Staff Profile

Current position:

Nov 2019 - October 2025, CRUK Career Development Fellow

Area of expertise:

Childhood Cancer Genomics

Qualifications:

PhD, Northern Institute for Cancer Research, Newcastle University

BSc, Pharmacology, Newcastle University

Previous position:

2010 - 2019, Genome Biologist, Leukaemia Research Cytogenetics Group (LRCG), Newcastle University

Memberships and committees:

VolTRAX Introduction Programme (VIP) membership (2017)

MinION Early Access Programme membership (2015)

Training and experience:

GATK Best Practices for Variant Discovery; Edinburgh University (2015)

One-month laboratory visit; R&D, Wellcome Trust Sanger Institute (2013)

Command Line Bioinformatics and High Throughput Sequencing Analysis; Bioinformatic Support Unit (BSU), Newcastle University (2013)

Four-month laboratory visit; Molecular Genetics Department, Munich Leukemia Laboratories (MLL) (2012)

My research interests have focused on exploring the genomic landscape of childhood cancer and leukaemia, to improve the risk-stratification of patients for treatment and provide a greater understanding of disease development and prevention in children. I have developed and utilised next generation sequencing (NGS) technologies to identify recurrent mutations, copy number abnormalities (CNA) and rearrangements of genes in childhood cancer and leukaemia using whole genome (WGS), whole exome (WES) and targeted sequencing approaches. My translational research output has facilitated the development of UK treatment stratification procedures, biomarker-driven pan-European clinical trials and identified targetable lesions in high-risk patients who would benefit from intensive or targeted therapy. Furthermore, these studies have identified patients with predisposition to disease and shed light on the mechanisms of cancer development through abnormalities involving the centromere or telomere of individual chromosomes. 

Following on from my previous research, I am currently developing methods to explore genetic variation within the centromere and telomere of individual chromosomes to determine their role in chromosomal instability and childhood cancer development. Through my CRUK Career Development Fellowship, I am developing approaches to isolate chromosomes-of-interest and assessing the utility of hybrid sequencing methods to deconvolute the genetic architecture of these highly repetitive genomic regions. Certain subtypes of childhood cancer may develop through genetic inheritance or somatic acquisition of abnormalities within repeat DNA sequence of the centromere or telomere, and these genetic features may facilitate chromosomal instability and the development and progression of childhood cancer.   

Staff supervision:

Dr Richard Yim - Research Associate/Bioinformatician

Dr Tom Creasey - PhD student

Current and past funding:

Cancer Research UK

Bloodwise

KidScan

Children with Cancer UK

JGW Patterson Foundation 

Student Supervision

PhD: Co-supervisor to two students (2014-2018, 2017-)

MRes: Supervised seven master's students between 2011-2020

BSc: Supervised five undergraduate students (Biomedical Sciences) between 2008-2020

Lecturing

BSc – BMS3010 and BGM3061 (Biomedical, Nutritional and Sports Sciences), seminar on pharmacogenomics 

