National Genotyping Center

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National Genotyping Center

• CeGen Bioinformatic support
• International Workshop on Pharmacogenomics and
  Pharmacogenetics Current Challenges
  and Bioinformatics Support
• Barcelona, July 11th-12th

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What is CeGen?

• CeGen is a technologic platform promoted by
  Genoma España, which aims to provide knowledge
  and infrastructure for affordable large-scale SNP
  genotyping projects.
• CeGen intended target are research groups in
  universities, hospitals, research centers and the
  industry.
• CeGen aims to contribute to a quantum leap in
  biomedical research through high added value
  services provided from Spain.

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CeGen services
SAMPLES
SELECTION of genome regions of interest
DNA EXTRACTION
SNP SEARCH
DNA QUANTITATION
CHOICE OF TECHNOLOGY
GENOTYPING
STATISTICAL ANALYSIS OF RESULTS AND CONSULTING
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Genotyping technologies
SNPlex
Illumina
Sequenom
TaqMan
1500 - 300 SNPs
400 - 40 SNPs
40 - 5 SNPs
10 - 1 SNPs
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OK, the users samples have been transformed into
millions of genotypes... What now?
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We could send these data to the users and let
them play with them...
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...O we can try to provide some added value. (O
both, of course) http//bioinformatica.cegen.upf.e
s/
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Bioinformatics at CeGeN

• Bioinformatics as a general service
• Selección de SNPs
• Analysis
• Tools for platforms and users
• Flexible SNP selection tool, including functional
  information prediction (PupaSNP)
• Powerful, flexible web interface for genotype
  data delivery, management, and analysis.

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Where does Bioinformatics play a role?
Coordination

• Pregenotyping
• SNP selection based on
• Function prediction
• Previous LD
• Known disease association

• Postgenotyping
• Data download
• Format changes
• Data analysis
• Customer support

Genotyping platforms BCN CNIO USC
CeGen Users
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Development of applications to help the users in
SNP selection and genotype analysis
SNPator (SNP Analysis To Results)
PupaSNP

• Pregenotyping
• SNP selection based on
• Function prediction
• Previous LD
• Known disease association

• Postgenotyping
• Data download
• Format changes
• Data analysis
• Customer support

Both applications executable through WebServers
(human-accessible) and WebServices (automated
access)
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Bioinformatics at CeGen http//bioinformat
ica.cegen.upf.es/
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Bioinformatics at CeGen http//bioinformat
ica.cegen.upf.es/
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Bioinformatics at CeGen http//bioinformat
ica.cegen.upf.es/
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SNPator an application for data handling and
analysis http//bioinformatica.cegen.upf.e
s/

• OVERVIEW
• Security-aware. Password protected.
• Project - oriented.
• Four user levels.
• Browser data download and analysis.
• Editor data upload.
• Designer database tailoring for specific
  studies.
• Administrator user and project administration.
• Guest users with limited options (ID guest
  Pswd guest)
• Three kinds of tools.
• Format changers (to upload and download data).
• Algorithms programmed from scratch.
• Background execution of usual software packages.

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SNPators basic architecture
POSTGENOTIPING
Client side
Web browser
Results
Queries
HTML PHP
HTML
Apache web server
PHP
HTML
PHP Programming language
Stream of data (SQL)
MySQL Database management system
Server side
Linux OS
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SNPators structure.

• Other
• applications
• ERP
• LIMS

• Output
• Raw data.
• Export formats (ARLEQUIN, MLINK / FASTLINK,
• GENEHUNTER, PHASE...)

• Database
• Info on
• SNPs
• SAMPLES.
• GENOTYPES
• ...

• Basic analysis
• Genotype frequencies
• Heterozygosity
• Allele frequencies
• HW equilibrium
• Haplotype frequencies

• Sample
• Processing
• Coordination
• Platforms

• Genomic Analysis
• LD measures and tests
• Haplotype blocks
• tagSNPs

Data Caring

• Disease/Complex Trait Analysis
• Association RR, OR, logistic models,
• multiple test corrections
• TDT hTDT, multiple test corrections.
• Linkage analysis shuttle to linkage programs.
• ... Future developements on new techniques.

CeGen Users
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SNPator a tool for data handling and analysis
http//bioinformatica.cegen.upf.es/
set up a new user
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How to contact CeGen
Contactar con el CEGEN
coordinacion.cegen_at_upf.edu
http//www.cegen.org