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The Association to Function Knowledge Portal: a genomic data resource for translating GWAS associations to biological effects

Award Number: U24HG011453
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Abstract Genome wide association studies (GWAS) have produced associations between many thousands of genetic variants and many hundreds of traits. The “functional effects” of most associations, however, have not yet been elucidated – that is, the causal variants and effector genes responsible for them, and the tissues and pathways through which they act, remain largely unknown. Over the past few years, three classes of genomic data have arisen for inferring the functional effects of GWAS associations: summary association statistics (effect sizes and p-values for associations between SNPs and traits), genomic annotations (assays of regulatory activity and genomic functional elements), and bioinformatic methods (computationally predicted functional effects). We argue that two gaps exist in the current resources that aggregate these data: first, no current resource aims to comprehensively curate and catalog all that is known, and all data or methods that could help predict, the functional effects of GWAS associations; second, existing resources are developed with (at best) limited involvement from experts who either originally generated the genomic data and/or understand how to best use them. We propose to address these gaps by building a new genomic community resource – the Association to Function Knowledge Portal (A2FKP) – using a general software platform we initially developed for type 2 diabetes. Our approach makes use of a key innovation to build a resource that is both high quality and comprehensive: we collaborate with disease expert communities to build dedicated knowledge portals for them, motivating them to contribute their data and expertise, and we then integrate these data alongside those of other communities, providing users with access a comprehensive resource. Specific aim 1 addresses gaps in the comprehensiveness and quality of the data aggregated by current resources regarding the functional effects of GWAS associations. It will establish and manage collaborations with a wide range of disease, data, and method experts, and then work with these communities to identify, aggregate, and curate data for 11 classes of disease. Specific aim 2 addresses gaps in current schemas and software platforms for the myriad types of data used for predicting the functional effects of GWAS associations. It will build pipelines for processing genetic and genomic datasets through bioinformatic methods for predicting the functional effects of GWAS associations, apply these pipelines to data aggregated in Aim 1, and transform their outputs to relationships among entities in a knowledge graph. The goal of specific aim 3 is to provide users with direct and visual access to the resources aggregated or computed in Aims 1 and 2. It will develop REST APIs and web portals for querying and visualizing data within the A2FKP. Significance: The project would produce a high quality and comprehensive genomic resource of data and methods for predicting the functional effects of GWAS associations. Easy access to such a resource will accelerate the pace by which GWAS associations can be translated to insights into complex disease.


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: 2024 ( Subtotal = $0 )
2024	2023	THE BROAD INSTITUTE, INC	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	3	3/25/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $684,620 )
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	001	3	6/30/2023	NON-COMPETING CONTINUATION	$684,620
2023	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	2	11/8/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $684,620

Issue Date FY: 2022 ( Subtotal = $684,283 )
2022	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	2	7/29/2022	NON-COMPETING CONTINUATION	$684,283
														Subtotal = $684,283

Issue Date FY: 2021 ( Subtotal = $710,735 )
2021	2021	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	1	9/16/2021	NEW	$710,735
														Subtotal = $710,735

Grand Total All Awards = $2,079,638

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The Association to Function Knowledge Portal: a genomic data resource for translating GWAS associations to biological effects

Award Number: U24HG011453

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

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