Breast Cancer Somatic Genetics Study (BASIS)

BASIS is an international collaboration, which aims to genetically characterise the most common class of breast cancer (known as ER+, HER2-), responsible for approximately 40 per cent of all cases of the disease.

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All cancers are caused by somatic mutations – mutations acquired over a lifetime. The BASIS team will use next-generation technologies to comprehensively catalogue all the somatic mutations in the genomes of 500 cases of breast cancer. This will shed new light on the biology of the disease, thereby opening the door for the development of new diagnostics and targeted treatments.

Overview

BASIS is led by Professor Mike Stratton and Dr Andy Futreal, from the Wellcome Trust Sanger Institute’s Cancer Genome Project. It will draw on its collaborating centres’ expertise in pathology, cancer genomics and sequencing, epigenomics, transcriptomics, bioinformatics and clinical translational research and the strength of its sample collections. The project forms part of the International Cancer Genome Consortium (ICGC), a collaboration designed to obtain comprehensive descriptions of genetic changes in 50 different tumour types and/or subtypes which are of clinical and societal importance across the globe.

Harnessing the latest sequencing technologies, BASIS will generate whole-genome sequences, which will be analysed to identify every instance of every class of mutation present in each of the 500 cancer samples collected. The mutations identified will encompass single letter changes; insertions or deletions of chunks of DNA; duplicated copies of stretches of the DNA; and rearrangements of the genome. By sequencing the DNA from both tumour and normal tissue samples taken from the same patient, the researchers will be able to root out those changes that are unique to the cancer.

Using these data, the team will have the statistical power to identify mutations that occur at a frequency greater than 3 per cent in the ER+, HER2- class of breast cancers. The types of mutations identified will provide insights into the mutagenic processes that produced them and offer clues to the aetiology of the disease. Complementary catalogues of epigenetic changes and mRNA and miRNA expression profiles will be generated for the same 500 cancer samples. The team will compare these data with equivalent data from other classes of breast cancer as well as other types of cancer.

At the same time, the BASIS project team will begin to translate its genomic findings by identifying somatic mutations specific to ER+, HER2- in the free DNA found circulating in patients’ bloodstreams. Using this method, the team hopes to be able to detect minimal residual disease in patients and use this information to refine prognoses and treatment regimes for women with breast cancer.

Data from the BASIS project will be made rapidly available, with minimal restrictions, to all scientific researchers as they are generated. Data will be available through a dedicated BASIS website, through the ICGC database system, as well as via the Sanger Institute’s Catalogue of Somatic Mutations in Cancer (COSMIC) database.