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1 The PhenX Project: Consensus Measures for Phenotypes & Exposures Erin M. Ramos, PhD MPH Division...
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Transcript of 1 The PhenX Project: Consensus Measures for Phenotypes & Exposures Erin M. Ramos, PhD MPH Division...
1
The PhenX Project: Consensus Measures for Phenotypes & Exposures
Erin M. Ramos, PhD MPH
Division of Genomic Medicine
NHGRI
9/8/15: NIH CDE Initiatives – Overview Webinar
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Standard Measures Needed – c2006
Combining studies increases ability to detect loci with moderate effect size (G x G; G x E interactions)
Replication of GWAS results
Potential for cross-study analysis and replication limited by lack of standardized measures
(www.broad.mit.edu/diabetes/scandinavs/type2.html)
Type 2 Diabetes GWAS (>380K SNPs)
The PhenX Project
• Goal: Produce an online resource of standard phenotypic & environmental exposure measures
• Cooperative Agreement (2007 U01 2013 U41)
• ~ 450 measures addressing 21 domains
• Protocols, data element dictionaries, data collections worksheets (www.phenxtoolkit.org)
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PhenX Definitions DOMAIN: Topical area with unifying
theme (organ system, complex disease)
Substance Use
MEASURE: Certain characteristic of, or relating to, a study subject Nicotine Dependence
PROTOCOL: Standard procedure recommended collecting and record a PhenX measure
Fagerstrom Test
COLLECTION: A set of measures with a shared characteristic, target population or topic. The measures may cut across research Domains.
Mental Health Research 4
Steering Committee
Steering Committee
NHGRINHGRI RTIRTI
NIH IC LiaisonsNIH IC
Liaisons
External Scientific
Panel
External Scientific
Panel
Cardiovascular DiabetesDemographics
CancerAnthropometrics
Environmental Exposures
Nutrition/Dietary SupplementsGastrointestinal NeurologyInfectious Disease
& Immunity
Ocular PsychosocialOral Health PsychiatricPhysical Activity & Fitness
Reproductive Health
Speech and HearingRespiratory Social
EnvironmentsSkin, Bone,
Muscle & Joint
Alcohol, Tobacco, Other Substances
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Rare Genetic Conditions
Obesity
Pregnancy and Pediatrics
TBD
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Selecting PhenX Measures
Criteria for selecting measures include: - Well-established and broadly
validated
- Low burden to participant & investigator
- Applicable across population groups
- Freely available protocols
- Useful to investigators who are not domain experts
WG refines scopeWG refines scope
SC defines scopeSC defines scope
WG selects prelim measures
WG selects prelim measures
Community Outreach
Community Outreach
WG selects final measures
WG selects final measures
PhenX CDEs and variables
21 Domains (demographics, diabetes, etc.)- 389 CDEs (CDEs are created for each protocol)- 11,961 variables
Substance Abuse and Addiction Collections- 121 CDEs- 3,009 variables
Mental Health Research Collections- 39 CDEs to date- 893 variables
Tobacco Regulatory Research Collections- 21 CDEs to date- 200 variables
10(Slide provided by C. Hamilton, PhenX PI)
Example of PhenX CDEs and Variables
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Protocol Name Protocol CDE NameProtocol CDE ID VARNAME
Birthplace of Grandparents
Maternal Grandmother Geographic Birth Place Text 2789935 PX010401_Maternal_Grandmother_Bi
rthplaceBirthplace of Grandparents
Maternal Grandmother Geographic Birth Place Text 2789935 PX010401_Maternal_Grandmother_Bi
rthplace_LocationBirthplace of Grandparents
Maternal Grandfather Geographic Birth Place Text 2789937
PX010401_Maternal_Grandfather_Birthplace
Birthplace of Grandparents
Maternal Grandfather Geographic Birth Place Text 2789937
PX010401_Maternal_Grandfather_Birthplace_Location
