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Revealing new short tandem repeat variation in the human population across sequencing technologies: towards rare disease diagnosis and discovery

Award Number: R00HG012796
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/07/2024
PERIOD OF PERFORMANCE END DATE: 05/31/2027

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Revealing new short tandem repeat variation in the human population across sequencing technologies: towards rare disease diagnosis and discovery - Abstract Short tandem repeats (STRs) are 1–6 bp repetitive and highly polymorphic DNA sequences. Expansions in dozens of STRs are associated with genetic disease. However, STRs are challenging to sequence and interpret, meaning that individuals with STR disease often go undiagnosed. In rare disease studies, it is now standard to prioritize candidate pathogenic SNVs, indels and SVs by excluding variants that have high allele frequencies in population-scale databases such as gnomAD. However, there is no such genome-wide database available for large STR expansions. I will produce a publicly available STR variation community resource, stratified by ancestry, to enable prioritization of candidate pathogenic STR expansions. Long-read sequencing technologies from PacBio and Nanopore have been heralded as the solution to accurately genotype long repeats because their reads can span the repetitive region. However, there are several challenges when genotyping STRS in long-reads that are not adequately addressed by existing approaches. I will develop a method to genotype STRs from long-read Oxford Nanopore sequencing data. It will discover informative reads using a combination of alignment and identifying repetitive regions in reads. It will then infer the genotype by integrating evidence from multiple reads, informed by my investigation of biases in these technologies. Drawing together new short and long-read computational approaches to calling STR expansions, and my population-scale STR catalog, with an emphasis on diverse and under-served populations, this proposal will establish a genetic diagnosis for hundreds of patients, while searching for new STR disease loci. I will analyze patient cohorts enriched for phenotypes associated with STRs from the UDN, University of Washington, Harry Perkins Institute of Medical Research and Children’s Mercy Hospital to solve cases and discover new disease- associated STRs in both short and long-read sequencing.


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 = $503,449 )
2025	2025	THE REGENTS OF THE UNIV. OF COLORADO	13001 E 17TH PL STE F428	AURORA	CO	80045	ADAMS	USA	Human Genome Research	001	4	8/26/2025	NON-COMPETING CONTINUATION	$249,000
2025	2025	THE REGENTS OF THE UNIV. OF COLORADO	13001 E 17TH PL STE F428	AURORA	CO	80045	ADAMS	USA	Human Genome Research	000	3	11/26/2024	EXTENSION WITH OR WITHOUT FUNDS	$249,000
2025	2024	THE REGENTS OF THE UNIV. OF COLORADO	13001 E 17TH PL STE F428	AURORA	CO	80045	ADAMS	USA	Human Genome Research	000	3	11/26/2024	EXTENSION WITH OR WITHOUT FUNDS	$5,449
														Subtotal = $503,449

Issue Date FY: 2024 ( Subtotal = $249,000 )
2024	2024	THE REGENTS OF THE UNIVERSITY OF COLORADO	13001 E 17TH PL STE F428	AURORA	CO	80045	ADAMS	USA	Human Genome Research	000	3	8/7/2024	EXTENSION WITH OR WITHOUT FUNDS	$249,000
														Subtotal = $249,000

Grand Total All Awards = $752,449

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Revealing new short tandem repeat variation in the human population across sequencing technologies: towards rare disease diagnosis and discovery

Award Number: R00HG012796

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/07/2024

PERIOD OF PERFORMANCE END DATE: 05/31/2027

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