Friday, April 26, 2024 4/26/2024

Enhancing gnomAD Sustainability: Implementing Site Reliability Engineering Principles for Genomic Data Infrastructure

Award Number: U24HG011450
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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Project Summary The Genome Aggregation Database (gnomAD) is a ubiquitous resource for basic research and clinical interpretation. The world’s largest genetic variation resource, the gnomAD dataset is used in virtually all clinical genetic diagnostic pipelines worldwide, and the website has over 20 million page views to date. Here we outline a proposal that will expand the gnomAD resource to millions of samples across diverse global populations. Our proposal will scale variant-calling and quality control to match this sample size, integrate statistical tools and other genomic resources critical to clinical interpretation, and ensure that the data we aggregate will continue to be shared freely with the biomedical community. To accomplish this we will apply a highly computationally efficient strategy to call all classes of variation (including SNVs, small indels, and the mutational spectrum of structural variants) across millions of sequenced samples enriched for under- represented ancestry groups. We will deploy a cloud-based framework for the efficient storage and automated quality control of these very large and heterogeneous sequence data sets using the massively parallel Hail architecture. We will leverage the scale of gnomAD to provide increasingly high-resolution maps of the depletion of functional variation across regions of the genome (highlighting genome regions where natural selection constrains DNA change) and provide statistical frameworks for quantitatively assessing whether the population frequency of a variant is consistent with pathogenicity, linking this information with evidence from the ClinVar resource. We will continue to share all of this data as rapidly and openly as possible with the biomedical community, long before publication. We will support and expand functionality in our widely accessed data browser as well as create scalable and publicly accessible datasets that integrate our variation data with clinical and functional genomic annotations, accessible through API frameworks to empower novel applications of the datasets. We will also provide resources and training to improve the use of gnomAD resources by the clinical genetics and wider biomedical communities.


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 = $2,321,100 )
2024	2024	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	4	1/12/2024	NON-COMPETING CONTINUATION	$2,321,100
2024	2023	THE BROAD INSTITUTE, INC	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	001	3	4/17/2024	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $2,321,100

Issue Date FY: 2023 ( Subtotal = $2,678,996 )
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	3	1/23/2023	NON-COMPETING CONTINUATION	$2,199,600
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	003	3	9/1/2023	SUPPLEMENT FOR EXPANSION	$234,996
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	002	3	8/11/2023	NON-COMPETING CONTINUATION	$0
2023	2023	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	001	3	2/16/2023	NON-COMPETING CONTINUATION	$244,400
														Subtotal = $2,678,996

Issue Date FY: 2022 ( Subtotal = $2,309,000 )
2022	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	002	2	7/27/2022	NON-COMPETING CONTINUATION	$0
2022	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	2	1/7/2022	NON-COMPETING CONTINUATION	$2,078,100
2022	2022	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	001	2	5/2/2022	NON-COMPETING CONTINUATION	$230,900
														Subtotal = $2,309,000

Issue Date FY: 2021 ( Subtotal = $2,187,000 )
2021	2021	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	1	2/8/2021	NEW	$2,187,000
														Subtotal = $2,187,000

Grand Total All Awards = $9,496,096

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Enhancing gnomAD Sustainability: Implementing Site Reliability Engineering Principles for Genomic Data Infrastructure

Award Number: U24HG011450

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

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