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Integrating T cell receptor features with gene expression profiles to define T cell specificity and differentiation

Award Number: R21AI169085
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 02/01/2022
PERIOD OF PERFORMANCE END DATE: 01/31/2025

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Integrating T cell receptor features with gene expression profiles to define T cell specificity and differentiation - ABSTRACT The objective of this proposal is to identify linkages between T cell receptor (TCR) sequences and transcriptional profiles across the human T cell landscape. This work is enabled by our recent development of the CoNGA algorithm, a graph theoretic approach that integrates TCR and gene expression (GEX) datasets, and by technological advances that have made it possible to profile both features in parallel at high throughput. Submitted in response to Notice of Special Interest NOT-AI-21-011 ( Secondary Analysis of Existing Datasets for Advancing Immune-mediated and Infectious Disease Research ), our proposal brings together a team of computational biologists and immunologists with a track record of successful collaboration. Our goal is to apply CoNGA on diverse T cell datasets to define the landmark TCR features and their correlated phenotypes in human T cells. In the first Aim, we will identify, acquire, pre-process, and standardize all large, publicly available single-cell datasets that feature linked gene expression and paired TCR sequence information. We will then run the CoNGA pipeline on these individual datasets, correlate the results with available study metadata, and make these results available for download. In the second Aim, we will perform a meta-analysis of the relationship between T cell receptor sequence and T cell transcriptional profile across the entire dataset (1,000+ donors and 1,000,000+ individual T cells). Completion of the work proposed here will lay the groundwork for a comprehensive atlas of the human T cell landscape and provide a valuable dataset for further development of analytical tools and methods. T cell features and sub-populations identified by CoNGA will provide new insight into the individual datasets while also illuminating the global landscape of GEX/TCR covariation.


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 = -$1 )
2025	2023	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	000	3	5/23/2025	NON-COMPETING CONTINUATION	-$1
														Subtotal = -$1

Issue Date FY: 2023 ( Subtotal = $223,720 )
2023	2023	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	002	3	1/30/2023	NON-COMPETING CONTINUATION	$223,720
2023	2022	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	000	1	10/14/2022	NEW	-$1
2023	2022	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	001	2	10/14/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$1
														Subtotal = $223,720

Issue Date FY: 2022 ( Subtotal = $287,500 )
2022	2022	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	000	1	2/8/2022	NEW	$287,500
2022	2022	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	001	1	5/27/2022	NEW	-$287,499
2022	2022	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Allergy and Infectious Diseases Research	002	2	5/27/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$287,499
														Subtotal = $287,500

Grand Total All Awards = $511,219

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Integrating T cell receptor features with gene expression profiles to define T cell specificity and differentiation

Award Number: R21AI169085

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 02/01/2022

PERIOD OF PERFORMANCE END DATE: 01/31/2025

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