• Bashton M, Hollis R, Ryan S, Schwab CJ, Moppett J, Harrison CJ, Moorman AV, Enshaei A. Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia. Scientific Reports 2020, 10, 45.
• Sinclair PB, Ryan S, Bashton M, Hollern S, Hanna R, Case M, Schwalbe EC, Schwab CJ, Cranston RE, Young BD, Irving JAE, Vora AJ, Moorman AV, Harrison CJ. SH2B3 inactivation through CN-LOH-12q is uniquely associated with B-cell precursor ALL with iAMP21 or other chromosome 21 gain. Leukemia 2019, 33, 1881-1894.
• Sinclair PB, Blair HH, Ryan SL, Buechler L, Cheng J, Clayton J, Hanna R, Hollern S, Hawking Z, Bashton M, Schwab CJ, Jones L, Russell LJ, Marr H, Carey P, Halsey C, Heidenreich O, Moorman AV, Harrison CJ. Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Haematologica 2018, 103, 634-644.
• Schwab C, Ryan SL, Chilton L, Elliott A, Murray J, Richardson S, Wragg C, Moppett J, Cummins M, Tunstall O, Parker CA, Saha V, Goulden N, Vora A, Moorman AV, Harrison CJ. EBF1-PDGFRB fusion in pediatric B-cell precursor acute lymphoblastic leukemia (BCPALL):genetic profile and clinical implications. Blood 2016, 127, 2214-2218.
• Lindsey JC, Hill RM, Schwalbe EC, Shrimpton ER, Howell CI, Rafiee G, Crosier S, Smith A, Ryan SL, Williamson D, Bailey S, Clifford SC. Molecular and Prognostic Heterogeneity within MYC and MYCN Amplified Medulloblastomas. In: International Symposium on Paediatric Neuro-Oncology (ISPNO). 2016, Liverpool, UK: Oxford University Press.
• Ryan SL, Matheson E, Grossmann V, Sinclair P, Bashton M, Schwab C, Towers W, Partington M, Elliott A, Minto L, Richardson S, Rahman T, Keavney B, Skinner R, Bown N, Haferlach T, Vandenberghe P, Haferlach C, Santibanez-Koref M, Moorman AV, Kohlmann A, Irving JA, Harrison CJ. The role of the RAS pathway in iAMP21-ALL. Leukemia 2016, 30, 1824-1831.
• Sinclair P, Cheng J, Raninga P, Hanna R, Hollern S, Enshaei A, Blair H, Nakjang S, Ryan S, Eswaran J, Buechler L, Heidenreich O, Harrison C. A Targeted Functional Clone Tracking Assay for the Identification of Tumour Suppressor Genes in BCP- ALL Implicates the Transcription Factors FOXO3 and PRDM1. In: 57th American Society of Hematology (ASH) Annual Meeting. 2015, Orlando, FL, USA: American Society of Hematology.
• Russell LJ, Jones L, Enshaei A, Rutherford J, Tonin S, Ryan S, Eswaran J, Papaemmanuil E, Tubio J, Campbell PJ, Moorman AV, Harrison C. Clincial and Genetic Landscapes Differ Between IGH-CRLF2 and P2RY8-CRLF2 Acute Lymphoblastic Leukaemia. In: 57th ASH Annual Meeting 2015. 2015, Orlando, USA: American Society of Hematology.
• Hill RM, Kuijper S, Lindsey JC, Petrie K, Schwalbe EC, Barker K, Boult JK, Williamson D, Ahmad Z, Hallsworth A, Ryan SL, Poon E, Robinson SP, Ruddle R, Raynaud FI, Howell L, Kwok C, Joshi A, Nicholson SL, Crosier S, Ellison DW, Wharton SB, Robson K, Michalski A, Hargrave D, Jacques TS, Pizer B, Bailey S, Swartling FJ, Weiss WA, Chesler L, Clifford SC. Combined MYC and P53 defects emerge at medulloblastoma relapse and define rapidly progressive, therapeutically targetable disease. Cancer Cell 2014, 27, 72-84.
• Li Y, Schwab C, Ryan S, Papaemmanuil E, Robinson HM, Jacobs P, Moorman AV, Dyer S, Borrow J, Griffiths M, Heerema NA, Carroll AJ, Talley P, Bown N, Telford N, Ross FM, Gaunt L, McNally RJ, Young BD, Sinclair P, Rand V, Teixeira MR, Joseph O, Robinson B, Maddison M, Dastugue N, Vandenberghe P, Haferlach C, Stephens PJ, Cheng J, Van-Loo P, Stratton MR, Campbell PJ, Harrison CJ. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 2014, 508, 98-102.
