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Haplotype-aware models of gene and isoform expression with application to genetic studies of disease in diverse populations

Award Number: R01GM140287
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: 03/01/2021
PERIOD OF PERFORMANCE END DATE: 11/30/2024

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Haplotype-aware models of gene and isoform expression with application to genetic studies of disease in diverse populations - Project Summary In recent years, there has been a deluge of data from genome-wide functional assays. Rapid expansion of computational techniques for mapping genetic correlates of intermediate molecular traits, such as gene expression, has offered opportunities to explore molecular mechanisms that underlie disease susceptibility. Here we will develop mechanistically justified statistical methods that enable allele-specific assessment of regulatory activity in individual genomes. We hypothesize that incorporating the dosage modifying effect of regulatory alleles into genetic association analyses will enhance the resolution of the current genotype-phenotype maps, and allow for a more refined mapping of the underlying biological mechanisms. Our proposal is organized into the following aims: Aim1: To derive biologically interpretable effect sizes for regulatory variants and to enable allele-specific prediction of gene and isoform dosage, we will develop haplotype-aware models of genetic regulatory variation and apply them to large-scale reference transcriptome datasets. Aim2: To enhance the resolution of the current genotype-phenotype maps, we will develop genetic association methods that incorporate expected allele dosages for genes and transcript isoforms and apply them to large biobank and GWAS data. Aim3: To improve generalizability of genetic association signals to understudied populations, we will develop genetic association methods that incorporate population-specific regulatory architecture of genes and transcript isoforms.


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 = $723,118 )
2024	2024	SEATTLE CHILDREN'S HOSPITAL	4800 SAND POINT WAY NE	SEATTLE	WA	98105	KING	USA	Biomedical Research and Research Training	005	4	2/9/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$762,351
2024	2024	SEATTLE CHILDREN'S HOSPITAL	4800 SAND POINT WAY NE	SEATTLE	WA	98105	KING	USA	Biomedical Research and Research Training	006	4	4/3/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$0
2024	2024	SEATTLE CHILDREN'S HOSPITAL	4800 SAND POINT WAY NE	SEATTLE	WA	98105	KING	USA	Biomedical Research and Research Training	007	4	5/15/2024	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$72,312
2024	2024	SEATTLE CHILDREN'S HOSPITAL	4800 SAND POINT WAY NE	SEATTLE	WA	98105	KING	USA	Biomedical Research and Research Training	002	4	11/17/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$650,806
2024	2023	SCRIPPS RESEARCH INSTITUTE	10550 N TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	004	3	2/9/2024	NON-COMPETING CONTINUATION	-$624,727
2024	2023	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	001	3	11/17/2023	NON-COMPETING CONTINUATION	$0
2024	2023	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	3	10/11/2023	NON-COMPETING CONTINUATION	$0
2024	2022	SCRIPPS RESEARCH INSTITUTE	10550 N TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	003	2	2/9/2024	NON-COMPETING CONTINUATION	-$137,624
														Subtotal = $723,118

Issue Date FY: 2023 ( Subtotal = $624,727 )
2023	2023	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	3	11/28/2022	NON-COMPETING CONTINUATION	$562,255
2023	2023	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	001	3	3/28/2023	NON-COMPETING CONTINUATION	$62,472
														Subtotal = $624,727

Issue Date FY: 2022 ( Subtotal = $627,102 )
2022	2022	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	001	2	8/3/2022	NON-COMPETING CONTINUATION	$62,710
2022	2022	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	2	12/13/2021	NON-COMPETING CONTINUATION	$564,392
														Subtotal = $627,102

Issue Date FY: 2021 ( Subtotal = $836,952 )
2021	2021	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	001	1	8/27/2021	SUPPLEMENT FOR EXPANSION	$179,726
2021	2021	SCRIPPS RESEARCH INSTITUTE, THE	10550 NORTH TORREY PINES RD	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	1	2/26/2021	NEW	$657,226
														Subtotal = $836,952

Grand Total All Awards = $2,811,899

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Haplotype-aware models of gene and isoform expression with application to genetic studies of disease in diverse populations

Award Number: R01GM140287

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: 03/01/2021

PERIOD OF PERFORMANCE END DATE: 11/30/2024

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