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GENCODE: comprehensive genome annotation for human and mouse

Award Number: U41HG007234
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2013
PERIOD OF PERFORMANCE END DATE: 09/13/2021

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GENCODE: comprehensive genome annotation for human and mouse - OVERALL - PROJECT SUMMARY The objective of the GENCODE consortium is to create a foundational reference genome annotation, in which all gene features in the human and mouse genomes are identified and classified with high accuracy based on biological evidence, and then to release these annotations for the benefit of biomedical research and genome interpretation. GENCODE aims for a better understanding of a `normal' human genome; using genome sequences of the most commonly used mouse strains will facilitate the most effective use of these key models for large-scale knockout analysis and disease-specific research. To produce regular annotation releases of high accuracy, GENCODE will continue to follow its well-established and conservative research design, supplemented by targeted investigations into the value of new technologies, new data and new sources of evidence. GENCODE focuses on protein-coding and non-coding loci, including their alternatively spliced isoforms and pseudogenes. Over the course of this proposal GENCODE will follow major directions in genomics, including graph- based genome representations, long-read transcriptome sequencing, connecting genes and the associated regulatory regions that affect their transcription, and identifying genes that are not present on the current reference assembly. The GENCODE consortium has four fundamental components: (1) a comprehensive gene annotation pipeline leveraging manual annotation; (2) an integrated approach to pseudogene identification and classification; (3) a set of computational methods to evaluate and enhance gene annotation; and (4) complementary experimental pipelines for validation and functional annotation. More specifically, in the next four years GENCODE aims to (1) extend the human and mouse GENCODE gene sets to as near completion as possible given current experimental technology; (2) deploy population-based genome annotation to ensure that any transcript isoform expressed in an individual human will be present in the reference annotation set; (3) extend the gene annotation to include core regulatory regions and tissue-specific enhancers from selected datasets; (4) to distribute GENCODE annotations and engage with community annotation efforts. Current popular distribution channels for GENCODE data including the GENCODE web site, the Ensembl and UCSC Genome Browsers, will be maintained. Finally, new mechanisms for prioritizing genes for manual annotation with community input will be established, with the long-term aim of establishing GENCODE as the standard annotation set for research and clinical genomics efforts.


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 = -$199,366 )
2025	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG				DEU	Human Genome Research	000	8	10/1/2024	NON-COMPETING CONTINUATION	-$199,366
														Subtotal = -$199,366

Issue Date FY: 2022 ( Subtotal = -$1,358,523 )
2022	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	000	8	3/17/2022	NON-COMPETING CONTINUATION	-$1,457,260
2022	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	001	8	3/25/2022	NON-COMPETING CONTINUATION	$1,457,260
2022	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	002	8	6/9/2022	NON-COMPETING CONTINUATION	-$1,358,523
														Subtotal = -$1,358,523

Issue Date FY: 2021 ( Subtotal = $0 )
2021	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	002	8	9/22/2021	NON-COMPETING CONTINUATION	$0
2021	2017	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG			DEU	Human Genome Research	001	5	2/1/2021	COMPETING CONTINUATION	$270,000
2021	2016	GENOME RESEARCH LTD	WELLCOME TRUST GENOME CAMPUS	SAFFRON WALDEN	ESSEX			GBR	Human Genome Research	000	4	2/1/2021	NON-COMPETING CONTINUATION	-$270,000
														Subtotal = $0

Issue Date FY: 2020 ( Subtotal = $2,226,969 )
2020	2020	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	000	8	9/11/2020	NON-COMPETING CONTINUATION	$2,226,969
														Subtotal = $2,226,969

Issue Date FY: 2019 ( Subtotal = $2,694,784 )
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	000	7	7/19/2019	NON-COMPETING CONTINUATION	$2,694,784
2019	2019	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	7	9/25/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,694,784

Issue Date FY: 2018 ( Subtotal = $2,513,651 )
2018	2018	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	002	6	6/11/2018	NON-COMPETING CONTINUATION	$2,513,651
2018	2017	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	5	1/4/2018	COMPETING CONTINUATION	$357,037
2018	2016	GENOME RESEARCH LTD	WELLCOME TRUST GENOME CAMPUS	SAFFRON WALDEN	ESSEX	CB10 1SA		GBR	Human Genome Research	000	4	1/4/2018	NON-COMPETING CONTINUATION	-$357,037
														Subtotal = $2,513,651

Issue Date FY: 2017 ( Subtotal = $2,638,258 )
2017	2017	EUROPEAN MOLECULAR BIOLOGY LABORATORY	MEYERHOFSTR. 1	HEIDELBERG	BADEN-WURTTEMBERG	69117		DEU	Human Genome Research	001	5	7/26/2017	COMPETING CONTINUATION	$2,638,258
2017	2016	GENOME RESEARCH LTD	WELLCOME TRUST GENOME CAMPUS	SAFFRON WALDEN	ESSEX	CB10 1SA		GBR	Human Genome Research	000	4	7/25/2017	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,638,258

Issue Date FY: 2016 ( Subtotal = $2,582,205 )
2016	2016	GENOME RESEARCH LIMITED	WELLCOME TRUST GENOME CAMPUS	CAMBRIDGE				GBR	Human Genome Research	000	4	3/28/2016	NON-COMPETING CONTINUATION	$2,582,205
														Subtotal = $2,582,205

Issue Date FY: 2015 ( Subtotal = $2,517,650 )
2015	2015	GENOME RESEARCH LIMITED	WELLCOME TRUST GENOME CAMPUS	CAMBRIDGE				GBR	Human Genome Research	000	3	5/14/2015	NON-COMPETING CONTINUATION	$2,517,650
														Subtotal = $2,517,650

Issue Date FY: 2014 ( Subtotal = $2,530,561 )
2014	2014	GENOME RESEARCH LIMITED	WELLCOME TRUST GENOME CAMPUS	CAMBRIDGE				GBR	Human Genome Research	000	2	7/9/2014	NON-COMPETING CONTINUATION	$2,530,561
														Subtotal = $2,530,561

Issue Date FY: 2013 ( Subtotal = $2,582,206 )
2013	2013	WELLCOME TRUST SANGER INSTITUTE	WELLCOME TRUST GENOME CAMPUS HINXTO	CAMBRIDGE				GBR	Human Genome Research	001	1	4/19/2013	NEW	$1,291,103
2013	2013	WELLCOME TRUST SANGER INSTITUTE	WELLCOME TRUST GENOME CAMPUS HINXTO	CAMBRIDGE				GBR	Human Genome Research	000	1	3/27/2013	NEW	$1,291,103
														Subtotal = $2,582,206

Grand Total All Awards = $18,728,395

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GENCODE: comprehensive genome annotation for human and mouse

Award Number: U41HG007234

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 04/01/2013

PERIOD OF PERFORMANCE END DATE: 09/13/2021

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