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Scalable methods for the characterization and analysis of families in large genomic datasets

Award Number: R35GM133805
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: 09/01/2019
PERIOD OF PERFORMANCE END DATE: 07/31/2024

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Scalable methods for the characterization and analysis of families in large genomic datasets - PROJECT SUMMARY Numerous studies of common genetic diseases in humans are now analyzing very large genomic datasets with information from up to 500,000 individuals. These large studies pose challenges to traditional analysis approaches—especially in terms of computational runtime scaling—but also afford opportunities for reﬁned in- ference, and necessitate the development of new computational methods. The program of research we will undertake focuses on the emerging opportunities of widespread relatedness in large studies. We are currently developing a method to efﬁciently infer identical by descent (IBD) sharing using an algorithm that does not require phased data. We are also ﬁnalizing a method that distinguishes among second degree relative types— half-sibling, avuncular, and grandparent-grandchild pairs. Building on these models, we will develop novel, efﬁcient methods to: (1) identify pedigrees that deﬁne close relationships within large datasets; (2) fundamen- tally advance genome-wide association studies (GWAS) by inferring the genomes of parents of sets of siblings and other relatives; (3) leverage recombination patterns in men and women to infer the parent-of-origin of hap- lotypes in a set of close relatives; and (4) infer haplotypes by jointly modeling both family- and population-level structure. Notably, no method we are aware of enables the reconstruction of parent haplotypes without parent data, and this will enable improved GWAS power by utilizing individuals for whom more complete health history information is known. Furthermore, few studies of parent-of-origin associations have been done in humans be- cause of the difﬁculty of obtaining parent data, but we will perform these analyses in large studies even without parent data. All software will be made freely available to the public and distributed under open source software licenses.


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 = $0 )
2025	2023	23ANDME INC	223 N MATHILDA AVE	SUNNYVALE	CA	94086	SANTA CLARA	USA	Biomedical Research and Research Training	000	5	3/25/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2021	CORNELL UNIVERSITY	341 PINE TREE RD	ITHACA	NY	14850	TOMPKINS	USA	Biomedical Research and Research Training	000	3	2/2/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $266,646 )
2023	2023	23ANDME INC	223 N MATHILDA AVE	SUNNYVALE	CA	94086	SANTA CLARA	USA	Biomedical Research and Research Training	000	5	8/2/2023	NON-COMPETING CONTINUATION	$266,646
														Subtotal = $266,646

Issue Date FY: 2022 ( Subtotal = $266,646 )
2022	2022	23ANDME INC	223 N MATHILDA AVE	SUNNYVALE	CA	94086	SANTA CLARA	USA	Biomedical Research and Research Training	001	4	9/19/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$266,646
2022	2021	CORNELL UNIVERSITY	341 PINE TREE RD	ITHACA	NY	14850	TOMPKINS	USA	Biomedical Research and Research Training	000	3	9/19/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $266,646

Issue Date FY: 2021 ( Subtotal = $357,730 )
2021	2021	CORNELL UNIVERSITY	341 PINE TREE RD	ITHACA	NY	14850	TOMPKINS	USA	Biomedical Research and Research Training	000	3	8/4/2021	NON-COMPETING CONTINUATION	$357,730
														Subtotal = $357,730

Issue Date FY: 2020 ( Subtotal = $357,730 )
2020	2020	CORNELL UNIVERSITY	341 PINE TREE RD	ITHACA	NY	14850	TOMPKINS	USA	Biomedical Research and Research Training	000	2	8/4/2020	NON-COMPETING CONTINUATION	$357,730
														Subtotal = $357,730

Issue Date FY: 2019 ( Subtotal = $357,730 )
2019	2019	CORNELL UNIVERSITY, INC	373 PINE TREE RD	ITHACA	NY	14850	TOMPKINS	USA	Biomedical Research and Research Training	000	1	8/27/2019	NEW	$357,730
														Subtotal = $357,730

Grand Total All Awards = $1,606,482

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Scalable methods for the characterization and analysis of families in large genomic datasets

Award Number: R35GM133805

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: 09/01/2019

PERIOD OF PERFORMANCE END DATE: 07/31/2024

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