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New open-source software judges accuracy of computer predictions of cancer genetics

January 10, 2020

Cancers are often made up of many cells which vary genetically to each other. These genetic differences mean the cancer may be particularly susceptible or resistant to a given treatment. As a result, identifying these variations can help clinicians decide which treatment is most likely to be successful for a specific patient.

Because simple clinical methods to test for genetic variation are vulnerable to missing a lot of cell-to-cell variability, recent computer tools have been developed to predict and characterise genetic diversity within clinical tumour samples. However, there is no existing common benchmarking approach to determine the most accurate computational methods.

The study, published in Nature Biotechnology, developed open-source software that can be used to judge the accuracy of computer predictions and establish this benchmark.

The team developed a simulation framework and scoring system to determine how accurately each algorithm predicted various measures of genetic diversity. These included: the proportion of cancerous cells in the tumour sample; the number of genetically different groups of cancerous cells in the tumour sample; the proportion of cells within each of these groups; which genetic mutations were in each group; and the genetic relationship between the groups.

"Our new framework provides a foundation which, over time as it is run against more tumours, will hopefully become a much-needed, unbiased, gold-standard benchmarking tool for assessing models that aim to characterise a tumour's genetic diversity," says joint-lead author Maxime Tarabichi, postdoc in the Cancer Genomics Laboratory at the Crick.

The researchers built upon an existing computer software to generate and analyse the 580 predictions in this research, adding new features to the software to create more realistic tumours. This tumour-simulation software and the marking framework are publicly available for other researchers to use either directly or to help develop their own scoring framework.

"Computer simulations in cancer genomics are helping us develop more accurate tools, as we understand where these tools perform well, and where they need improvement," says author Peter Van Loo, group leader in the Cancer Genomics Laboratory at the Crick. "Further developing these tools, so they more closely match real-life tumours, should ultimately help clinicians better match patients with personalised medicines."
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Notes to Editors

  • The tools referenced above can be accessed online: https://github.com/adamewing/bamsurgeon
    http://search.cpan.org/~boutroslb/NGS-Tools-BAMSurgeon-v1.0.0/https://github.com/mateidavid/phase-tools
    https://github.com/asalcedo31/SMC-Het_Scoring/smc_het_eval
    http://mtarabichi.shinyapps.io/SMCHET

  • For further information, contact: press@crick.ac.uk or +44 (0)20 3796 5252

  • The Francis Crick Institute is a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease. Its work is helping to understand why disease develops and to translate discoveries into new ways to prevent, diagnose and treat illnesses such as cancer, heart disease, stroke, infections, and neurodegenerative diseases.

    An independent organisation, its founding partners are the Medical Research Council (MRC), Cancer Research UK, Wellcome, UCL (University College London), Imperial College London and King's College London.

    The Crick was formed in 2015, and in 2016 it moved into a brand new state-of-the-art building in central London which brings together 1500 scientists and support staff working collaboratively across disciplines, making it the biggest biomedical research facility under a single roof in Europe.

    http://crick.ac.uk/

  • The Big Data Institute is located in the Li Ka Shing Centre for Health Informatics and Discovery at the University of Oxford. It is an interdisciplinary research centre that focuses on the analysis of large, complex data sets for research into the causes, consequences, prevention and treatment of disease. Research is conducted in areas such as genomics, population health, infectious disease surveillance and the development of new analytic methods. The Big Data Institute is supported by funding from the Medical Research Council, the UK Research Partnership Investment Fund, the National Institute for Health Research Oxford Biomedical Research Centre, and philanthropic donations from the Li Ka Shing and Robertson Foundations. Further details are available at http://www.bdi.ox.ac.uk



The Francis Crick Institute

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