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PG4AD: Scaling up pangenome graph for genotyping complex structural variations for Alzheimer's disease genetics

Award Number: U01AG098387
ORGANIZATION: NATIONAL INSTITUTE ON AGING
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 03/01/2026
PERIOD OF PERFORMANCE END DATE: 02/28/2029

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PG4AD: Scaling up pangenome graph for genotyping complex structural variations for Alzheimer's disease genetics - PROJECT SUMMARY/ABSTRACT The Human Pangenome Reference Consortium (HPRC) has built a tremendously valuable resource of high- quality human pangenome reference assemblies of individuals and their corresponding pangenome graph that greatly reduced reference biases. However, uptake and utilization of the HPRC pangenome resources by the human genetics community for the analysis of complex structural variations (SV) remains limited. Most existing SV methods are based on existing catalogs of known SVs represented in linear reference-based VCF files, and thus still suffer from reference biases. Lack of methods and tools for better leveraging the reference pangenome graph is a critical gap that hinders the realization of the full potential of pangenome-enabled genetic studies, including those for Alzheimer’s disease (AD) and other complex traits. We will address these challenges by developing path-based algorithms for genotyping complex SVs and extending the pangenome reference using AD genetics data. We will translate our expertise and experience in developing positional Burrows-Wheeler transform (PBWT) algorithms to its pangenome counterpart, the GBWT (Graph Burrows- Wheeler transform), a proven data structure already in use in the HPRC consortium. First, we will develop GBWT-block-based methods for identifying frequent and long SV haplotype in pangenome graphs for genotyping and panel smoothing. Second, we will develop SV genotype imputation methods based on pangenome GBWT. Third, we will apply the developed methods to the Alzheimer’s disease sequencing project (ADSP) data to empower AD genetics research. We will build PG4ADSP, an expanded approximate reference pangenome panel and its PBWT from ADSP data. We will identify frequent and long SV haplotypes in ADSP and conduct SV-GWAS to identify SV loci associated with AD risks. Finally, we will rigorously evaluate our methods and build software for broad use. Successful completion of this project will broaden the adoption of HPRC resources by the human genetics and AD genetics community.


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: 2026 ( Subtotal = $556,359 )
2026	2026	UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON	7000 FANNIN ST FL 9	HOUSTON	TX	77030	HARRIS	USA	Aging Research	000	1	2/17/2026	NEW	$556,359
														Subtotal = $556,359

Grand Total All Awards = $556,359

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PG4AD: Scaling up pangenome graph for genotyping complex structural variations for Alzheimer's disease genetics

Award Number: U01AG098387

ORGANIZATION: NATIONAL INSTITUTE ON AGING

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 03/01/2026

PERIOD OF PERFORMANCE END DATE: 02/28/2029

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