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The construction and utility of reference pan-genome graphs

Award Number: U01HG010961
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: 02/04/2023
PERIOD OF PERFORMANCE END DATE: 02/29/2024

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The construction and utility of reference pan-genome graphs - PROJECT SUMMARY The current human reference genome, GRCh38, plays a central role in medical and population human genetics. It primarily models a single human individual and is missing hundreds of thousands of large structural variations segregating in the population. This underrepresentation of genetic diversity leads to various artifacts in data analysis and significantly hampers our understanding of the functional and medical relevance of these large human variations, which may collectively have pervasive impact. To address this issue, we will extend our previous work on sequence graphs and alignment algorithms and construct a pan-genome reference graph from hundreds of long-read human assemblies that more completely represent genetic diversity. Specifically, we will (1) design a reference graph model with a stable coordinate system compatible with GRCh38 and develop toolkits and libraries to interact with this model; (2) develop minimizer-based sequence-to-graph alignment algorithms for short and long sequences; (3) incrementally construct a reference graph by mapping assemblies to an existing graph and updating the graph; and (4) develop a graph-based genotyping algorithm and apply it to short-read based projects to call structural variations missed by the current pipelines. Upon completion, the proposed project could replace the current practices based on a linear genome and will enable the profiling and study of complex human variations missed in most current research.


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 = -$310,773 )
2024	2023	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	000	3	7/22/2024	SUPPLEMENT FOR EXPANSION	-$310,773
														Subtotal = -$310,773

Issue Date FY: 2023 ( Subtotal = $801,988 )
2023	2023	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	002	3	6/26/2023	SUPPLEMENT FOR EXPANSION	$801,988
2023	2023	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	003	3	7/21/2023	SUPPLEMENT FOR EXPANSION	$0
2023	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	3	6/23/2023	NON-COMPETING CONTINUATION	$0
2023	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	3	12/6/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $801,988

Issue Date FY: 2022 ( Subtotal = $800,001 )
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	002	3	5/2/2022	NON-COMPETING CONTINUATION	$80,003
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	3	3/9/2022	NON-COMPETING CONTINUATION	$719,998
2022	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	2	1/19/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $800,001

Issue Date FY: 2021 ( Subtotal = $800,000 )
2021	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	2	3/29/2021	NON-COMPETING CONTINUATION	$800,000
														Subtotal = $800,000

Issue Date FY: 2020 ( Subtotal = $800,000 )
2020	2020	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	1	2/20/2020	NEW	$800,000
														Subtotal = $800,000

Grand Total All Awards = $2,891,216

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The construction and utility of reference pan-genome graphs

Award Number: U01HG010961

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: 02/04/2023

PERIOD OF PERFORMANCE END DATE: 02/29/2024

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