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Population-Scale Clinical Genomics

Award Number: OT2OD027070
ORGANIZATION: OFFICE OF THE DIRECTOR, NIH
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: OTHER
PERIOD OF PERFORMANCE START DATE: 09/21/2019
PERIOD OF PERFORMANCE END DATE: 02/28/2025

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Population-Scale Clinical Genomics - The production of genomic data for the All of Us Research Program (AoU) is an unprecedented opportunity to support a comprehensive precision medicine effort that benefits the entire U.S. population. With the participation from patients, family members, researchers and clinicians, this opportunity will impact clinical management by directing patient care, enabling pre-symptomatic genetic testing of relatives, guiding familyplanning measures, and triggering healthcare interventions. We propose to create the HudsonAlpha Consortium for Population Genomics (HACPG) for AoU as a platform for high quality microarray, sequence, and clinical interpretation of high-value variants. The HACPG will leverage the experience and breadth of our clinical team and consortium members to allow accurate and cost-effective production of annotated variant data from the largest number of cases and samples possible. The data we generate will be formatted and transferred to the program Data Resource Center (DRC) to facilitate return of clinical results to the Genetic Counseling Resource as directed by the program. Our overarching strategy in developing this proposal is to combine best-in-field teams to form a consortium dedicated to enabling scalable genomics in an evolvable platform. This platform will easily support advancements in the genomics field, efficiently combining existing technical and analytic resources. Our efforts will facilitate a path to move unbiased genetic testing such as whole-genome sequencing to routine use in healthcare and lifestyle management. The roles and relationships of HACPG consortium members are summarized below (Fig 1.1). HACPG is a collaboration between HudsonAlpha Institute for Biotechnology (lead institution, sequencing, and clinical validation laboratory), Rutgers University (sample intake, quality control and genotyping), University of Utah (data analysis), Fabric Genomics (clinical reporting) and Helix (return of results and value add). With the significant expansion of sequencing volume in years 2-5 of AoU, the HACPG will expand to include Baylor College of Medicine Human Genome Sequencing Center Clinical Lab (HGSC-CL) to provide a known and trusted partner to expand the capacity of the consortium to support the requested volumes (see Letters of Support 7.4 to 7.6 in Section 7). As lead institution, HudsonAlpha Institute for Biotechnology benefits from a unique background. HudsonAlpha was founded ten years ago with a mission to improve genomic literacy and support the application of genomic technologies in education, research, healthcare and economic development. Since its founding, HudsonAlpha has grown significantly in each of its mission areas and has made significant contributions to the genomics field. Some key highlights and unique accomplishments with references to the relevant sections of our proposal are: • HudsonAlpha established the first CAP-accredited, CLIA licensed lab offering whole-genome sequencing (WGS) and currently has capacity for sequencing over 70,000 clinical genomes per year (please see Section 2.C.1). • HudsonAlpha has generated ~30X+ genomes from thousands of individuals and returned definitive diagnoses for hundreds of patients through our UDN and CSER programs (please see Section 3). • HudsonAlpha is co-leading the Alabama Genomics Health Initiative; a program that mirrors many of the features of AoU and has provided vital early perspectives on population scale programs that utilize multiple technologies (please see Section 3). • Although HudsonAlpha has resources to support the full AoU scope of work, we have made strategic partnerships to provide the best available options and flexibility to AoU, especially in the later years of the program (please see this section and Figure 1.1). • HudsonAlpha has production-scale experience with the Illumina NovaSeq 6000 demonstrated by more than 25,000 whole-genomes or equivalents in the first half of 2018 (please see Section 2.C). • We have deve


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 = -$1,555 )
2025	2022	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	Trans-NIH Research Support	000	1	1/22/2025	SUPPLEMENT FOR EXPANSION	$0
2025	2022	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	Trans-NIH Research Support	001	1	7/25/2025	SUPPLEMENT FOR EXPANSION	-$1,555
														Subtotal = -$1,555

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2022	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	Trans-NIH Research Support	000	1	4/11/2024	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2022	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	Trans-NIH Research Support	000	1	8/3/2023	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $2,607,081 )
2022	2022	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	Trans-NIH Research Support	003	1	9/7/2022	SUPPLEMENT FOR EXPANSION	$2,607,081
2022	2019	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	National Center for Advancing Translational Sciences	002	1	9/7/2022	NEW	$0
2022	2019	HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	National Center for Advancing Translational Sciences	001	1	8/30/2022	NEW	$0
2022	2019	HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	National Center for Advancing Translational Sciences	000	1	10/28/2021	NEW	$0
														Subtotal = $2,607,081

Issue Date FY: 2021 ( Subtotal = $0 )
2021	2019	HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY	601 GENOME WAY	HUNTSVILLE	AL	35806	MADISON	USA	National Center for Advancing Translational Sciences	000	1	4/30/2021	NEW	$0
														Subtotal = $0

Grand Total All Awards = $2,605,526

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Population-Scale Clinical Genomics

Award Number: OT2OD027070

ORGANIZATION: OFFICE OF THE DIRECTOR, NIH

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: OTHER

PERIOD OF PERFORMANCE START DATE: 09/21/2019

PERIOD OF PERFORMANCE END DATE: 02/28/2025

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