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Calling germline and mosaic variants from long genomic and RNA-seq reads

Award Number: R01HG014175
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2025
PERIOD OF PERFORMANCE END DATE: 06/30/2029

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Calling germline and mosaic variants from long genomic and RNA-seq reads - PROJECT SUMMARY The rapidly reduced cost and increased base quality of long sequence reads enable the accurate calling of germline and mosaic sequence variations thanks to phasing and the power to resolve repetitive regions. Although multiple callers have been developed for long-read variant calling, tools are still missing for several important applications such as variant calling from long RNA-seq reads, mosaic small variant calling for long reads and accurate mosaic structural variant calling. In addition, existing tools often target one type of variants and treat small variants, structural variants and phasing as separate problems. This reduces the power of long reads and makes the current tools difficult to use for biologists. Here, we plan to address these issues with three proposals: (1) developing a variant caller for calling germline variants, mosaic mutations and RNA editing events from long RNA-seq reads; (2) improving the accuracy of mosaic and somatic structural variant calling using pangenome graphs and the de novo assembly of the normal bulk sample; (3) jointly calling germline/mosaic small/structural variants from long genomic reads by using integrated phasing and local realignment or reassembly methods. Upon completion, this proposal will result in new computational tools for tasks not achievable with current methods and for the calling of most types of variants to higher accuracy.


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 = $501,618 )
2025	2025	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	000	1	8/15/2025	NEW	$501,618
														Subtotal = $501,618

Grand Total All Awards = $501,618

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Calling germline and mosaic variants from long genomic and RNA-seq reads

Award Number: R01HG014175

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/01/2025

PERIOD OF PERFORMANCE END DATE: 06/30/2029

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