Birthplace of Grandparents
Paternal Grandmother Geographic Birth Place Text 2789939 PX010401_Paternal_Grandmother_Bir
thplaceBirthplace of Grandparents
Paternal Grandmother Geographic Birth Place Text 2789939 PX010401_Paternal_Grandmother_Bir
thplace_LocationBirthplace of Grandparents
Paternal Grandfather Geographic Birth Place Text 2789941 PX010401_Paternal_Grandfather_Birt
hplaceBirthplace of Grandparents
Paternal Grandfather Geographic Birth Place Text 2789941 PX010401_Paternal_Grandfather_Birt
hplace_Location
1 Protocol, 4 CDEs, 8 variables
(Slide provided by C. Hamilton, PhenX PI)
Closing thoughts
Lessons learned- Identifying NIH IC Liaisons early was important- Personalized emails are most effective for outreach- Evaluating update/adoption of PhenX is not easy
2,000 Registered Users, 97 FOAs
- Science changes, re-evaluate content often (PhenX Expert Review Panels) and have strong versioning system
Looking ahead- Protocol translations, education & outreach- dbGaP mapping, EHR integration, participate in trans-NIH
CDE efforts
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Acknowledgments
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NHGRI - Brenda Iglesias (Program
Analyst) PhenX Steering Committee
- Mary Marazita, Co-Chair- Cathy McCarty, Co-Chair- Sharon Terry, Member
WG Chairs / Members NIH Liaisons Other Liaisons: HHS, DoD, CDC,
FDA, VA NIDA lead – Kevin Conway TRSP lead – Kay Wanke NIMH lead – Greg Farber NHLBI lead – Ellen Werner
RTI Team- Carol Hamilton (Principal
Investigator)- Tabitha Hendershot (Co-
Investigator)- Amanda Riley (Project
Manager)- Darigg Brown- Wayne Huggins- Debbie Maiese- Destiney Nettles- Helen Pan- Mike Phillips- Toolkit team- Communications team- Logistics team
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Contact Information
Erin M. Ramos, PhD MPH Program Director, Division of Genomic Medicine
National Human Genome Research Institute
5635 Fishers Lane, Suite 4076, MSC 9305
Bethesda, MD 20892-9305
Tel: 301.451.3706
Toolkit Stats (July 2015)
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• Number of Registered Users: 1,949• Number of Countries that Accessed PhenX : 155• Number of Visits: 713,446• Number of Unique Visits: 118,695• Average Visits Per Day: 301• Report Downloads: 4,830• Register Your Study: 16• Publications Citing PhenX: 94• Number of Funding Opportunities: 97
PhenX at ASHG Annual Meeting 2015
ASHG Invited Sessions on October 7, 2015 “Human Phenotypes for Researchers, Clinicians,
and Patients” Moderator: Jonathan Haines Speakers: C. McCarty, A. Kho, H. Rehm, B.
Patrick-Lake
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Add Value by PhenX/dbGaP Mapping
Huge # of variables in dbGaP (160,188) Fewer # of variables in PhenX (16,112) Mapping Comparable Variables Only
PhenX var => dbGAP var (harmonizable) same concept dbGAP var => PhenX var (harmonizable) same concept
Tools- In-house web-based wrapper using NCBI search API- Drill down using dbGaP search pages
Evaluating effectiveness of two mapping procedures Establish a schedule based on results
20(Slide provided by C. Hamilton, PhenX PI)
PhenX Phase II Improve Toolkit Content
- 4 new domains- Review/Update PhenX domains
Extend Capabilities- Chinese and Spanish translations- Web-based protocols, Explore EHR Integration
Mapping PhenX Measures to studies in dbGaP- Identify opportunities to combine studies
Collaborations and Outreach
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“A complete understanding of disease also requires…high-quality phenotypic data. Obtaining phenotypic data that are both thorough and accurate enough to be analyzed in conjunction with genomic and environ mental data requires meticulous application of phenotyping methods, improved definitions of phenotypes, new technologies, and the consist ent use of data standards (http://www.phenx.org).”
Green and Guyer, 2011