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Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory code

Award Number: U01HG012069
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 05/01/2026
PERIOD OF PERFORMANCE END DATE: 05/31/2027

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Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory code - ABSTRACT A central challenge in human genomics is to interpret the regulatory functions of the noncoding genome, and to identify and interpret variants with regulatory functions. In this project we plan to leverage recent advances in experimental functional genomics (including single cell methods and high throughput perturbation methods) alongside recent progress in deep learning models of gene regulation, to make fundamental progress on these problems. We have assembled a team of investigators with diverse and complementary expertise – in deep learning, single-cell genomics, cellular QTLs and GWAS, and high throughput validations – to build, test, and implement predictive models for interpreting disease associations. Specifically, we aim to (1) Develop interpretable base-resolution deep-learning models for regulatory sequences; (2) Predict and validate cell type- specific effects of regulatory variants on molecular phenotypes and disease; (3) Collaborate with the IGVF Consortium to build nucleotide-level regulatory maps. Our ultimate goal in this project will be to create a nucleotide-resolution cis-regulatory map of the human genome to connect disease variants to functions and phenotypes, in diverse cell types, states, and spatial contexts.


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 = $702,605 )
2026	2026	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	5	8/21/2026	SUPPLEMENT FOR EXPANSION	$702,605
2026	2025	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	5	8/10/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $702,605

Issue Date FY: 2025 ( Subtotal = $712,816 )
2025	2025	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	5	7/16/2025	NON-COMPETING CONTINUATION	$712,816
														Subtotal = $712,816

Issue Date FY: 2024 ( Subtotal = $712,815 )
2024	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	4	6/5/2024	NON-COMPETING CONTINUATION	$712,815
														Subtotal = $712,815

Issue Date FY: 2023 ( Subtotal = $727,363 )
2023	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	3	6/5/2023	NON-COMPETING CONTINUATION	$727,363
														Subtotal = $727,363

Issue Date FY: 2022 ( Subtotal = $727,363 )
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	2	7/5/2022	NON-COMPETING CONTINUATION	$727,363
														Subtotal = $727,363

Issue Date FY: 2021 ( Subtotal = $352,213 )
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	1	8/24/2021	NEW	$352,213
														Subtotal = $352,213

Grand Total All Awards = $3,935,175

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Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory code

Award Number: U01HG012069

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 05/01/2026

PERIOD OF PERFORMANCE END DATE: 05/31/2027

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