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Isoform-level probabilistic transcriptome-wide association to undercover neurogenetic mechanisms underlying complex psychiatric traits

Award Number: R01MH121521
ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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PROJECT SUMMARY/ABSTRACT As large-scale genome-wide association studies (GWAS) rapidly identify associations with neurodevelopmental and psychiatric traits, the major defining challenge of the post-GWAS era is to rigorously define the neurobiological mechanisms underlying disease-associated genetic variation at scale. To this end, we and others have recently developed methods to directly integrate GWAS results with large-scale tissue-specific expression quantitative trait loci (eQTL) reference panels, enabling a transcriptome-wide association study (TWAS) – a powerful approach to identify genes whose expression is associated with genetic risk for disease. In parallel, emerging evidence has strongly implicated alternative splicing – a form of genetic regulation capable of generating an exponential number of unique RNA transcript isoforms from a single gene – as an important mechanism that exhibits dynamic patterns across development and is disrupted in the brains on individuals affected by psychiatric diseases, including autism and schizophrenia. Yet, no studies have systematically characterized the genetic regulation of isoform expression in human brain or its association with genetic risk for psychiatric disorders. This proposal seeks to develop a novel, isoform-level TWAS approach (iso-TWAS) to identify transcript-isoforms whose cis-regulated expression is associated with psychiatric disease risk. We will compile a large-scale functional genomic reference panel incorporating genotype and isoform quantifications from RNA-seq data of more than 3800 human brain samples, which we will leverage to perform iso-TWAS along with traditional gene-level TWAS for a host of neuropsychiatric traits. We will directly integrate isoform quantification uncertainties as well as probabilistic fine-mapping within our iso-TWAS framework, in order to ensure the robustness of resulting associations. We hypothesize that isoform-level characterization will provide substantially greater resolution to detect candidate biological mechanisms underlying psychiatric GWAS loci. Finally, predicted SNP-isoform-disease associations will be experimentally validated using genome-engineering in primary human neural progenitor cell (phNPC) lines followed by long-read RNA-sequencing and detailed cellular phenotyping. Together, these studies will systematically characterize a critical, yet underexplored area of genomic regulation in human brain, thereby providing novel insights into psychiatric disease mechanisms and identifying potential neurobiological targets for therapeutic development and intervention.


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: 2024 ( Subtotal = $559,676 )
2024	2024	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Mental Health Research Grants	000	5	12/28/2023	NON-COMPETING CONTINUATION	$559,676
														Subtotal = $559,676

Issue Date FY: 2023 ( Subtotal = $632,856 )
2023	2023	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Mental Health Research Grants	001	4	1/30/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$632,856
2023	2023	TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE	3451 WALNUT ST STE 440A	PHILADELPHIA	PA	19104	PHILADELPHIA	USA	Mental Health Research Grants	004	4	4/10/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$774,117
2023	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	003	3	4/10/2023	NON-COMPETING CONTINUATION	-$731,712
2023	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	000	3	1/27/2023	NON-COMPETING CONTINUATION	$0
2023	2021	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	002	2	4/10/2023	NON-COMPETING CONTINUATION	-$42,405
														Subtotal = $632,856

Issue Date FY: 2022 ( Subtotal = $731,712 )
2022	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	000	3	1/13/2022	NON-COMPETING CONTINUATION	$658,540
2022	2022	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	001	3	5/23/2022	NON-COMPETING CONTINUATION	$73,172
														Subtotal = $731,712

Issue Date FY: 2021 ( Subtotal = $688,988 )
2021	2021	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90095	LOS ANGELES	USA	Mental Health Research Grants	000	2	12/17/2020	NON-COMPETING CONTINUATION	$620,089
2021	2021	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90024	LOS ANGELES	USA	Mental Health Research Grants	001	2	6/9/2021	NON-COMPETING CONTINUATION	$68,899
														Subtotal = $688,988

Issue Date FY: 2020 ( Subtotal = $691,796 )
2020	2020	UNIVERSITY OF CALIFORNIA, LOS ANGELES	10889 WILSHIRE BLVD STE 700	LOS ANGELES	CA	90095	LOS ANGELES	USA	Mental Health Research Grants	000	1	1/3/2020	NEW	$691,796
														Subtotal = $691,796

Grand Total All Awards = $3,305,028

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Isoform-level probabilistic transcriptome-wide association to undercover neurogenetic mechanisms underlying complex psychiatric traits

Award Number: R01MH121521

ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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