Centre for Cancer Research & Cell Biology

Bioinformatics and Imaging

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Enabling Technologies

Bioinformatics and Imaging

The Cancer Bioinformatics and Imaging group consists of scientists with expertise across a broad spectrum of subjects including Computational Biology, Computer Vision, Machine Learning, Data Integromics, Systems and Network Biology.

The group is leading on high-throughput big data analysis in cancer genomics, molecular oncology and tissue pathology for molecular diagnostics and precision medicine.

With a focus on solid cancers, they provide a vital key in deciphering the complex genomic and phenotypic landscape of cancer, and in identifying prognostic and predictive biomarkers. This is strongly allied to the rapid developments in molecular pathology and the translation of new genomic and tissue-based tests into practice. Digital pathology, image analysis and tissue informatics provide important technologies to support high throughput computerised analysis of solid tumour tissue samples and to understand the complex interplay between genotype and phenotype.

The aim of the group is to lead internationally on the development of novel computational and statistical methods in the analysis of genomic and image data, and to support interdisciplinary collaborative research by working closely together with biologists, oncologists and pathologists within the Centre for Cancer Research and Cell Biology (CCRCB).

Key Research Areas

  • Computational biology and biostatistics;
  • Pathway analysis, causal inference of regulatory networks, and integration of genetics and genomics data;
  • Digital pathology, tissue imaging, image analysis and tissue biomarker discovery;
  • High-throughput analysis of genomic and image data;
  • Quantitative methods in linking genomes to targeted therapeutic compounds;
  • Data “Integromics”;
  • The development of new computational methods and their application to translational cancer research.

Areas of Research Focus

Next Generation Sequencing and Genomics

Using the high-throughput sequencing platforms centred within the Northern Ireland Molecular Pathology Laboratory (NI-MPL), we generate a wealth of data across a range of cancer specific projects. Using the latest analytics software, in-house algorithms and novel high performance computing architectures, research is undertaken across a range of solid cancers including prostate, breast, gastrointestinal and brain tumours. 

Key hypotheses are generated and tested with the aim of generating novel genomic biomarkers and multivariate signatures for cancer diagnostics and prognostics.

Data Integromics and PICAN

Through collaboration with the Northern Ireland Biobank (NIB), NI-MPL and Digital Pathology, the Cancer Informatics team have also developed a novel bioinformatics integration platform called PICAN (Pathology Integromics in Cancer) for the management of clinical, phenotypic and genotypic data from cancer tissues.  This allows novel but complex biomarker signature analysis across large numbers of tissue samples.  Recent initiatives aim to build new compute architectures and big data pipelines to enhance data search and accelerate biomarker discovery in cancer genomics.

Tissue Imaging, QuPath and Immuno-Oncology Algorithms

The group has a strong interest in tissue and biomarker imaging and works closely with the NI-MPL and the NIB to drive innovative solutions in cancer research. We have established one of the most extensive digital pathology laboratories in the UK, with scanning technologies, image and tissue microarray (TMA) management software, along with image analysis software for quantitative biomarker discovery, validation and translation. Expansion of this capability will be possible through a recent £3.9m grant as part of the CRUK Accelerator programme.  We have developed QuPath – a sophisticated image analysis platform for the high resolution analysis of tissues and cells.    This is now supporting a wide range of cancer biomarker imaging programmes within the Centre and is allowing us to develop novel approaches to quantifying immune cell response in cancer patients, as powerful prognostic and predictive markers in disease.

This strong track record is underpinned by strong industrial links, primarily through PathXL Ltd which was spun out from these activities and is now a leading digital pathology software company with customers worldwide. It has been working closely with the group on automated tumour identification using image analysis and has established TissueMark™ as a leading software platform for tumour markup and analysis in molecular diagnostics and next generation sequencing

Educating the Next Generation of Bioinformaticians

Finally, the group takes a leading role in the education, training and mentoring of students, staff and scientists to provide them with a deeper knowledge and understanding of modern methods in bioinformatics, computational biology and tissue imaging.   This includes a comprehensive MSc course in Bioinformatics and Computational Genomics aimed at establishing the next generation of bioinformaticians and equipping researchers with the tools necessary to drive discovery in genomics, molecular diagnostics and translational cancer research.

 

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