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Workflow optimization and capacity expansion for molecular newborn screening

Award Number: NU88EH001339
ORGANIZATION: NATIONAL CENTER FOR ENVIRONMENTAL HEALTH
OPDIV: CDC
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: HEALTH SERVICES
PERIOD OF PERFORMANCE START DATE: 09/30/2022
PERIOD OF PERFORMANCE END DATE: 09/29/2024

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Workflow optimization and capacity expansion for molecular newborn screening - Approximately 50,000 babies in the state of Utah are screened annually for conditions that are not readily apparent at birth but require immediate medical treatment. As new disorders are added to the NBS panel, molecular testing workflows and testing platforms require modernization to allow scalable panel expansion. Modernization also allows the integration to best practice solutions to ensure screening performance optimization. The purpose of this project is to optimize processes and workflows for molecular NBS analyses. Specifically, we propose (1) upgrades to our qPCR platform to allow the introduction of improved diagnostic algorithms (detection or calling algorithms), the integration into the Laboratory Information Management System (LIMS) and introducing a scalable qPCR for expanded multiplexing, (2) the establishment of cloud computing resources for genomic analyses and data storage, and (3) integration of genomic variant results and reporting into the Laboratory Information Management System (LIMS). Specifically, we propose improvements targeting molecular screening applications and second and third tier workflows by improving the performance of existing tests for current conditions (SCID and SMA) with the long-term goal of expanding the capacity and capability of our screening laboratory with the inclusion of additional conditions or markers in this platform. Improvements in the second tier testing applications for SCID as well as the disorder agnostic exome based NGS testing workflow will introduce efficiencies and result in turn-around-time (TAT) improvements. We propose to modernize our current qPCR instrumentation to allow for (1) the adoption of closed analytical instrument workflows, (2) the direct integration into the LIMS and (3) the adoption of a testing platform allowing the expansion of multiplex assays for conditions such as CMV infection. Primary outcomes include upgrades to a qPCR instrumentation platform to allow for expanded multiplexing and LIMS integration, establishing and configuration of AWS cloud computing resources for bioinformatics analyses and data storage, and the development of a genomic module in the LIMS. All primary outcomes will result in screening performance improvements including decreased TAT and a reduction in repeat screening requirements. Accurate interpretation of complex biomarker profiles requires both the development of analytic and interpretive tools and total management of complex data systems. In this matter our program recently developed a WES-based test for secondary screening that can be applied to any current and future disorders on the NBS panel. We propose transitioning our pipeline to a cloud-based platform allowing the dynamic allocation of computational resources on demand and remote access. Both measures would improve TAT for these second or third tier testing modalities. Additionally, we propose the required implementation of a genomic module within our LIMS that will store and display genomic variant results, generate a NBS genomic variant report, and send out this report electronically to clinical specialists. The proposed work described in this grant will benefit all newborns and their families in Utah as well as babies born in Utah from surrounding states. The awarded funds will provide the capability of the Utah NBS Program to implement process and workflow optimizations for qPCR instrumentation, AWS cloud computing resources for bioinformatics analyses and data storage, and development of a genomic module in the LIMS.


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 = -$239,149 )
2025	2023	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	02	2	9/25/2025	ADMINISTRATIVE SUPPLEMENT ( + OR - ) (DISCRETIONARY OR BLOCK AWARDS)	-$239,149
2025	2022	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	02	2	9/25/2025	ADMINISTRATIVE SUPPLEMENT ( + OR - ) (DISCRETIONARY OR BLOCK AWARDS)	$0
														Subtotal = -$239,149

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2023	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	01	2	11/27/2023	ADMINISTRATIVE SUPPLEMENT ( + OR - ) (DISCRETIONARY OR BLOCK AWARDS)	$0
2024	2022	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	01	2	11/27/2023	ADMINISTRATIVE SUPPLEMENT ( + OR - ) (DISCRETIONARY OR BLOCK AWARDS)	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $368,294 )
2023	2023	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	00	2	6/2/2023	NON-COMPETING CONTINUATION	$368,294
2023	2022	UTAH DEPARTMENT OF HEALTH AND HUMAN SERVICES	195 N 1950 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	00	2	6/2/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $368,294

Issue Date FY: 2022 ( Subtotal = $383,744 )
2022	2022	DEPARTMENT OF HEALTH UTAH	288 N 1460 W	SALT LAKE CITY	UT	84116	SALT LAKE	USA	Laboratory Leadership, Workforce Training and Management Development, Improving Public Health Laboratory Infrastructure	00	1	7/24/2022	NEW	$383,744
														Subtotal = $383,744

Grand Total All Awards = $512,889

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Workflow optimization and capacity expansion for molecular newborn screening

Award Number: NU88EH001339

ORGANIZATION: NATIONAL CENTER FOR ENVIRONMENTAL HEALTH

OPDIV: CDC

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: HEALTH SERVICES

PERIOD OF PERFORMANCE START DATE: 09/30/2022

PERIOD OF PERFORMANCE END DATE: 09/29/2024

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