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New methods for studying thousands of complete human and vertebrate genomes

Award Number: R01HG014490
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/26/2025
PERIOD OF PERFORMANCE END DATE: 06/30/2029

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New methods for studying thousands of complete human and vertebrate genomes - PROJECT SUMMARY / ABSTRACT We propose to advance comparative genomics through three interconnected aims. In Aim 1, we will scale genome alignment and analysis capabilities to accommodate the rapidly growing number of available vertebrate genomes, projected to reach ~10,000 species within four years. We propose developing a highly scalable, automated pipeline for species-tree construction from raw genome assemblies, reworking the genome-based HAL format, and introducing a new column-based alignment format (TAF) to facilitate efficient representation and analysis of large-scale alignments. To demonstrate these improvements, we will create and share the deepest ever vertebrate alignments, focusing on predictions of evolutionary selection. In Aim 2, we address the challenge of aligning telomere-to-telomere (T2T) human genome assemblies. We will develop novel repeat-aware alignment algorithms and graph models to enable a more complete alignment, starting with human centromeres and extending to other heterochromatic sequence. We will integrate these methods into our pangenome construction process to facilitate T2T alignment within the human pangenome. Aim 3 focuses on disentangling the genetics of the 1q21.1 region, which is associated with various neurodevelopmental disorders, as an exemplar of a difficult segmental duplication. We will analyze T2T ape and human genomes to create a comprehensive 1q21 pangenome, develop efficient methods for high-resolution genome reconstruction of patient-derived cell lines with 1q21.1 copy number variations, and test the functional consequences of identified genetic alterations using hiPSC-derived cerebral cortex organoids. By combining advanced genomic analysis, efficient sequencing protocols, and functional studies, we aim to significantly advance our understanding of genome evolution, improve our ability to analyze complex genomic regions, and potentially lead to improved diagnostics and therapeutic strategies for neurodevelopmental disorders associated with the 1q21.1 region. Together, these advancements will empower the community to conduct more comprehensive comparative genomic analyses, leading to a deeper understanding of genome evolution across vertebrates and humans and its implications for human health.


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 = $610,815 )
2026	2026	UNIVERSITY OF CALIFORNIA SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	2	8/14/2026	NON-COMPETING CONTINUATION	$610,815
														Subtotal = $610,815

Issue Date FY: 2025 ( Subtotal = $633,116 )
2025	2025	UNIVERSITY OF CALIFORNIA SANTA CRUZ	1156 HIGH ST	SANTA CRUZ	CA	95064	SANTA CRUZ	USA	Human Genome Research	000	1	9/26/2025	NEW	$633,116
														Subtotal = $633,116

Grand Total All Awards = $1,243,931

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New methods for studying thousands of complete human and vertebrate genomes

Award Number: R01HG014490

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/26/2025

PERIOD OF PERFORMANCE END DATE: 06/30/2029

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