The University of Southampton
Medicine

Dr William J Tapper BSc, PhD

Associate Professor in Genomic Informatics

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Dr William Tapper is an Associate Professor in Genomic Informatics within the Faculty of Medicine at the University of Southampton.

Dr. Tapper was appointed Senior Research Fellow in Genomic Medicine within the School of Medicine in 2014. A graduate of the University of Wales, Swansea, he joined the Genetic Epidemiology Group at University of Southampton in 1998. He investigated the identification of disease genes using genome wide patterns of linkage disequilibrium and completed his PhD in 2004 under the supervision of Professors Newton Morton and Andrew Collins.

Dr. Tapper now leads a Genomic Informatics Group and works closely with Professors Nick Cross, Diana Eccles, Surinder Sahota, Jonathan Strefford, Sarah Ennis and Andy Collins. His group specialises in identifying and understanding the genetic basis of a wide range of diseases using bioinformatic and statistical analysis of next generation sequencing data and genome wide association data. His work benefits from strong collaborative links with several colleagues at the University of Southampton. He is based in the Duthie building at Southampton General hospital and attracts postgraduate and postdoctoral staff with strengths in statistics and bioinformatics. Individuals interested in joining his group should contact Dr. Tapper directly.

Qualifications

PhD, Genetic Epidemiology, University of Southampton 2004
BSc, Genetics, University of Wales, Swansea 1998

Appointments held

Associate Professor in Genomic Informatics (March 2017 - present)

Senior Research Fellow in Genomic Informatics (2014 – 2017

Senior Research Fellow: Development and application of a bioinformatics pipeline to identify somatic mutations in haematological malignancies. (2012-2014)

Research Fellow: Genome-wide association study of Myeloproliferative Neoplasms. (2010-2012)

Research Fellow: Comparing induction therapies and chromosomal abnormalities for the MRC Myeloma 9 clinical trial (2009-2010)

Research Fellow: Genome-wide association study of early onset breast cancer. (2007-2009)

Research Fellow: Development of a novel approach for meta-analysis of association data. (2007)

Research Fellow: Linkage disequilibrium (LD) in the human genome. (2004-2006)

Research Assistant: Development, construction and description of LD maps and location databases. (1998-2003)

Research

Responsibilities

Publications

Teaching

Contact

Research interests

My research involves statistical and bioinformatic approaches aimed at identifying and understanding the genetic basis of a wide range of human diseases.

 

Research areas include:

1) Identification of genes associated with breast cancer prognosis

Genome wide association studies (GWAs) have been very effective in identifying genetic variants that predispose to a wide range of diseases. In collaboration with Professor Eccles, Dr Tapper supervises a meta-analysis of GWAs of breast cancer prognosis that includes a unique cohort of early onset breast cancer. They are investigating the relationship between the genetic factors identified and clinical factors such as oestrogen receptor status, tumour grade and size. In addition, they are developing a new model for predicting breast cancer prognosis that combines genetic factors with established clinical factors.

2) Identification of somatic abnormalities in Myeloproliferative neoplasms (MPN) by exome sequencing

Cancer cells can be traced back to a fertilized egg through mitotic cell divisions. During this process they acquire a set of mutations that are not present in the germline. These somatic mutations can be divided into drivers and passengers. The drivers contribute to oncogenesis by conferring a growth advantage which is positively selected by the tissue microenvironment while the passengers are neutral and are not involved in the cancer. Dr Tapper aims to identify these driver mutations and the cancer genes they reside in by exome sequencing tumour and germline pairs from patients with Myeloproliferative neoplasms (MPN). MPNs are a group of related hematological disorders that are characterised by an excess proliferation of one or more myeloid cell lineages and a tendency to transform to acute myeloid leukemia.

3) Genome wide association study of essential thrombocythemia (ET) and polycythemia vera (PV) to investigate whether germline variation influences disease subtype

MPNs are classified by which myeloid cell lineage(s) is predominantly expanded in the peripheral blood, namely erythrocytes in PV and platelets in ET. Sequencing studies have revealed that somatic mutations in one or more of several genes (eg. JAK2V617F, TET2, EZH2, CBL, ASXL1, RUNX1, TP53, DNMT3A, NRAS, U2AF1, SFRS2, ZRSR2, etc) drive the clonal proliferation. In contrast, very few genes/variants (e.g. SF3B1, SETBP1, JAK2 exon 12) have been identified that are mutated specifically within haematologically-defined disease entities such as ET and PV. In collaboration with Professor Cross, Dr Tapper is performing a genome-wide association study of ET and PV cases with somatic JAK2V617F mutations to investigate whether germline variation is associated with these phenotypic subtypes of MPN.

