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Development of a system to protect and concentrate large DNA for genome analysis

Award Number: R15GM155799
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/06/2024
PERIOD OF PERFORMANCE END DATE: 07/31/2027

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Development of a system to protect and concentrate large DNA for genome analysis - PROJECT SUMMARY/ABSTRACT Structural variation alters approximately 3.4 times more base pairs than point mutations within the human genome. Structural variations, such as amplification, deletion, inversions, or translocations, alter genes and non-genic regions in several different diseases, such as Huntington’s, Parkinson’s, Charcot-Marie-Tooth, cancer, chromoplexia, and undiagnosed genetic diseases. Long molecule read lengths are beneficial for studying complex disease genetics. Many diseases involve multiple genetic variants and regulatory elements, and longer reads provide a more comprehensive view of the genomic regions associated with disease susceptibility, enabling the identification of variants and potential disease mechanisms. A significant obstacle in the field is DNA length prior to sequencing and physical mapping. Longer molecules are necessary to span large variations, with enough unique information on each side to determine the size and genetic information within the variation. Our long-term goal is to develop a system to protect and concentrate huge DNA molecules for physical mapping or sequencing systems to analyze genomes for structural variations. The overall objective of this application is to protect and concentrate whole S. cerevisiae and E. coli chromosomes. Once the system is tested with S. cerevisiae and E. coli, this system will be used for more complex samples. Our central hypothesis is that sizeable DNA molecules can be protected in an inverted insert and concentrated in a 3D- printed device with an acrylamide roadblock. The rationale for this project is to create a method to protect and concentrate huge DNA molecules since no available system currently exists. To accomplish this, we put forth the following specific aims: 1) Develop an inverted insert to protect DNA during cell lysis. 2) Develop a roadblock to concentrate chromosomal DNA. This project is innovative as it a) utilizes 3D printing to create a device and allows rapid modifications to the device, b) uses a roadblock to slow down the progression of DNA so DNA can be concentrated in the solution, c) protects DNA inside the inverted insert during cell lysis, so the DNA remains full length, and d) develops a system to protect and concentrate large DNA molecules (200 kb - 5 Mb). The significance of this project is devising a system to concentrate large DNA molecules that can span large variations within a genome with enough unique information on either side of the variation to discern variations associated with different diseases, enhance sequencing efficiency, improve genome assembly, and aid in phasing and haplotype reconstruction.


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 = $0 )
2026	2024	UNIVERSITY OF NEBRASKA	905 W 25TH ST	KEARNEY	NE	68849	BUFFALO	USA	Biomedical Research and Research Training	000	1	2/23/2026	NEW	$0
														Subtotal = $0

Issue Date FY: 2024 ( Subtotal = $394,857 )
2024	2024	UNIVERSITY OF NEBRASKA	905 W 25TH ST	KEARNEY	NE	68849	BUFFALO	USA	Biomedical Research and Research Training	000	1	8/6/2024	NEW	$394,857
														Subtotal = $394,857

Grand Total All Awards = $394,857

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Development of a system to protect and concentrate large DNA for genome analysis

Award Number: R15GM155799

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/06/2024

PERIOD OF PERFORMANCE END DATE: 07/31/2027

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