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Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes

Award Number: U24HG007497
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes - PROJECT SUMMARY The characterization of the full spectrum of genetic variation from whole-genome sequencing (WGS) data is essential for genome research and precision medicine. Recent technological advances have led to substantially improved sensitivity in detecting and characterizing structural variants (SVs) and the generation of highly contiguous phased genomes; however, some genomic regions (e.g., short arms of acrocentric chromosomes, pericentromeric regions and regions containing complex SVs) remain extremely difficult to accurately assemble and genotype. The Investigators of this project are well qualified to tackle this problem. They have worked together for well over a decade to make substantial advances toward comprehensive SV discovery and improved genome assemblies by combining data from multiple technologies and developing new tools for analyzing and integrating these data. This competing renewal for a community resource has four aims. In Aim 1, computational methods will be developed to optimize SV discovery through accurate genome assembly - in the absence of parental sequencing data - and will be applied to 426 samples from all 26 diverse populations of the 1000 Genomes Project (1kGP) where long-read sequencing data are available from both the Human Genome Structural Variation Consortium (HGSVC) and Human Pangenome Reference Consortium (HPRC) efforts. Aim 2 will develop pipelines that will provide the most comprehensive, rapid and low-cost genotyping of SVs in short-read datasets. This will be made possible from the incorporation of pooled Strand-seq data and inversions in 1000 individuals from the 1kGP. Aim 3 will develop pipelines and resources for SV imputation, genotyping, and functional characterization that can be used for future association studies. Proof-of-principle studies will be conducted on the 1kGP, and an autism spectrum disorder (ASD) cohort. Aim 4 will develop a fine-resolution SV resource containing precise breakpoint information and biologically relevant annotations. New visualization and analytical tools will be built into the International Genome Sample Resource (IGSR), making the data and tools acquired from this project widely available and in a manner that preserves the complexities of SVs. As a part of Aim 4, we also outline a plan to provide dedicated user training for our tools and datasets in different geographical locations and multiple times a year to maximize research community awareness and adoption. Taken together, our community resource project will provide valuable methods and tools for benchmarking SV discovery and genotyping across WGS datasets in the human genomic research and clinical domains.


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	2024	JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	001	9	3/4/2025	COMPETING CONTINUATION	$139
2025	2022	JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	8	3/4/2025	NON-COMPETING CONTINUATION	-$139
														Subtotal = $0

Issue Date FY: 2024 ( Subtotal = $1,888,152 )
2024	2024	JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	9	5/28/2024	COMPETING CONTINUATION	$1,888,152
														Subtotal = $1,888,152

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2022	JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	8	8/7/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $2,695,990 )
2022	2022	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	8	7/21/2022	NON-COMPETING CONTINUATION	$2,695,990
														Subtotal = $2,695,990

Issue Date FY: 2021 ( Subtotal = $2,695,991 )
2021	2021	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	001	7	6/2/2021	NON-COMPETING CONTINUATION	$2,695,991
2021	2020	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	6	3/15/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,695,991

Issue Date FY: 2020 ( Subtotal = $2,695,991 )
2020	2020	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	6	6/12/2020	NON-COMPETING CONTINUATION	$2,695,991
														Subtotal = $2,695,991

Issue Date FY: 2019 ( Subtotal = $2,867,579 )
2019	2019	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	001	5	9/13/2019	COMPETING CONTINUATION	$0
2019	2019	THE JACKSON LABORATORY	600 MAIN ST	BAR HARBOR	ME	04609	HANCOCK	USA	Human Genome Research	000	5	7/31/2019	COMPETING CONTINUATION	$2,867,579
														Subtotal = $2,867,579

Grand Total All Awards = $12,843,703

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Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes

Award Number: U24HG007497

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

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