Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types

Abstract Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC’s Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors’ presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

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Abstract 2214: Development and validation of PredicineATLAS, a 600-gene liquid biopsy panel for simultaneous detection of TMB and genomic alterations in Immuno-Oncology

10.1158/1538-7445.am2019-2214 ◽

2019 ◽

Author(s):

Zhixin Zhao ◽

Amy Chang ◽

Tak Cheung ◽

Feng Xie ◽

Carlos Montesinos ◽

...

Keyword(s):

Liquid Biopsy ◽

Simultaneous Detection ◽

Genomic Alterations ◽

Development And Validation

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Abstract 2214: Development and validation of PredicineATLAS, a 600-gene liquid biopsy panel for simultaneous detection of TMB and genomic alterations in Immuno-Oncology

10.1158/1538-7445.sabcs18-2214 ◽

2019 ◽

Author(s):

Zhixin Zhao ◽

Amy Chang ◽

Tak Cheung ◽

Feng Xie ◽

Carlos Montesinos ◽

...

Keyword(s):

Liquid Biopsy ◽

Simultaneous Detection ◽

Genomic Alterations ◽

Development And Validation

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An automated high throughput solution for DNA extraction and bisulfite-conversion from high volume liquid biopsy specimens – sample preparation for epigenetic analysis

10.21203/rs.2.11948/v2 ◽

2019 ◽

Author(s):

Sebastian Rausch ◽

Oliver Hasinger ◽

Thomas König ◽

Anne Schlegel ◽

Gunter Weiss

Keyword(s):

Dna Extraction ◽

High Throughput ◽

Liquid Biopsy ◽

Analytical Techniques ◽

High Volume ◽

Magnetic Bead ◽

Bisulfite Conversion ◽

Manual Method ◽

Automated Method ◽

Biopsy Specimens

Abstract Objective: DNA methylation analysis via real-time PCR or other analytical techniques requires purified bisulfite converted DNA. We report on an automated high throughput solution for DNA extraction, bisulfite-conversion, and purification of 96 samples with an input volume of up to 3.5mL of plasma or urine, using reagents from the commercially available Epi BisKit. Results: Magnetic bead-based DNA extraction, bisulfite conversion at high temperature, and efficient DNA purification was conducted on a customized commercially available liquid-handling platform. A highly interlaced 4x24 sample protocol was implemented for DNA extraction, elution in a 96-well plate, efficient bisulfite-conversion and extensive purification. The resulting bisulfite-converted DNA was stored in a 96-well format, ready for PCR set-up or other down-stream applications. The automated method is a walk-away solution for processing 96 samples in 7h30min. Performance of the method was validated by comparison with the standard manual method of the Epi BiSKit using technical and biological samples. Overall DNA yield was assessed with a standardized ß-actin assay. The automated workflow demonstrated equivalent performance to the manual method for technical, plasma and urine samples. It may provide a new standard for effective high-throughput preparation of bisulfite-converted DNA from a variety of high volume liquid biopsy specimens.

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