In 2001, the aims of the BµG@S (Bacterial Microarray Group at St George's) facility were to establish a multi-collaborative bacterial microarray facility for the purposes of making available DNA microarray technology to the microbial pathogen research community in the UK over a period of 5 years. The timeliness of making whole genome and whole species arrays widely and rapidly available in the post-genomic era was self-evident. Access to and training in high-throughput technology addressed both fundamental and applied issues in pathogen biology, pathogenesis, virulence, molecular epidemiology and public health.
The facility planned initially to make microarrays for 12 bacterial genomes in the first 2 years and make them accessible for the duration of funding. Other arrays will be made, as sequence becomes available, creating a flexible and evolving resource that meets the clearly documented needs of the community and which fills a technological and time-frame gap. The urgent need, indeed demand, for microarrays, was highlighted at several Wellcome Trust meetings on functional genomics (e.g. Mycobacterium tuberculosis, Campylobacter jejuni and Neisseria meningitidis), necessitated their manufacture in the shortest timeframe practicable following the availability of the genome sequences; this proposal was structured to meet such imperatives. Our experience in designing and producing the PCR products for an initial complete genome microarray for M.tuberculosis together with the production of a C.jejeuni microarray allowed us to realistically expect to achieve this timetable.
The BµG@S facility provided training in the use of microarrays by:-
- training individuals in the labs through short visits;
- group training in specially organised training courses twice a year (but subject to demand);
- annual update user-group scientific meetings;
- publication of detailed working protocols, on a website for user group access.
- provided an impetus and focus for common format array data to promote standardisation for ease of access to future international databases; e.g. ArrayExpress (EBI);
- promote sharing of data with user groups via a secure website, further enhancing research productivity and preventing duplication of research;
- through established collaborations with expert groups in computing and mathematical modelling of data sets, it has tested and provided new analysis and visualisation tools;
- implemented improvements in technologies; thus providing a core knowledge-base that can keep abreast of and exploit technological advances and make them available;
- up-date existing genome arrays as new genome information were validated and developed universal- or pan-species arrays; e.g. include all the strain differences for C.jejuni or a pan-pathogenic mycobacterial array with sequences from M.tuberculosis,
M.leprae, M.bovis, M.avium and M.avium subsp.paratuberculosis and M.ulcerans;
- acted as a pilot-study for larger-scale functional genomics initiatives including those based on the human genome sequence.
The BµG@S facility aims to foster a multi-collaborative network of interdisciplinary research groups that can exploit genome sequence information and provide an international lead in pathogen functional genomics. This facility thus provides an enabling and a material resource for microarrays based on a dynamic scientific interaction between the facility scientists, the user groups, collaborating expert groups and public institutions holding databases (Sanger Centre: Dr Julian Parkhill and EBI: Drs Helen Parkinson and Alvis Brazma). A network of users have thus advanced both the technology and the quality of biological information that accrues from microarrays. There is no intention to make this facility a factory, simply to provide arrays on demand. Instead, we have established networks of collaborating groups using the arrays for each pathogen.
The BµG@S facility provides an interdisciplinary, collaborative approach unified by a broad common goal. It also provides a reference point for data collection and comparison, together with quality control and standards, which in this case focuses on one particular technology, rather than a broader functional genomics centre including proteomics and structural genomics. The purpose of training is to aid dissemination of technologies within and between communities and also to build up the researcher base.