Transnational access activities of the European Sequencing and Genotyping Infrastructure
The integrated ESGI infrastructure consists of seven major European genome centres from the following countries
- France (CNG, Inserm, Evry),
- Germany (CAU, Kiel and MPIMG, Berlin),
- Spain (CNAG and CRG, Barcelona, Spain)
- Sweden (UU, Uppsala, Sweden)
- United Kingdom (WTSI, Hinxton).
Home page: www.esgi-infrastructure.eu
ESGI will offer access to high-throughput sequencing technologies of the second and third generation as well as to medium- and high-multiplex genotyping platforms. The users of the infrastructure will be supported by members of the ESGI consortium in key steps of the analysis of their biological samples. This may include training in sample preparation for sequencing and/or genotyping, the sequencing/genotyping process itself, raw data analysis as well as support in in-depth, multilayered analysis of biological data, depending on the project and facility involved.
ESGI will fund accepted projects for transnational access. ESGI funding includes full cost coverage of consumables, instruments, personnel supporting the project etc., and additionally includes funding of travel, lodging and subsistence costs of external users.
Modality of access:
A research team of one or more researchers given access to the infrastructure under the project is defined as an external user or a user group. Each user group is led by a user group leader. The external user or user group leader and majority of the users of a group must work in an institution established in a EU Member State or Associated State and in a country other than the country(ies) where the legal entity(ies) operating the infrastructure is(are) established. Only those users or user groups that are entitled to disseminate the foreground they will potentially generate under transnational access projects are eligible for project application. Applicants must provide a clear statement on potential dissemination of results.
Access is provided to a wide variety of projects selected based on applications that will be validated by external review. Proposals for transnational access projects to access ESGI facilities can be made according to the deadlines published by ESGI.
The infrastructure can respond to a broad range of projects with varying numbers of samples to be processed. ESGI will consider only large-scale projects with associated costs ranging from 50,000-250,000 Euros for review. Therefore, applicants must clearly describe the number of samples and analyses planned for the project using the online submission form. Otherwise, the application would not be acceptable. The projects of users accessing the infrastructure will be distributed between the sites according to the general capacities and competencies of the respective laboratories. In general, ESGI will provide external users access to its facilities for up to three months. Data sharing is essential to disseminate knowledge; therefore ESGI requires data sharing at a minimum at the time of publication of results, by default via the EGA (European Genome-Phenome Archive) or other archives at the European Bioinformatics Institute (Partner 4), which supports protection of sample providers by data access control. ESGI users must explain in their proposals how they would share data produced by ESGI with other scientific researchers.
Unit of access:
The units of access for sequencing and genotyping depend on the technologies applied. The access being offered comprises sample preparation, sequencing and/or genotyping and data analysis. The units of access for sequencing are gigabases. The units of access for genotyping involve a defined minimum number of DNA samples and SNPs to perform efficiently the specific assays at the different installations. SNP assays comprise Illumina genome-wide SNP arrays, targeted Illumina SNP arrays, and Sequenom?s mass spectrometry (iPLEX) method. Applicants are encouraged to provide estimated units of access numbers in addition to the exact description of samples and analyses needed for the study. ESGI recommends contacting the transnational access work-package coordinator before submission of proposals to clarify the dimension and specific needs of potential projects.
The selection of access projects will be through an open competition, which will be carried out every year. An independent project selection committee is responsible for the evaluation of the proposals. Five relevant expert scientists expert in human genetics and genomics in general will be chosen to evaluate each project proposal in light of on-going international research. They will be supported by a management committee to verify eligibility and the access costs associated with a proposal, and to aid in the selection of the partner facilities or sites that will provide access to a particular project. Based on the evaluation of the proposals, ESGI facilities will finally decide on accepting projects for transnational access.
