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A fast, scalable, cost-effective, single-stranded library protocol for cell-free DNA

Award Number: R43CA239933
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/16/2019
PERIOD OF PERFORMANCE END DATE: 08/31/2020

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A fast, scalable, cost-effective, single-stranded library protocol for cell-free DNA - Project Summary Liquid biopsy is a potentially powerful, non-invasive approach for detecting, classifying and monitoring tumors by capturing cell-free DNA molecules found circulating in blood and other bodily fluids. Any next-generation sequencing (NGS) based approach requires an efficient protocol for converting cell-free DNA into a sequencing library. Nearly all currently available NGS library preparation methods target exclusively double-stranded DNA. However, the benefits of a single-stranded DNA library approach are well described: higher efficiency and fidelity, less length bias, recovery of nicked double-stranded fragments, and retention of the native ends of each molecule, i.e. no DNA end repair. Despite the benefits, single-stranded library generation has not been widely adopted because the only existing protocols are expensive, complicated, and time- consuming. Claret Bioscience has developed an innovative new single-stranded approach (SRSLY) that is fast, efficient, simple to follow, and cost-effective. The protocol is carried out in a single tube and can convert cell-free DNA into a sequence-ready product in less than three hours. We propose to develop the SRSLY protocol for clinical analysis by optimizing the reaction conditions for cell-free DNA isolated from blood plasma. With data from our sequencing libraries, we will investigate the added utility of retaining the native ends of cell-free DNA molecules for reconstructing higher resolution nucleosome ‘maps’, as well as recovering populations of short cell-free DNA – either nicked fragments lost to other methods or linker molecules thought to be associated with regulatory elements with potential significance in disease processes. In collaboration with medical oncologists at UCSF, we will analyze cell-free DNA from a study of GI cancer patients through their course of treatment and integrate our sequencing-based metrics with other metrics of tumor progression to learn the utility of our method in a clinical setting. We aim to develop a scalable, cost-effective protocol that supports all NGS liquid biopsy analyses in current use and provide data suitable for new discovery.


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: 2021 ( Subtotal = $0 )
2021	2019	CLARET BIOSCIENCE LLC	567 ASPEN RD	BIRMINGHAM	MI	48009	OAKLAND	USA	Cancer Detection and Diagnosis Research	000	1	2/22/2021	NEW	$0
														Subtotal = $0

Issue Date FY: 2019 ( Subtotal = $299,918 )
2019	2019	CLARET BIOSCIENCE LLC	567 ASPEN RD	BIRMINGHAM	MI	48009	OAKLAND	USA	Cancer Detection and Diagnosis Research	000	1	9/16/2019	NEW	$299,918
														Subtotal = $299,918

Grand Total All Awards = $299,918

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A fast, scalable, cost-effective, single-stranded library protocol for cell-free DNA

Award Number: R43CA239933

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/16/2019

PERIOD OF PERFORMANCE END DATE: 08/31/2020

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