• Schwab C, Andrews R, Chilton L, Elliott A, Keil G, Richardson S, Ryan SL, Wragg C, Moppett J, Cummins M, Goulden N, Vora AJ, Moorman AV, Harrison CJ. EBF1-PDGFRB Fusion in Paediatric Acute Lymphoblastic Leukaemia (ALL): Genetic Profile and Clinical Implications. In: 56th ASH Annual Meeting and Exposition. 2014, San Francisco, California: American Society of Hematology.
• Clayton J, Cheng J, Ryan S, Harrison CJ, Sinclair P. Oncogenomic Screening Strategies to Identify Tumour Suppressor Genes on Chromosome 12 in Acute Myeloid Leukaemia. In: 56th ASH Annual Meeting and Exposition. 2014, San Francisco, CA: American Society of Hematology.
• Schwab C, Andrews R, Chilton L, Elliott A, Richardson S, Ryan SL, Logan A, Fielding AK, Goulden N, Vora AJ, Moorman AV, Macartney CA, Harrison CJ. SSBP2-CSF1R Is a Recurrent Fusion in B-Other Acute Lymphoblastic Leukaemia with Variable Clinical Outcome. In: 56th ASH Annual Meeting and Exposition. 2014, San Francisco, California: American Society of Hematology.
• Ryan SL, Schwalbe EC, Cole M, Lu Y, Lusher ME, Megahed H, O'Toole K, Nicholson SL, Bognar L, Garami M, Hauser P, Korshunov A, Pfister SM, Williamson D, Taylor RE, Ellison DW, Bailey S, Clifford SC. MYC family amplification and clinical risk-factors interact to predict an extremely poor prognosis in childhood medulloblastoma. Acta Neuropathologica 2012, 123(4), 501-513.
• Ellison DW, Kocak M, Dalton J, Megahed H, Lusher ME, Ryan SL, Zhao W, Nicholson SL, Taylor RE, Bailey S, Clifford SC. Definition of Disease-Risk Stratification Groups in Childhood Medulloblastoma Using Combined Clinical, Pathologic, and Molecular Variables. Journal of Clinical Oncology 2011, 29(11), 1400-1407.
• Rand V, Parker H, Russell LJ, Schwab C, Ensor H, Irving J, Jones L, Masic D, Minto L, Morrison H, Ryan S, Robinson H, Sinclair P, Moorman A, Strefford J, Harrison CJ. Genomic characterization implicates iAMP21 as a likely primary genetic event in childhood B-cell precursor acute lymphoblastic leukemia. Blood 2011, 117(25), 6848-6855.
• Schwalbe EC, Lindsey JC, Straughton D, Hogg TL, Cole M, Megahed H, Ryan SL, Lusher ME, Taylor MD, Gilbertson RJ, Ellison DW, Bailey S, Clifford SC. Rapid Diagnosis of Medulloblastoma Molecular Subgroups. Clinical Cancer Research 2011, 17(7), 1883-1894.
• Ryan SL, Rand V, Schwab C, Morrison H, Matheson E, Minto L, Rahman T, Keavney B, Bown N, Skinner R, Schnittger S, Santibanez-Koref M, Grossmann V, Kohlmann A, Irving J, Harrison CJ. Ras Signalling Pathway and Novel Target Genes Related to Down Syndrome Contribute to the Development of B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) in iAMP21 Patients. In: 53rd Annual Meeting and Exposition of the American Society of Hematology (ASH). 2011, San Diego, California, USA: American Society of Hematology.
• Schwab CJ, Jones LR, Morrison H, Ryan SL, Yigittop H, Schouten JP, Harrison CJ. Evaluation of Multiplex Ligation-Dependent Probe Amplification as a Method for the Detection of Copy Number Abnormalities in B-Cell Precursor Acute Lymphoblastic Leukemia. Genes, Chromosomes & Cancer 2010, 49(12), 1104-1113.
• Lu Y, Ryan SL, Elliott DJ, Bignell GR, Futreal PA, Ellison DW, Bailey S, Clifford SC. Amplification and overexpression of Hsa-miR-3ob, Hsa-miR-30d and KHDRBS3 at 8q24.22-q24.23 in medulloblastoma. PLoS ONE 2009, 4(7), e6159.