of Medicine)

Dr Ana Rodríguez-Vicente – Visiting Fellow (Universidad de Salamanca)

Mr Miqdad Rajibali – Welcome Trust PhD Student

Mr Lee Brown – Visiting Masters Student (Cranfield University)


Mr Anton Parker – Visiting Scientist (Royal Bournemouth Hospital)

Mr Alistair McIntosh – Visiting Undergraduate Project Student (Birmingham University)

Dr Qian An – Postdoctoral Fellow (now at Portsmouth University)

Faculty of Medicine Committees

School of Cancer Sciences – Vice-Chair of the CRUK Clinical Centre Executive Committee (since 2018)

School of Cancer Sciences – Member of the CRUK Clinical Centre Executive Committee (2014-2018)

School of Cancer Sciences – Chair of the Lab Management Committee (2014-2018)

School of Cancer Sciences – Member of the Faculty IT Strategy Group (2012 - 2016)

School of Cancer Sciences - Member of the Faculty Website Strategy Group (2011 - 2016)

Faculty of Medicine – Academic member of the Postdoctoral Association (PDA) Committee

Faculty of Medicine – PDA Website Manager (2010 - 2016)

Faculty of Medicine – Postdoctoral Mentoring Working Group, (2010 - 2016)

National Responsibilities

Scientific Secretary of the UK CLL Forum (since 2016)

Chairperson of the UK CLL Scientific Workshop (since 2013)

Executive Member of the UK CLL Forum (since 2013)

Member of the UK CLL Biobank Research Governance Committee (since 2012)

Member of the UK CLL Trials Committee (since 2011)

British Society of Haematology member (BSH, since 2009)

UK Childhood Leukaemia Research Group member (2004-2009)

BSHG Scientific Committee member (2005-2011)

BSHG Annual Meeting Organisational Committee member (2005-2011)

Member of the British Society of Human Genetics (BSHG, 1995-2013)

Member of the Association of Clinical Cytogeneticists (1994-2013)

International Responsibilities

American Society of Hematology (ASH, since 2009)

American Association for Cancer Research (active membership since 2001)

Member of the European Research Initiative on CLL (ERIC) (2008- present)

‘Novel Mutations’ Project co-lead for ERIC (2010- present)

 

Editorial Board member –

‘Exploration of Targeted Anti-tumor Therapy’

'Cancer Genomics and Proteomics’

‘Journal of Carcinogenesis and Mutagenesis’

'Journal of Hematology'

'Open Journal of Genomics'

 

Journal Reviewing

Including: Annals of Oncology, Blood, Blood Advances, Blood Cancer Journal, Bioinformatics, BMC Medical Genomics, British Journal of Cancer, British Journal of Haematology, Critical Reviews in Oncogenesis, Cytogenetics and Genome Research, Genes Chromosome and Cancer, Haematologica, Human Molecular Genetics, International Journal of Cancer, Journal of Clinical Oncology, Journal of Medical Genetics, Journal of Pathology, Lancet Haematology, Leukemia, Leukemia and Lymphoma, Leukemia Research, Molecular Genetics, Nature Communications, Nature Genetics, Oncogene.

Conference Organizer / Reviewer

Including: British Society of Human Genetics, European Haematology Association, International Workshop on CLL, British Society of Haematology.

 

Grant reviewing for funding bodies

Wellcome, MRC, Blood Cancer UK, KKLF, AICR, CRUK, Myeloma UK, Children with Cancer, Nederlands National Fund for Scientific Research, Czech Science Foundation, Polish National Academy of Academic Exchange, Indian Biomedical Research Fellowship Programme, Wellcome Trust – India, DBT Alliane, Leukemia and Lymphoma Society, NIH P01

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Articles

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Conferences

Letters/Editorials

Review

Module co-ordinator for the MSc in Genomic Medicine, Precision medicine module.

Personnel Academic Tutor for BM4 and BM5 medical students and PGT students of the Genomic Medicine MSc.

Facilitator on the BM4 graduate medicine programme

Project supervisor for BMedSci, MMedSci, MSc, undergraduate and rotation students.

Assessment marker for MSc, iPhD projects

Faculty of Medicine PhD Programme. Internal examiner, PhD supervisor, project supervisor and marker, lecturer.

Faculty of Medicine Intercalated BMedSci Programme. Project supervisor and marker

University of Southampton Inter-Professional Common Learning. Facilitator.

University of Southampton Bachelor of Medicine BM4. Facilitator.

Professor Jonathan C Strefford
Somers Cancer Research Building Southampton General Hospital Mailpoint 824 Tremona Road Southampton SO16 6YD

Room Number: SGH//MP824

Facsimile: (023) 8120 5152

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