copyright openhelix. no use or reproduction without express written consent1

Copyright OpenHelix. No use or reproduction without express written consent 1

dbGaP

The Database of Genotypes and Phenotypes

Materials prepared by:

Cynthia Perreault-Micale, Ph.D.

Dorothy S. Reilly, Ph.D.

www.openhelix.com

Updated: Q4 2010Version 2


NCBI dbGaP Agenda

Introduction & Credits Basic Searching & Browsing Report Types Analysis Reports Advanced Searching Summary Exercises

dbGaP: www.ncbi.nlm.nih.gov/gap

http://www.ncbi.nlm.nih.gov/gap


Many Contribute dbGaP Studies

Launched Dec. 2006 Major contributors include: National Eye Institute’s Age Related Eye Disease Study, The Genetic Association Information Network (GAIN), & many more!


Data Content & Organization

Many types of studies are included

2 types of access - open & controlled

Open access: studies, documents, variables, analyses

Controlled access: de-identified phenotypes & genotypes for individual study subjects

Specific authorization process for controlled access requests


Multiple Data Types - Stable Identifiers

phs = Studies

phd = study Documents

phv = phenotypic Variables

pha = genotype-phenotype Analyses

pht = dataseTs

Study number phs000007.v1.p1

“v” data version “p” participant

set version

Unique identifiers assigned

These numbers increase whendata changes


Citing a Study in dbGaPBMC Medical Genetics 8:S7, 2007

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17903306

URL with uniquestudy ID number


dbGaP Homepage Resources


ImportantLinks

GettingStarted

Access to dbGaP Data

Tutorial, Overview, FAQs & Submission instructions Apply for Controlled Access, FTP site, Browse Studies RSS Feed, Conduct Codes, Security Procedures & Contact Us

Start Searches& Help


dbGaP Homepage Additional Resources

List ofLatest Studies

GettingStarted

Contact

Categorized list of NCBIresources

Popularresources

Featuredresources

NCBIinformation

Additionalaccess

Genetics &Medicine


NCBI Homepage - The Interlinked Entrez Network

http://www.ncbi.nlm.nih.gov

dbGaP

All Databases

dbGaP results

An Entrez Global Query - results in all databases


Results Utilize Many Handy Entrez Features

Manyhelpful

tools & links

Search box & menu

Display Settings Categorized results

For more information about Entrez search functions:• OpenHelix Entrez Overview tutorial (www.openhelix.com) • NCBI Entrez documentation (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp; http://www.ncbi.nlm.nih.gov/Entrez/tutor.html)


dbGaP Credits

Nature Genetics 39:1181, 2007http://www.nature.com/ng/journal/v39/n10/full/ng1007-1181.html

Nature Genetics 39:1045, 2007http://www.nature.com/ng/journal/v39/n9/full/ng2127.html

Many additional sources of information

Click FAQ link on homepage


NCBI dbGaP Agenda




Accessing Studies from dbGaP Homepage


List AllStudies

Browse AllStudies


Browsing Studies from dbGaP Homepage

Resulttabs

Choose how many items

per page

Click to returnto homepage

Next page of results

Click Apply


Browsing Studies - Study Information

Colored icons indicateVariable, Document &

Analysis Reports available


Browsing Studies - More Study Information

Many typesof studies

A variety of study types: Exome Sequencing,

Family, Single Patient, Longitudinal, and more.

Parent-Offspring trios: Data are collected from parent-

parent-offspring sets.

Case-Control Studies: Identify individuals with a disease of interest and a control group without the disease. The frequency or levels of an attribute [eg,

specific genotype] are compared between these

groups.


