SEARCHbreast: A virtual resource to facilitate sharing breast cancer materials and knowledge to benefit the 3Rs

Aims

This project will develop a searchable database of resources related to breast cancer that scientists can share to minimise repetition of animal studies and maximise the use of available in vivo data through meta-analysis.

Background

Animals are used to address a range of questions about the development, metastasis and treatment of breast cancer. The UK has an active breast cancer research community and there is an opportunity to further apply the 3Rs by facilitating the sharing of data, models, materials and expertise. A web-based bioinformatics search portal will be developed to facilitate this, allowing researchers to mine and integrate in vivo data from a range of sources

Research details and methods

A secure, searchable database will be developed which can easily interface with other online cancer resources. It will include technical information on collecting and preserving animal tissue and study designs to minimise animal use for various breast cancer models. 

Related content

We will develop a searchable secure database of animal resources related to breast cancer and a specialist bioinformatics resource. The database architecture will have an access layer with a web server and a storage layer with a MySQL database server. It will be populated by information obtained from collaborators. This will host technical information and detailed SOPs, developed by the scientific coordinator, the applicants and their collaborators to unify procedures, collect and preserve animal materials and provide information on how to estimate the fewest numbers of animals needed in various breast cancer models. Access from external users will be password protected to prevent inappropriate use.

The SEARCHbreast bioinformatics portal will be online enabling researchers to mine and integrate published data on animal studies in breast disease from multiple different sources. This will be based on existing structure developed by Dr Chelala (http://bioinformatics.breastcancertissuebank.org/ and www.pancreasexpression.org). This will allow scientists to perform fast meta-analysis on publicly available data, overcome possible data analysis obstacles and avoid duplication of work, not only being more time and cost-effective but also impacting on the 3Rs.

The resource will be established using Open Source BioMart technology (www.biomart.org) which enables the resource to be easily integrated with complementary resources e.g. Ensembl (www.ensembl.org), international efforts in cancer research e.g. International Cancer Genome Consortium (ICGC; www.icgc.org) and the Cancer Biomedical Bioinformatics Grid caBIG (http://cabig.cancer.gov/). Interoperability with ICGC and caBIG will promote the SEARCHbreast bioinformatics resource not only within the UK, but also internationally. Our Institutes have facilities for professional hosting of planned workshops and webinars. We will manage the project by fortnightly teleconferences and six monthly face to face meetings.

Morrissey B, Blyth K, Carter P, Chelala C, Jones L, Holen I, Speirs V (2017). The Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) Framework: Encouraging Reduction, Replacement, and Refinement in Animal Research. PLoS Biol  15(1): e2000719 doi:10.1371/journal.pbio.2000719

Speirs V (2016). Opinion: Reuse and Reduce. The Scientist Read the article

Speirs V, Morrisey B, Holen I, Blyth K, Carter P, Chelala C, Jones L (2016). SEARCHBreast: An online resource designed to increase the efficiency of using materials derived from breast cancer studies in animals. J Pathol 240(1):120 doi:10.1002/path.4755

Morrissey B, Holen I, Chelala C, Carter P, Jones L, Blyth K, Speirs V (2016). Introducing SEARCHBreast: a virtual resource to facilitate sharing of surplus animal material developed for breast cancer research. npj Breast Cancer 2(16020) doi:10.1038/npjbcancer.2016.20

Carter P, Blyth K, Holen I, Jones L, Morrissey B, Speirs V, Chelala C (2016).  The SEARCHBreast portal: A virtual bioresource to facilitate the sharing of surplus animal materials derived from breast cancer studies. Open Journal of Bioresources, 3(1),p.e4 doi:10.5334/ojb.21

Blyth K, Carter P, Morrissey B, Chelala C, Jones L, Holen I, Speirs V (2016). SEARCHBreast: a new resource to locate and share surplus archival material from breast cancer animal models to help address the 3Rs. Breast Cancer Res Treat. 156(3):447-52  doi:10.1007/s10549-016-3785-0

Morrissey B, Blyth K, Carter P et al. (2016) SEARCHBreast: a new online resource to make surplus material from in vivo models of breast cancer visible and accessible to researchers.  Breast Cancer Research, 18:59  doi:10.1186/s13058-016-0716-2  Read the paper

Blyth K, Carter P, Morrissey B, Chelala C, Jones L, Holen I, Speirs V (2016) SEARCHBreast: a new resource to locate and share surplus archival material from breast cancer animal models to help address the 3Rs. Breast Cancer Research and Treatment, 156(3): 447-52  doi:10.1007/s10549-016-3785-0 Read the paper

Morrissey B, Blyth K, Carter P et al. (2015) SEARCHBreast Workshop Proceedings: 3D modelling of breast cancer. Alternatives to Laboratory Animals – ATLA, 43(6): 367-75. Read the paper

Speirs V (2015). Animal research: share surplus animal tissue. Nature, 522(7555):156. doi:10.1038/522156c Read the paper

 

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Infrastructure grant

Grant reference number

NC/L001004/1

Award date:

Feb 2014 - Aug 2016

Grant amount

£495,766

Primary 'R'

Reduction

Scientific Discipline

Cells and systems
Cancer

Technologies/approach

Bioinformatics

Keywords

Meta-analysis