Monday, November 25, 2024 11/25/2024

Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor

Award Number: U24CA180996
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Abstract Bioconductor is an ecosystem of more than 1,500 open-source software and data packages for the statistical analysis and comprehension of high-throughput genomic data. It is widely used by the cancer genomics research community for statistical analysis and visualization. This software ecosystem is supported by core data classes and methods, reused by both users and developers, that provide convenient representations and efficient operations for many kinds of high-throughput molecular data. Falling sequencing costs and single-cell assays enable increasingly resolved study of the molecular biology of cancer, through combined assaying of DNA sequence, epigenetics, gene expression, protein, and other aspects, even at the single-cell level, for a single specimen. These developments present new challenges in complexity, size, and interpretability of the data. The overarching goal of this project is to create and adapt core Bioconductor software infrastructure to meet these challenges, through the following aims. First, we develop infrastructure for the analysis of single-cell multi-omic experiments. Second, we implement FAIR principles for improved somatic variant prioritization, by defining performant data architecture that harmonizes and integrates the large amount of experimental and annotation data available through Bioconductor. Users of our system will be able to create provenance-rich interoperable reports on structural and functional contexts of somatic variants for use in prioritization. Third, we develop scalable infrastructure for the curation, distribution, maintenance, discoverability, and usability of cancer data resources within and externally to Bioconductor. Finally, we develop a program of user training and new outreach approaches to support adoption of advanced Bioconductor infrastructure by developers of new cancer-related packages and existing packages critical to the cancer research community.


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 = $0 )
2024	2023	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 W 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	002	11	4/29/2024	NON-COMPETING CONTINUATION	$0
2024	2023	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 W 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	001	11	12/14/2023	NON-COMPETING CONTINUATION	$0
2024	2023	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 W 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	000	11	11/21/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $703,381 )
2023	2023	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	003	11	8/24/2023	NON-COMPETING CONTINUATION	$703,381
2023	2022	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	002	10	8/23/2023	NON-COMPETING CONTINUATION	$0
2023	2021	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 W 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	001	9	11/2/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$250,289
2023	2020	HEALTH RESEARCH, INC.	ELM & CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	8	11/2/2022	NON-COMPETING CONTINUATION	-$250,289
														Subtotal = $703,381

Issue Date FY: 2022 ( Subtotal = $1,020,084 )
2022	2022	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	005	10	9/12/2022	SUPPLEMENT FOR EXPANSION	$318,602
2022	2022	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	004	10	9/9/2022	NON-COMPETING CONTINUATION	$701,482
2022	2021	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	001	9	1/31/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$271,396
2022	2021	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	003	9	2/4/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	-$271,396
2022	2020	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	002	8	2/4/2022	NON-COMPETING CONTINUATION	$271,396
2022	2020	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	8	1/31/2022	NON-COMPETING CONTINUATION	-$271,396
														Subtotal = $1,020,084

Issue Date FY: 2021 ( Subtotal = $569,363 )
2021	2021	RESEARCH FOUNDATION OF THE CITY UNIVERSITY OF NEW YORK	55 WEST 125TH ST FL 7	NEW YORK	NY	10027	NEW YORK	USA	Cancer Cause and Prevention Research	006	9	8/31/2021	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$569,363
2021	2020	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	005	8	8/31/2021	NON-COMPETING CONTINUATION	$0
2021	2020	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	8	12/17/2020	NON-COMPETING CONTINUATION	$0
2021	2019	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	004	7	8/4/2021	COMPETING CONTINUATION	$184,240
2021	2019	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	002	7	7/27/2021	COMPETING CONTINUATION	-$231,767
2021	2018	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	001	6	7/27/2021	NON-COMPETING CONTINUATION	$231,767
2021	2018	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	003	6	8/4/2021	NON-COMPETING CONTINUATION	-$184,240
														Subtotal = $569,363

Issue Date FY: 2020 ( Subtotal = $704,932 )
2020	2020	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	002	8	8/20/2020	NON-COMPETING CONTINUATION	$704,932
2020	2019	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	001	7	4/2/2020	COMPETING CONTINUATION	$231,767
2020	2018	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	6	4/2/2020	NON-COMPETING CONTINUATION	-$231,767
														Subtotal = $704,932

Issue Date FY: 2019 ( Subtotal = $693,486 )
2019	2019	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	7	9/13/2019	COMPETING CONTINUATION	$693,486
														Subtotal = $693,486

Issue Date FY: 2018 ( Subtotal = $479,384 )
2018	2018	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	001	6	8/30/2018	NON-COMPETING CONTINUATION	$479,384
2018	2017	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	5	7/18/2018	NON-COMPETING CONTINUATION	$0
														Subtotal = $479,384

Issue Date FY: 2017 ( Subtotal = $691,625 )
2017	2017	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	21st Century Cures Act - Beau Biden Cancer Moonshot	001	5	9/13/2017	SUPPLEMENT FOR EXPANSION	$67,933
2017	2017	HEALTH RESEARCH, INC.	ELM AND CARLTON ST	BUFFALO	NY	14263	ERIE	USA	Cancer Cause and Prevention Research	000	5	8/14/2017	NON-COMPETING CONTINUATION	$623,692
														Subtotal = $691,625

Issue Date FY: 2016 ( Subtotal = $632,853 )
2016	2016	HEALTH RESEARCH, INC - ROSWELL PARK DIVISION	666 ELM STREET	BUFFALO	NY	14203	ERIE	USA	Cancer Cause and Prevention Research	002	4	8/18/2016	NON-COMPETING CONTINUATION	$632,853
2016	2015	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE NO J6-330	SEATTLE	WA	98109	KING	USA	Cancer Cause and Prevention Research	001	2	12/30/2015	NON-COMPETING CONTINUATION	-$696,669
2016	2015	HEALTH RESEARCH, INC - ROSWELL PARK DIVISION	666 ELM STREET	BUFFALO	NY	14203	ERIE	USA	Cancer Cause and Prevention Research	000	3	12/30/2015	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$696,669
														Subtotal = $632,853

Issue Date FY: 2015 ( Subtotal = $696,669 )
2015	2015	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE NO J6-330	SEATTLE	WA	98109	KING	USA	Cancer Cause and Prevention Research	000	2	8/7/2015	NON-COMPETING CONTINUATION	$696,669
														Subtotal = $696,669

Issue Date FY: 2014 ( Subtotal = $749,248 )
2014	2014	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE NO J6-330	SEATTLE	WA	98109	KING	USA	Cancer Cause and Prevention Research	000	1	8/21/2014	NEW	$749,248
														Subtotal = $749,248

Grand Total All Awards = $6,941,025

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Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor

Award Number: U24CA180996

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

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