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PheMAP: Measured, Automated Profile to Facilitate High Throughput Phenotyping

Award Number: R01GM139891
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 01/01/2021
PERIOD OF PERFORMANCE END DATE: 11/30/2025

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PheMAP: Measured, Automated Profile to Facilitate High Throughput Phenotyping - Electronic health records (EHRs) are a powerful and efficient tool for biological discovery globally. However, a vital step for EHR-based research is valid, accurate, and reliable phenotyping (i.e., correctly identifying individuals with a particular trait of interest). Conventional approaches to phenotyping are ad hoc, domain expert dependent, rule-based, and usually specific to EHR environments. However, each requires an extensive investment of time and resources to develop due to the heterogeneity, complexity, inaccuracy, and frequent fragmentation of EHRs. The lack of general, automatic, and portable approaches to enable accurate high- throughput phenotyping is a critical barrier that hampers our ability to leverage valuable clinical data in EHRs for better healthcare. We propose a new generalizable high-throughput approach: Phenotyping by Measured, Automated Profile (PheMAP) that we have developed from public resources and will further refine and implement across various EHRs. We recognize that mass information about phenotypes is often described in significant detail and continuedly accumulated within publicly available resources (e.g., MedlinePlus and Wikipedia). We hypothesize this information can be retrieved, filtered, organized, measured, and formalized into standard EHR phenotype profiles. Indeed, we have used such an ensemble approach to integrate four generalizable online medication resources (e.g., SIDER and RxNorm) to create MEDI--a resource linking 2,136 medications and 13,304 indications. In preliminary studies, we extended this strategy to phenotyping and created a prototype PheMAP. For each phenotype, we identified relevant clinical concepts and weighted each based on its importance to the phenotype. We then mapped all associated concepts to commonly-used clinical terminologies. Our preliminary studies showed an average consistency of 98.6%±0.8% between our early-stage PheMAP and three validated eMERGE algorithms (Type 2 Diabetes, dementia, and hypothyroidism). We seek support to refine and optimize PheMAP and develop tools to allow researchers to implement PheMAP efficiently in different EHRs. This will allow researchers to rapidly and accurately determine the status of thousands of phenotypes for millions of individuals with minimal human intervention. Since PheMAP is created using independent resources that are more generalizable than a local clinical dataset, the implementation will generate more consistent outcomes in different EHRs for large-scale analyses.The work we propose is a necessary step toward being able to conduct high-throughput genome-wide and phenome-wide association analyses (GWASs and PheWASs). We will use data from multiple biobanks to accomplish these tasks. Specifically, we will achieve the following goals in this grant: 1.refine PheMAP and conduct large-scale validation, 2. implement PheMAP and perform representative GWASs and PheWASs, 3. Use PheMAP to conduct GWASs for unstudied or understudied diseases and phenotypes, and 4. Share PheMAP to facilitate research using EHRs.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = -$17,188 )
2026	2024	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	000	4	5/20/2026	NON-COMPETING CONTINUATION	-$17,188
														Subtotal = -$17,188

Issue Date FY: 2024 ( Subtotal = $432,500 )
2024	2024	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	000	4	11/21/2023	NON-COMPETING CONTINUATION	$389,250
2024	2024	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	001	4	6/17/2024	NON-COMPETING CONTINUATION	$43,250
														Subtotal = $432,500

Issue Date FY: 2023 ( Subtotal = $432,500 )
2023	2023	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	000	3	12/20/2022	NON-COMPETING CONTINUATION	$389,250
2023	2023	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	001	3	2/21/2023	NON-COMPETING CONTINUATION	$43,250
														Subtotal = $432,500

Issue Date FY: 2022 ( Subtotal = $432,500 )
2022	2022	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	001	2	6/29/2022	NON-COMPETING CONTINUATION	$43,252
2022	2022	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	000	2	11/23/2021	NON-COMPETING CONTINUATION	$389,248
														Subtotal = $432,500

Issue Date FY: 2021 ( Subtotal = $432,500 )
2021	2021	VANDERBILT UNIVERSITY MEDICAL CENTER	1161 21ST AVE S STE D3300 MCN	NASHVILLE	TN	37232	DAVIDSON	USA	Biomedical Research and Research Training	000	1	12/23/2020	NEW	$432,500
														Subtotal = $432,500

Grand Total All Awards = $1,712,812

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PheMAP: Measured, Automated Profile to Facilitate High Throughput Phenotyping

Award Number: R01GM139891

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 01/01/2021

PERIOD OF PERFORMANCE END DATE: 11/30/2025

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