Parco Tecnologico Padano

Via Einstein

Lodi

Italy
Laboratory (ies) involved:

• PTP Genomics Platform (PGP),
• PTP Statistical Genomics and Bioinformatics Unit
• From Q4 2010 small P3 experimental animals facilities (provided though Istituto Zooprofilattico di Lodi)

Research topics

• Genetics and genomics applied to livestock

Contact person

John Williams

Science Director

john.williams@tecnoparco.org

Activities and services

>> Genomics Platform:

The PTP Genomics Platform is an ISO9001 and SINAl17025 accredited laboratory that has a fully integrated sample handling, genome analysis and data processing capacity. The heart of the upstream sample handling and processing capability has 3 TECAN FREEDOM EVO robots for sample preparation, DNA extraction and setting up reactions. These robots are integrated with a powerful LIMS system (SQL-LIMS v5.1) and Oracle database through a bar-coded system for sample tracking. The sample handling and LIMS interfaces with a biorepository for the storage of DNA samples.

Genome analyses offered include Sanger sequencing and re-squencing, low through-put SNP genotyping is based on “SnapSHOT” and microsatellite marker analysis offered on an ABI 3730 platform. Medium throughput SNP genotyping with custom designed SNP panels is offered via IIlumina BeadXpress, and quantitative PCR and allele discrimination assays on a ABI7900. This capability is being extended with the installation of latest generation high throughput genotyping and sequencing equipment, which will offer to the project high throughput sequencing at the level of 300MB sequence per run with paired-end sequence reads currently of 100bp and Illumina Infinium genotyping with the capacity of 300K custom SNP panels and 1.2M SNP dedicated genotyping panels.

>> The Statistical Genomics and Bioinformatics Unit.

The Statistics unit develops and manages genomic databases, complex project management bioinformatics systems, and undertakes the development and implementation of new statistical methods for analysis of complex genomic data. A shared Linux cluster of 280 Opteron AMD cores operating at 2.2 GHz is dedicated to bioinformatic applications. The system is composed by ten chassies of six blades discless each one equipped with an Infiniband 4X network card and 8GB of RAM (total 480GB RAM). The storage facilities can be accessed through a fiber channel network and the total available space is up to 20 TB.

Bioinformatics and Statistical tools are offered to process and store and analyse the data generated in the project. Bioinformatic pipelines and custom databases linked to user friendly internet based user interfaces can be created to manage data produced in projects, particularly for projects involving large and complex data sets. Statistical tools can be developed to build, optimise and validate analysis models through simulation. The tolls can then be applied to real data produced in the project.

>> Research Hotel

Associated with the Genomics and Bioinformatics/Statistical Platforms, wet and dry laboratories are available at PTP for visiting scientists to carry out research projects supported by expert staff, and to receive training.

>> Animal Experimentation facilities(provided by Instituto Zooproflattico de Lombadia e Emila Romana (IZLER))

IZLER is constructing a new state of the art laboratory facility including a small P3 experimental animal facility which will be a flexible multi-purpose unit able to house small farm species (sheep, goats and pigs). This facility will be commissioned mid-2010 and will be available for NADIR studies by Q4 2010.

Description of the access to provide

1)Remote accessunder which the experimental design is completed by Email exchange, and if necessary virtual meetings between client and the Genomics and Statistical Platforms. Samples are then shipped to the Genome Platform where samples are processed and genomic analysis completed. Data is then either returned to the client in an agreed format, or passed to the Statistical Platform for additional analysis as agreed with client at the project set-up stage.

2)On Site Access. PTP is a fully integrated research organisation and can offer the opportunity for visiting scientists to carry out research on site. On site projects would be initiated as for remote access with the development of the project protocols via Email and virtual meetings. Once the project design is agreed the client would spend time at PTP to carry out some or all of the project activities. Thus wet-lab facilities could be provided for sample generation and processing, and bioinformatics and statistical support available to assist and train the client in data processing and analysis.

Genomic Platform:

• DNA, RNA extraction and storage,
• High and low throughput genotyping, (SNPs, micro-satellite markers, AFLPs)
• High and low throughput sequencing
• Transcriptomics, (by custom Combimetrix array, sequence tags)
• Real-Time PCR; detection and quantification of animal pathogens (viral, bacterial pathogens)

Bioinformatic and Statistical facilities:

• Statistic and quantitative genetics e.g. for project design, complete data analysis, interpretation of results
• Computer simulation procedures e.g. testing epidemiological models, mechanisms of genetic resistance
• Bioinformatics support, e.g. data processing, comparative analysis
• Database design and maintenance

“Research hotel”

• Laboratory and computational facilities to carry out molecular genetic studies

NUMBER of projectsaccepted:

Availability of 58 laboratory days,

Estimated 15-20 genomics projects.

Conditions of participant involvement

After the end of each project the candidate will:

• Submit a short report
• Fill a questionnaire available on-line at: http://cordis.europa.eu/fp7/capacities/questionnaire_en.html
• The participant is entitled to publish the results of its work at the infrastructure in the open literature.All publications resulting from the project should acknowledge this EC-support by mentioning : “The research leading to these results has received funding from the European Community‘s Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 228394”
• Proprietary research (research where results are not generally available to the public or only made available under confidentiality arrangements) cannot be supported.
• Travel and subsistence expenses linked to the access will be reimbursed upon approval of the report. Reimbursements will be done according to administrative rules of each hosting organisation.
• For more information about transnational access conditions, see the ANNEX III to the Grant Agreement - Infrastructures

Infrastructure ethical rules

Studies on live animals producing samples for genomic studies must have been conducted in compliance with national and local ethical regulations.

Permission to use samples must have been obtained from the owner

Recent publications

• Juling, K., Schwarzenbacher, H., Williams, J.L. and Fries, R. (2006) A major genetic component of BSE susceptibility BMC Biology, 4:33 doi:10.1186/1741-7007-4-33
• Sironi, L., Williams, J.L., Moreno-Martin, A.M., Ramelli, P., Stella, A., Jianlin, H., Weigend, S., Lombardi, G., Cordioli, P. and Mariani, P. (2008) Susceptibility of different chicken lines to H7N1 highly pathogenic Avian Influenza virus and the role of Mx gene polymorphism coding amino acid position 631. Virology 380 152-156. doi:10.1016/j.virol.2008.07.022
• Baxter, R., Craigmile, S.C., Haley, C., Douglas, A., Williams, J.L. and Glass, E.J. (2009) BoLA-DR Peptide binding pockets are fundamental for foot-and-mouth disease virus vaccine design in cattle. Vaccine doi:10.1016/j.vaccine.2009.09.131
• Juling, K., Schwarzenbacher, H., Frankenberg, U., Ziegler U, Groschup M., Williams, J.L. and Fries. R. (2008) Characterisation of a 320-kb region containing the HEXA gene on bovine chromosome 10 and analysis of its association with BSE susceptibility Animal Genetics 39 400-406