4) Identification of genes mutated in regions of acquired uniparental disomy (aUPD) in Myeloproliferative neoplasms (MPN)

Acquisition of uniparental disomy (aUPD) is a common genetic mechanism by which a pathogenic mutation on a single allele is converted to homozygosity, thereby providing a clonal advantage over heterozygosity. It is a frequent occurrence in myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN) and myelodysplastic/myeloproliferative neoplasia (MDS/MPN), examples being aUPD of the long arms of chromosomes 4, 7 and 11 which result in homozygosity of mutations in TET2, EZH2 and CBL respectively. To identify additional regions of recurrent aUPD and the genes targeted, Dr Tapper analyses genome-wide SNP array data and next generation sequence data from MPN patients and healthy controls.

5) To understand why the FIP1L1-PDGFRA gene fusion is seen predominantly in males

The great majority (>80-90%) of patients with somatically acquired PDGFRA or PDGFRB fusion genes are male but the underlying reason for this remains obscure. In collaboration with Professor Cross, Dr Tapper is comparing whole exome data from FIP1L1-PDGFRA cases at diagnosis and remission to identify somatic changes that may account for the gender differences. To investigate the hypothesis that a specific inherited genetic factor is responsible for the male excess associated with PDGFR fusion genes Dr Tapper is also analysing SNP array data.

6) Clonal hierarchy in multiple myeloma by single cell exome sequencing

Multiple myeloma (MM) is a plasma cell malignancy characterised by marked genomic abnormalities that define disease subsets. Of these, 1q21 chromosomal amplification (amp1q21) associates with poor prognosis, but as yet it is not known how the lesion demarcates tumour behaviour. In collaboration with Professor Sahota, Dr Tapper is analysing single cell whole exome data to define intraclonal variation in a case with 1q21 MM. Their aim is to distinguish between early and late changes to identify likely disease initiating events that may serve as better therapeutic targets and markers of residual disease.

7) Identification of gene fusion in myeloid malignancies using RNA sequencing

Dr Tapper supervises a PhD studentship on the application of RNA sequencing to detect gene fusions and to investigate aberrant RNA splicing.

 

 

 

Academic unit(s)

Human Development and Health Academic Units

Affiliate academic unit(s)

Cancer Sciences Research group

PhD Supervision

Dr Tapper currently supervises one full time PhD student and has co-supervised a second PhD student who completed in 2012. Dr Tapper has informally contributed to the supervision of several other PhD students.

PhD, RNA sequencing for investigation of gene fusions and splicing, supervised by Dr Tapper and Professor’s Cross and Ennis, funded by C. Benson donation

Faculty of Medicine

‘Head of Field (Genetics)’ for BMedSc Projects.

Organisation of Human Genetics seminar series.

Organisation of annual lecture in honour of Professor Patricia Jacobs.

Organisation of a university-wide one day symposium on ‘Next Generation Sequencing’.

Member of the advisory committee for the Bioinformatics Core facility led by Dr Woelk.

 

 

Articles

Letters/Editorials

Book Chapter

 

Joint module lead in ‘Bioinformatics, Interpretation, and Data Quality Assurance in Genome Analysis’ for the MSc in Genomic Medicine.

Lecturing, demonstrating, and exam marking for the MSc in Genomic Medicine.

Lecturing, tutoring and exam marking in Biochemistry for the Bachelor of Surgery (BM5)

Outreach lecturing to international year 12 students from Itchen college.

 

 

Dr William J Tapper
Human Development and Health Academic Unit
Faculty of Medicine
University of Southampton
Duthie Building (MP 808)
Southampton General Hospital
Tremona Road
Southampton SO16 6YD
Email: W.J.Tapper@southampton.ac.uk

Room Number:SGH/Duthie/MP808

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