Given that the proposals contain the information required for review as described above, the principal criteria for evaluation of external referees will be:
1. scientific excellence of the proposal and potential impact of the proposed project;
2. the quality of previous work, e.g. the clinical and other phenotype data of samples to be analysed by ESGI;
3. accessible biological samples that can be transformed into high quality nucleic acids;
4. the potential of the collection to advance knowledge of genetics and molecular mechanisms of disease and/or advance prevention and treatment strategies;
5. the cost of the project to ESGI in comparison to the benefits described above.
6. ethics approval and consent to exchange nucleic acids samples and to share data across frontiers.
Ethical and legal issues associated with proposals will be reviewed following the project scientific selection, using ELSI experts external to the infrastructure as well as the relevant expertise available within our infrastructure consortium.
Transnational access project types offered by ESGI
ESGI integrates the capacity for large-scale genomics analyses and technical expertise in sequencing and genotyping technology of leading European genome research centres. The centres have all been founded by national investments in sequencing and genotyping infrastructures to participate in national and international collaborative research projects in genome research and particularly in disease-related genetic studies, and in some cases to provide services for the scientific community.
The institutes are well known for their activities in high-throughput sequencing and genotyping and offer state of the art technologies and data analysis methodologies in this field. They are well equipped and experienced for successfully performing genetics and functional genomics on a genome-wide scale and for targeted analyses in large sets of DNA or other nucleic acids samples. The centres are applying standard operational procedures and information management systems for handling of biological samples, production sequencing and genotyping, and quality assurance and management of the produced data on a routine basis.
The individual wet-lab facilities will enrich transnational projects by additionally bringing in their leading expertise in bioinformatics, database technology, statistical genetics and biobanking.
The integrated ESGI infrastructure provides access to world-class sequencing and genotyping facilities of high quality matching a wide range of needs of external users of the European scientific community.
The ESGI infrastructure is designed to particularly support external users in:
Main Sequencing applications:
- whole-genome sequencing;
- targeted re-sequencing (mutations, SNPs, CNVs);
- epigenetic analysis (MeDIP-seq, MBD-seq, bisulphite-seq);
- ChIP-seq; RNA-seq; miRNA-Seq; microbial sequencing.
Sequencing technologies currently being applied:
- HiSeq2000/Genome Analyzer IIx (IIlumina),
- SOLiD (ABI) and
- 454 (Roche).
Main Genotyping applications:
- replication studies of re-sequencing studies by medium-scale genotyping;
- detection of CNVs;
- detection of allele-specific expression;
- genome-wide DNA-methylation analysis;
- GWAS (genome-wide association studies).
Genotyping technologies currently being applied:
- Illumina Golden Gate and VeraCode assay (48-1536 SNPs);
- Sequenom iPlex;
- Illumina Infinium Bead Arrays, up to 2.5 million SNPs or 450K CpG sites.
ESGI has a large capacity to meet the demands of the European research community in sequencing and genotyping. Studies can be performed at one or more facilities as required.
The following technical and biological applications will particularly be offered for access by the linked facilities of the ESGI infrastructure:
Max-Planck Institute for Molecular Genetics (MPIMG, Berlin, Germany):
Single- and paired-end read sequencing by Illumina. Focus on ChIP-Seq and RNA-Seq methods to study mechanisms of gene regulation. Biological expertise focuses on cancer genomics, mouse genomics, metabolic and age-related diseases, drug development and nutrigenomics. Access will in particular be offered to projects dealing with the elucidation of fundamental mechanisms of genome regulation in mammalian model organisms and functional studies in target tissues or cells of metabolic disorders and ageing processes.
Christian-Albrechts-University (CAU, Kiel, Germany):
454 sequencing (microbial sequencing, amplicon resequencing). SOLiD-fragment and SOLiD-mate pair sequencing (Life Technologies). Three HiSeq machines from Illumina are available supporting the full Illumina sequencing portfolio. In terms of sequencing applications, the institute has specialised on the analysis of targeted resequencing (especially whole-exome) data. Illumina GoldenGate and Infinium genotyping for validation studies. Sequenom (multi-plex, 384 well format) and TaqMan (single-plex, 384 well format) high-throughput genotyping for interrogating custom sites. Expertise in clinical genetics is centred on immunology, inflammatory barrier diseases and cancer. Access will in particular be offered to projects dealing with re-sequencing studies.
