Personalised bioinformatics for cancer
Several global initiatives such as the Cancer Genome Atlas and the International Cancer Genome Consortium have successfully characterised the genomes of thousands of cases of the most common cancer types. This analysis has provided a mutational landscape of human cancer, offering important biological and clinical insights. Importantly, the generated knowledge has immediate translational impact in the diagnosis, monitoring and treatment of cancer. The EU-funded PanCanRisk project aimed to make use of the extensive genomic cancer data available nowadays to enhance the search for novel susceptibility genes. As the project fellow Dr Ceres Fernandez-Rozadilla explains “PanCanRisk is centred on the idea of cancer as a disease that has very specific molecular features, irrespective of the location where it arises. Thus, it is plausible to hypothesise that genetic susceptibility is common between different types of cancer.″ Pan-cancer analyses The PanCanRisk consortium combined expertise in bioinformatics, statistics, experimental and clinical science. Partners developed bioinformatics tools to exploit available large-scale cancer datasets to discover novel genetic variants and genes implicated in cancer susceptibility. These have been extensively validated in two further independent cohorts and, following sound functional analyses, they seem to be implicated in disease development. One of the highlights of the project is the eDiVa pipeline which incorporates a disease knowledge database with several new prediction and quality control tools. In an era where genomic information has become day-to-day practice for clinicians, eDiVa can be used to support them in diagnosis, decision-making and treatment choice by helping them interpret genomic information more efficiently. eDiVa is distributed under an open source license for genomic-based cancer risk assessment in a clinical setting. The immediate translational impact of PanCanRisk One of the main aims of the project was devoted to creating better diagnostic tools towards better screening programmes and personalised medicine approaches. “We have been successful in identifying and functionally validating two genes that modulate the risk of developing both breast and colorectal cancers. We have also designed a panel of circulatory biomarkers that can help detect and hence, diagnose some types of cancer sooner,″ continues Dr Fernandez-Rozadilla. These findings are of extreme importance for risk prediction as carriers of pathogenic variants in these genes will have a considerable risk of developing breast and/or colorectal cancers. With regards to the circulatory biomarkers, these could be potentially used to complement current screening strategies to increase our power to detect early cancer cases, which have a better prognosis. The PanCanRisk project has provided unprecedented knowledge on cancer risk. The generated platform harnesses the diagnostic power of genome sequencing in everyday clinical practice with immediate benefits in patient classification, monitoring and therapeutic interventions. PanCanRisk strategies could be extended to drug sensitivity evaluation and pharmacogenomics that will undoubtedly improve clinical management of patients. In his view of the future, Dr Fernandez-Rozadilla believes that “the bench-to-bedside component of PanCanRisk alongside its computational approach have the power to change the way cancer risk is assessed in the clinic.″
Keywords
PanCanRisk, cancer, risk, genomic, bioinformatics, biomarker