Browsing Studies - Right Side Options

Filtersinactive

Find related data

Recent activity

HandyLinks


Browsing Other Record Types



Basic Searching from Homepage

prostate cancer

Our basic search example: prostate cancer


Basic Search Results

Number of results & access by record type

Search term


NCBI dbGaP Agenda




Study Report Access

phs000130

phs = Studies

Search Results:

Enter Study ID

phs000130

Click here


Study Report

NIDDK IBD Genetics Consortium Crohn’s Disease Genome-Wide Association Study

Accession: phs000130.v1.p1

We will enlarge each section next

auth. data access req.

study name, #,navigation tabs

Search within study,

Associated Substudies, if available

description

auth. access data

public data (FTP)

criteria, molecular

history, publications

diseases (MeSH)

study attribution


Study Report: Description

Linked Logos

May also see studyversion history

Navigation tabs

Study type &number of participants


Study Report: Data Access

Authorized access data- rules for this study

Public data - FTP


Study Report: Criteria & Molecular


Study Report: Study History & Publications


Study Report:Diseases, Attribution, Access

Research Use Statements


Sample Variable Report phv = phenotypic Variables

Access

Click here


Sample Document Report phd = study Documents

Navigation

Document Name& Accession

Search

Study Name& Accession


Associated Datasets

Name & Accession

Similar organization

pht = dataseTs

Description

Dataset type

Dataset Summary


NCBI dbGaP Agenda



Analysis Methods


Sample Analysis Report

Analysis Plots

http://gmed.bu.edu/about/index.html“Please note that all associations. . . are considered "candidate associations" pending replication in additional studies.”

Details

Publications

pha001340.1

Enter ID into homepage search box

pha = genotype-phenotype Analyses

Study version history

Browser


Analysis Report & Genome BrowserdbSNP homepage:http://www.ncbi.nlm.nih.gov/projects/SNP/

Click here


Analysis Browser

zoomscroll

Controls

NCBI Service Utility menu: SNP Genotype, Entrez SNP,

Sequence Viewer,Map Viewer

HTML view to maximize, print or save

Toggleexpanded

or compacted

Close that data track

Highlight top ten SNP hits


Analysis Browser - More Features

Other buttons allow you to close particular windows Mouse over many items for tool tips & links


Browse SNPs

sample size, P-value rankallele freq., call rateLink to dbSNP record

Scroll over

Mouse over bin to see SNP record

highlightedGWAS catalog page# in bin = # markers

tested, + for 10 or more


Analysis Browser - Customizing Your Display

We will remove the GWAS Catalog Chromosome 3 SNP Bins reference track & highlight the top ten SNPs on the Sequence Viewer

Clickhere

One referencetrack removed

Top ten SNPshighlighted


NCBI dbGaP Agenda




Advanced Searching TIPS

Use the Boolean operators AND, OR and NOT. They must be capitalized.

Words can be truncated with * (asterisk): fibro*

Add quotes, as in “fibroblast growth factor”, for complete phrase, exact word order

(Use with caution, can be TOO restrictive)



Advanced Search Example

heart rate AND exercise

Our advanced search example: heart rate AND exercise


Search Results: Heart Rate AND Exercise

Limits: exclude or include specific types of records

Advanced search: similar functions, & several more

Click to open the dbGaP Advanced Search form


dbGaP Advanced Search Form

Limits, SearchDetails, Help

Back to homepage

Search History

Search Builder

Help

Help

Multiple easy options in a single query form


dbGaP Advanced Search - Search Builder

Click Searchor Preview

Term added toSearch box

Click here

heart rate

Choose Boolean

Repeat steps as many times as needed to build query We will add the term “AND exercise[Variable]”

Search Builder


dbGaP Advanced Search - Search Builder Results

Query: (heart rate[Variable]) AND exercise[Variable]


dbGaP Advanced Search - Search History

Search History

Most RecentQueries

Click to access

Combine, view, delete or save previous searches

#1 AND #2

Click Searchor Preview

Click here to learn more about My NCBICopyright OpenHelix. No use or reproduction without express written consent 48

Saving Searches in My NCBI

Register & log in to My NCBI

Click here to save search in My NCBI

About My NCBISave


NCBI dbGaP Agenda




Summary of NCBI’s dbGaP

Many groups contribute data



Data Organized into Uniform Report Types

Stable identifiers assigned

Genome browserprovided


NCBI dbGaP Agenda

