Sunday, June 29, 2025 6/29/2025

Stanford Mendelian Genomics Research Center

Award Number: U01HG011762
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: 07/15/2021
PERIOD OF PERFORMANCE END DATE: 04/30/2026

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Stanford Mendelian Genomics Research Center - Rapid advances in genomics have ushered in new opportunities for Mendelian disease discovery and diagnosis. In the last decade, exome and genome sequencing have moved from the research domain to clinical practice. These approaches have identified new disease genes and causative variants for ~30% of individuals suffering from a rare genetic disease. We believe that the systematic application of promising new genomics assays coupled with innovative computational approaches will foster discovery benefitting the 70% of symptomatic individuals without a genetic diagnosis. To this end we will apply long-read whole genome sequencing, RNA-sequencing, epigenomics assays, metabolomics and targeted in vitro and in vivo assays to evaluate a cohort of undiagnosed individuals suspected to have a Mendelian disorder. Our approach will be augmented through the development and application of computational strategies enabling improved gene and phenotype matching, integrative multi-omics analysis, and variant interpretation. This work is expected to establish a new frontier in Mendelian disease discovery. Our Mendelian Genomics Research Center (MRGC) team has developed key prior expertise and leadership in the use of diverse state-of-the-art experimental and computational methods for the diagnosis and discovery of Mendelian disorders. We hypothesize that the next phase of Mendelian genomics research will be defined by assessing and deploying the most effective ‘omics’ strategies. We propose that ongoing and iterative integration of functional genomics data into the translational genomics toolkit will significantly increase discovery of new gene and variant disease associations beyond the capabilities of DNA-sequencing assays alone. To facilitate this, we will comprehensively study 400 individuals and their immediate family members (N= 900 total) with Mendelian disease where exome sequencing has not yielded a genetic diagnosis. These represent a select cohort of hard to solve cases intractable to DNA sequencing to date. In Aim 1, individuals recruited into the study will undergo short-read and long-read whole genome sequencing, RNA-seq, ATAC-seq and MethylC-seq across multiple commonly used cell/tissue types as well as metabolomics and lipidomics assays. This dataset will define a holistic view of emerging genomics approaches for Mendelian disease diagnosis and facilitate evaluation of the relative merits of each approach. In Aim 2, we focus on computational innovations that will improve integration of these multi-omics data in gene and variant interpretation by integrating functional genomics outliers and advanced statistical learning approaches. These methods will be applicable broadly across the MGRC and the world. In Aim 3, we apply state-of-the-art targeted approaches including massively-parallel reporter assays, induced-pluripotent stem cell functional genomics, CRISPR screens for modifier genes and engineered mouse models to detect and validate novel causal variants and genes. Work at our site will potentiate the broad impact of the MGRC by providing a platform for functional genomics research, validation and diagnosis in Mendelian 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: 2025 ( Subtotal = $2,781,357 )
2025	2025	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	002	5	5/13/2025	NON-COMPETING CONTINUATION	$2,781,357
2025	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	4	4/28/2025	NON-COMPETING CONTINUATION	$0
2025	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	4	3/13/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,781,357

Issue Date FY: 2024 ( Subtotal = $2,932,868 )
2024	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	003	4	8/9/2024	SUPPLEMENT FOR EXPANSION	$154,400
2024	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	4	4/23/2024	NON-COMPETING CONTINUATION	$2,551,654
2024	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	002	4	5/29/2024	NON-COMPETING CONTINUATION	$226,814
2024	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	3	11/24/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,932,868

Issue Date FY: 2023 ( Subtotal = $2,838,036 )
2023	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	3	5/5/2023	NON-COMPETING CONTINUATION	$2,838,036
														Subtotal = $2,838,036

Issue Date FY: 2022 ( Subtotal = $2,840,303 )
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	001	2	5/9/2022	NON-COMPETING CONTINUATION	$2,840,303
2022	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	1	11/19/2021	NEW	$0
														Subtotal = $2,840,303

Issue Date FY: 2021 ( Subtotal = $2,836,860 )
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Human Genome Research	000	1	7/15/2021	NEW	$2,836,860
														Subtotal = $2,836,860

Grand Total All Awards = $14,229,424

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Stanford Mendelian Genomics Research Center

Award Number: U01HG011762

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: 07/15/2021

PERIOD OF PERFORMANCE END DATE: 04/30/2026

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