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Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements

Journal article
Authors H. J. He
E. V. Stein
Y. Konigshofer
T. Forbes
F. L. Tomson
R. Garlick
E. Yamada
T. Godfrey
T. Abe
K. Tamura
M. Borges
M. Goggins
S. Elmore
M. L. Gulley
J. L. Larson
L. Ringel
B. C. Haynes
C. Karlovich
P. M. Williams
A. Garnett
Anders Ståhlberg
Stefan Filges
L. Sorbara
M. R. Young
S. Srivastava
K. D. Cole
Published in Journal of Molecular Diagnostics
Volume 21
Issue 4
Pages 658-676
ISSN 1525-1578
Publication year 2019
Published at Sahlgrenska Cancer Center
Institute of Biomedicine, Department of Pathology
Wallenberg Centre for Molecular and Translational Medicine
Pages 658-676
Language en
Links dx.doi.org/10.1016/j.jmoldx.2019.03...
Keywords liquid biopsies, quantification, accuracy, rare, bias, kits, Pathology
Subject categories Pathology

Abstract

We conducted a multilaboratory assessment to determine the suitability of a new commercially available reference material with 40 cancer variants in a background of wild-type DNA at four different variant allele frequencies (VAFs): 2%, 0.50%, 0.125%, and 0%. The variants include single nucleotides, insertions, deletions, and two structural variations selected for their clinical importance and to challenge the performance of next-generation sequencing (NGS) methods. Fragmented DNA was formulated to simulate the size distribution of circulating wild-type and tumor DNA in a synthetic plasma matrix. DNA was extracted from these samples and characterized with different methods and multiple laboratories. The various extraction methods had differences in yield, perhaps because of differences in chemistry. Digital PCR assays were used to measure VAFs to compare results from different NGS methods. Comparable VAFs were observed across the different NGS methods. This multilaboratory assessment demonstrates that the new reference material is an appropriate tool to determine the analytical parameters of different measurement methods and to ensure their quality assurance.

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