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Pre-analytical factors affecting ctDNA analysis in early and locally advanced breast cancer

Award Number: U01CA243078
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/18/2019
PERIOD OF PERFORMANCE END DATE: 08/31/2025

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Pre-analytical factors affecting ctDNA analysis in early and locally advanced breast cancer - PROJECT SUMMARY Circulating tumor DNA (ctDNA) analysis has enabled noninvasive tumor genotyping for patients with advanced metastatic cancers. There is now growing interest in replicating this success in patients with early stage cancers. ctDNA analysis could enable blood-based minimal residual disease detection in patients receiving treatment and early detection of cancers in pre-symptomatic individuals. However, ctDNA levels are 10s-100s fold lower in localized cancers than in metastatic cancers, limiting the sensitivity of current assays. This is further confounded by pre-analytical variability such as differences in blood collection and processing and DNA extraction. For example, inappropriate or delayed blood processing can cause peripheral cell lysis and dilute ctDNA fraction in blood samples. In early stage cancer patients where ctDNA levels are already quite low, this can cause false-negative results. The effects of pre-analytical factors on ctDNA detection in patients with localized cancers are not well understood. To address this gap, we propose a study of 180 patients with early and locally advanced breast cancer to investigate three aspects of pre-analytical variation: 1) DNA extraction methods (Aim 1), 2) blood collection tubes and processing protocols (Aim 2) and 3) long-term storage of plasma and extracted DNA (Aim 3). We will investigate these factors using two assays we have recently developed: 1) a quality assessment assay that measures total cell-free DNA concentration and fragment size and 2) TARgeted DIgital Sequencing (TARDIS), an assay that simultaneously measures up to 30 patient-specific founder mutations in plasma DNA to quantify ctDNA levels. By leveraging multiple mutations for each patient, improving error suppression and minimizing loss of input DNA material, TARDIS enables sensitive detection and precise quantification of ctDNA in patients with localized cancers and improves limit of detection by 10-100 fold over current assays. Minimal residual disease detection and early detection using ctDNA analysis hold tremendous promise to individualize cancer treatment and to improve outcomes. Our study will clarify pre-analytical factors that could be critical to the success of future clinical studies across localized cancers of multiple subtypes.


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 = $0 )
2025	2023	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	000	5	3/4/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2023	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	000	5	3/7/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $349,281 )
2023	2023	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	001	5	9/7/2023	NON-COMPETING CONTINUATION	$349,281
2023	2022	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	000	4	11/18/2022	NON-COMPETING CONTINUATION	$0
														Subtotal = $349,281

Issue Date FY: 2022 ( Subtotal = $349,281 )
2022	2022	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	003	4	8/26/2022	NON-COMPETING CONTINUATION	$349,281
2022	2021	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	002	3	12/10/2021	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$536,825
2022	2020	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE	445 N 5TH ST	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	001	2	12/10/2021	NON-COMPETING CONTINUATION	-$419,136
2022	2019	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE	445 N 5TH ST	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	000	1	12/10/2021	NEW	-$117,689
														Subtotal = $349,281

Issue Date FY: 2021 ( Subtotal = $371,103 )
2021	2021	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6401	MADISON	WI	53715	DANE	USA	Cancer Treatment Research	001	3	9/7/2021	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$371,103
2021	2020	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE, THE	445 N 5TH ST STE 600	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	000	2	9/7/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $371,103

Issue Date FY: 2020 ( Subtotal = $419,136 )
2020	2020	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE, THE	445 N 5TH ST STE 600	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	001	2	8/25/2020	NON-COMPETING CONTINUATION	$419,136
2020	2019	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE, THE	445 N 5TH ST STE 600	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	000	1	3/12/2020	NEW	$0
														Subtotal = $419,136

Issue Date FY: 2019 ( Subtotal = $440,008 )
2019	2019	TRANSLATIONAL GENOMICS RESEARCH INSTITUTE, THE	445 N 5TH ST STE 600	PHOENIX	AZ	85004	MARICOPA	USA	Cancer Treatment Research	000	1	9/18/2019	NEW	$440,008
														Subtotal = $440,008

Grand Total All Awards = $1,928,809

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Pre-analytical factors affecting ctDNA analysis in early and locally advanced breast cancer

Award Number: U01CA243078

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

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

PERIOD OF PERFORMANCE START DATE: 09/18/2019

PERIOD OF PERFORMANCE END DATE: 08/31/2025

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