database of Genotype and Phenotype

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database of Genotype and Phenotype
http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
ap

• Kim Pruitt
• (for Matt Mailman)
• NCBI

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Overview

• Phenotype
• Genotype
• Genotype X Phenotype Association

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Overview

• Phenotype
• Data tables
• Columns are phenotypes
• Rows are individuals
• Documents (ie protocols, data collection forms)
• Parts of documents linked to variables
• Data dictionary
• Genotype
• Genotype X Phenotype Association

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Overview

• Phenotype
• Genotype
• Genotype files directly from vendor
• Intensity files (ie .CEL)
• Genotype X Phenotype Association

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Overview

• Phenotype
• Genotype
• Genotype X Phenotype Association
• Various statistical models and methods
• P-value or LOD score for each marker
• Filters by P-value, HWE, minor allele frequency
• Map phenotypes onto genomic sequence

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Overview

• Phenotype
• Genotype
• Genotype X Phenotype Association
• Obvious expansion potential
• More species different types of association data
  (QTL)
• Critically important to archive all data
• Submit primary data to appropriate public
  archive!
• Probe DB primers, resequencing amplicons
• dbSTS STS markers
• Maps UniSTS Map Viewer
• GenBank ESTs

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dbGaP Web Site

• two levels of access - open and controlled
• open access to non-sensitive data
• study summaries and documents
• measured variables and data elements
• analysis reports
• genome browser
• controlled access provides oversight and
  accountability for use of sensitive datasets
  involving personal information
• De-identified phenotypes and genotypes for
  individual subjects
• Pedigrees

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Browse Studies
http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
ap
Link back to dbGaP homepage
Description of dbGaP
Instructions
Link to study report
List of variables in study
List of documents in study
Automated query to PubMed for genome-wide
association study articles
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Browse Studies by Disease
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Advanced Search
Fields to be searched
Add any number of search criteria
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Study Report
Citeable unique stable identifier
Genotype x phenotype association or
linkage analyses
search this study
Link to variable report
History Publications Attribution Access Rules
Links back to submitter website
Criteria for inclusion/exclusion
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Variable Report
Citeable unique stable identifier
Documents containing a section that has been
linked to this variable
Statistical summary of values for this variable
P-value is red if cases differ from controls
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Variable Report (continued)
Document name
Section of document that has been linked to this
variable
Link to document
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Analysis Report
Link back to report for measured or derived
variable that was analyzed
Genome browser of analysis results
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Genome Browser of Analysis Results
Slider filters results less significant than
threshold
2MB bins colored to represent the
most Significantly associated marker
Click on bin of interest to zoom in and see
association in context with other objects mapped
to the same genomic region
LINK
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Genome Browser Higher Resolution
Collapse table
P-value of genotyped marker
Scroll via boxes above
Add maps
CFH gene has been associated with AMD in several
studies
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Coming Soon

• Studies
• Early 2007
• Michael J. Fox Foundation Parkinsons Disease
  Study (LEAPS)
• NINDS Stroke and ALS
• Spring 2007
• GAIN (Genetic Association Information Network)
• Framingham SHARe first two generations
• NIDDK GoKinD and EDIC
• Summer 2007
• Framingham SHARe third generation
• Late 2007- Early 2008
• GEI (Genes and Environment Initiative)
• Features
• Search analysis results by
• Gene
• SNP or microsatellite marker
• Genomic region
• Filter analysis results by
• P-value

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Acknowledgements

• Phenotype
• Rinat Bagoutdinov
• Luning Hao
• Mas Kimura
• Jimmy Jin
• Natasha Popova
• Stephanie Pretels
• Karl Sirotkin
• Jack Wang
• Matt Mailman

• Genotype
• Mike Feolo
• Lon Phan
• David Shao
• Ming Ward
• Steve Sherry
• XML
• Kim Tryka
• Laura Kelly
• Jeff Beck

• Authorized Access
• Steve Sherry
• Eugene Yaschenko
• Valdimir Soussov
• Misha Kimmelman
• Don Preuss
• Al Graeff
• Jim Ostell

http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
ap
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Document HTML
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Document PDF
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Multiple maps can be displayed to elucidate what
is already known in a particular genomic region