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Methods for improving clinical diagnostic by detection, prediction, interpretation and prioritization of aberrant transcriptome variations

Award Number: R01LM013437
ORGANIZATION: NATIONAL LIBRARY OF MEDICINE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/03/2020
PERIOD OF PERFORMANCE END DATE: 07/31/2025

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Methods for improving clinical diagnostic by detection, prediction, interpretation and prioritization of aberrant transcriptome variations - The goal of this research program project is to develop methods to improve clinical diagnosis of children with rare Mendelian disorders. Even with the most advanced standard-of-care genetic test of exome sequencing (ES) diagnostic rate is still below 50%. One reason for this rate is that mutations in non-protein coding regions or those that are synonymous (code for the same protein) are generally discarded even though these could be deleterious due to their effect on the processing of RNA transcribed from the underlying gene. We propose 2 complementary methods to help improve clinical diagnosis: The first is “RNA-first”, where our algorithms suggest which clinically accessible tissue (CAT) to use for RNA sequencing, then compare the results to a larger pool of donors to detect which RNA processing variations may be deleterious. The second is a “DNA-first” approach where we develop “RNA splicing code” models that predict the effect of genetic variations on RNA processing in a given tissue of interest. The two approaches, “RNA-first” and “DNA-first”, will be combined into a clinical diagnostic pipeline at the Children Hospital of Philadelphia (CHOP) and applied to solve undiagnosed cases at CHOP and other centers, including the NIH’s Undiagnosed Disease Network (UDN).


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	2023	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT STREET	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Medical Library Assistance	000	4	12/18/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $339,916 )
2023	2023	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Medical Library Assistance	000	4	7/25/2023	NON-COMPETING CONTINUATION	$339,916
														Subtotal = $339,916

Issue Date FY: 2022 ( Subtotal = $339,881 )
2022	2022	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Medical Library Assistance	000	3	8/1/2022	NON-COMPETING CONTINUATION	$339,881
														Subtotal = $339,881

Issue Date FY: 2021 ( Subtotal = $346,597 )
2021	2021	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Medical Library Assistance	000	2	7/15/2021	NON-COMPETING CONTINUATION	$346,597
														Subtotal = $346,597

Issue Date FY: 2020 ( Subtotal = $347,736 )
2020	2020	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Medical Library Assistance	000	1	8/3/2020	NEW	$347,736
														Subtotal = $347,736

Grand Total All Awards = $1,374,130

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Methods for improving clinical diagnostic by detection, prediction, interpretation and prioritization of aberrant transcriptome variations

Award Number: R01LM013437

ORGANIZATION: NATIONAL LIBRARY OF MEDICINE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/03/2020

PERIOD OF PERFORMANCE END DATE: 07/31/2025

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