Wellcome Trust Sanger Institute (WTSI, Hinxton, UK):
Single- and paired-end read sequencing by Illumina HiSeq. Sequenom genotyping at small numbers of custom sites (iPLEX technology). Access projects will focus on analysis of genetic variation (whole genome and exome), in particular sequence analyses of samples from (isolated) populations. Available access unit types are (a) units of 16 full genomes sequenced at 6x coverage, with analysis including detection of genetic variants jointly in the full set of samples, and imputation of these into further genotyped samples from the same population ? this design maximises the total number of variants found in a large sample set for fixed cost, and is particularly appropriate for studies based on genetic isolates, (b) units of 32 exomes sequenced at high depth (average typically > 50x), including detection of genetic variants, (c) Genotyping in units of 20 SNPs in 380 DNA samples, suitable for validation and replication studies. Suitable project sizes are in the range of 5-10 units.
Centre National de GÚnotypage (CNG, Evry/Paris, France):
Single- and paired-end read sequencing by Illumina. Sequenom genotyping for validation analyses (iPLEX technology). Focus on epigenetic applications. Expertise in metabolic diseases, cancer, genetic variation analysis and genetic epidemiology. Access will in particular be offered to projects dealing with functional studies in target tissues of metabolic disorders (RNAs-seq, Chip-seq or FAIRE-seq of target tissues); exome sequencing (for ENU induced mouse models of human metabolic and neuro-degenerative diseases and family based exome sequencing for monogenetic disorders); genotyping of medium number of SNPs (20 to 60) from GWAS studies for validation in relevant disease associated endophenotypes.
Centre Nacional de AnÓlisis Gen˛mica (CNAG, Barcelona, Spain):
Single- and paired-end read sequencing by Illumina. Focus on whole-genome sequencing and targeted re-sequencing, epigenetic analysis (ChIP-seq, MeDIP-seq, MBD-seq, bisulphite-seq) and RNA-seq and mi-RNA-Seq. Focus on cancer, asthma, inflammatory and infectious diseases. Access will in particular be offered to projects dealing with the elucidation of fundamental mechanisms of genome regulation in mammalian model organisms and projects dealing with re-/exome-sequencing.
Centro de Regulaciˇ Gen˛mica (CRG, Barcelona, Spain):
Medium- large scale genotyping (Illumina) for validation of sequencing studies, e.g. complementing the activities of CNAG. Available access unit types are (a) units of 4 samples for 1M Infinium (Illumina) genotyping (suitable project sizes are multiples of 4 units); (b) units of 480 samples for genotyping of 768 SNPs on the IlluminaGoldenGate platform; (c) units of 480 samples for genotyping of 96 SNPs on IlluminaGoldenGateVeracode platform. The facility has expertise in cancer, neurodegenerative disorders (Parkinson?s disease and Alzheimer?s disease), and neuropsychiatric diseases (mood disorders, anxiety disorders, eating disorders). Access will be offered in conjunction with projects of the other ESGI facilities.
Uppsala University (UU, Uppsala, Sweden):
Single- and paired-end read sequencing, (Illumina, SOLiD). Focus on genome, exome or targeted sequencing, MBD-sequencing, bisulphite-sequencing. Medium-scale and genome-wide genotyping (Illumina) and DNA methylation analysis. Expertise in the analysis of allele-specific expression by genotyping, ?digital karyotyping? by sequencing epigenomic studies of leukaemia and genetics of autoimmune diseases. Access will in particular be offered to projects dealing with the analysis of allele-specific gene expression.
Contact for further questions: contact