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Cancer Genomics Projects: The Collection

The cancer genome has been sequenced for more than a decade. This has created an abundance of relevant information that can be used to find novel drug targets and match patients to the most effective treatments. Unsurprisingly, sifting through all the data produced by the growing number of cancer genomics studies has presented a major hurdle in the field.

Nevertheless, several projects are now successfully gathering and sharing molecular information about cancer, most of which are openly accessible to researchers. This in turn has created a vast catalogue of known cancerous mutations.

The Cancer Genome Project

The Cancer Genome Project is part of the cancer, ageing and somatic mutation research based at the Wellcome Trust Sanger Institute in the UK. It was launched in 2000 by Michael Stratton. The project combines knowledge of the human genome sequence with high throughput mutation detection techniques. The goal is to characterise cancer genes, mutational processes and patterns of clonal evolution in human tumours.

The group is made up of internal partners, including Ultan McDermott and Serena Nik-Zainal, each having a different area of focus to assist the projects overall aim of cataloguing different cancer genomes. The mutation information that is gathered by the team is inputted into the COSMIC database, otherwise known as the “Catalogue Of Somatic Mutations In Cancer”. It holds millions of mutations across thousands of cancer types and is continuously growing, both in content and scope.

The International Cancer Genome Consortium

The International Cancer Genome Consortium is a voluntary scientific organisation that provides a collaborative forum for the world’s leading cancer and genomics researchers. It was launched in 2008 and is one of the most ambitious biomedical research efforts since the Human Genome Project. Essentially, the aim of the programme is to provide a comprehensive description of the somatic genomic abnormalities present in a broad range of human tumours. The catalogues are produced by members and made freely available to qualified researchers, enabling scientists around the world to use the information to improve how cancer is diagnosed, treated and prevented.

The Pan-Cancer Analysis of Whole Genomes Consortium

The Pan-Cancer Analysis of Whole Genomes study is an international collaboration to identify common patterns of mutations in over 2,600 whole cancer genomes from the International Cancer Genome Consortium. The project is focussed on the nature and consequences of variations in both coding and non-coding regions, specifically on cis-regulatory sites, non-coding RNAs and large-scale structural variations. The research activities have been coordinated by a series of working groups made up of more than 700 scientists.

The Cancer Genome Atlas

The Cancer Genome Atlas Program was a joint effort between the National Cancer Institute and the National Human Genome Research Institute, both of which are part of the US Department of Health and Human Services. The project began in 2006 and consisted of the molecular characterisation of over 11,000 cancer cases from 33 different cancer types. Researchers were brought together from diverse disciplines and multiple institutions, which enabled the project to generate over 2.5 petabytes of genomic, epigenomic, transcriptomic and proteomic data. Much of the information gained from this project has already led to improvements in the ability to diagnose, treat and prevent cancer. The data remains publicly available for the research community.

The Pan-Cancer Atlas

The Pan-Cancer Atlas project aimed to examine the full set of tumours characterised by the Cancer Genome Atlas Program. It also incorporated new information from the Multi-Center Mutation Calling Multi-Tumour Completion effort, which identified cancer-related mutations in the whole Cancer Genome Atlas dataset by analysing the differences between DNA sequences of tumours and normal samples. As a result, the Pan-Cancer Atlas was able to focus on three main cancer-related themes – cell-of-origin, oncogenic processes and pathways. The data remains publicly available and continues to facilitate new discoveries about cancer.

Genomics Evidence Neoplasia Information Exchange

The Genomics Evidence Neoplasia Information Exchange (GENIE) is a project by the American Association for Cancer Research. It is a publicly accessible international cancer registry of real-world data assembled through sharing between several of the leading global cancer centres. Cancer genomics sequencing data is collected, standardised and linked with clinical outcomes obtained during routine medical practice. The goal of the project is to provide the research community with the statistical power necessary to improve clinical decision making, especially in terms of rare variants or rare subtypes of the disease.

100,000 Genomes Project

Genomics England is a company owned and funded by the Department of Health and Social Care in the UK. It was set up to deliver its flagship 100,000 Genomes Project, which was also contributed to by the Wellcome Sanger Trust, Cancer Research UK and the Medical Research Council. This involved sequencing the whole genomes from 100,000 NHS patients to improve the diagnosis of cancer and rare diseases An additional aim of the project was to set up a genomic medicine service for the NHS that would enable new scientific discoveries and benefit patients.

In 2018, six years after its announcement, the 100,000 Genomes project reached its goal. Subsequently, the UK became the first nation in the world to apply whole genome sequencing at scale in direct health care, as well as providing access to high quality clinical and genomic data for research with the intent to improve patient outcomes. The project laid foundations for the NHS Genomic Medicine Service, which has a long-term plan of sequencing 500,000 whole genomes by 2024.

Therapeutically Applicable Research to Generate Effective Treatments

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) programme aims to determine the molecular changes that drive childhood cancers. It applies a comprehensive genomic approach and uses data to guide the development of effective and less toxic cancer therapies. The programme is run by the Office of Cancer Genomics, within the National Cancer Institute. The TARGET data portal enables the research community to search, download and analyse information and share knowledge to facilitate the discovery of novel targets that could be used to treat the most prevalent childhood cancers.

Cancer Genomics: From Diagnosis to Treatment

Image credit: ICR

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Big Data / Cancer / Cancer Research