Dataset Information

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

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.

SUBMITTER: He HJ

PROVIDER: S-EPMC6626992 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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

He Hua-Jun HJ Stein Erica V EV Konigshofer Yves Y Forbes Thomas T Tomson Farol L FL Garlick Russell R Yamada Emiko E Godfrey Tony T Abe Toshiya T Tamura Koji K Borges Michael M Goggins Michael M Elmore Sandra S Gulley Margaret L ML Larson Jessica L JL Ringel Lando L Haynes Brian C BC Karlovich Chris C Williams P Mickey PM Garnett Aaron A Ståhlberg Anders A Filges Stefan S Sorbara Lynn L Young Mathew R MR Srivastava Sudhir S Cole Kenneth D KD

The Journal of molecular diagnostics : JMD 20190502 4

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 ...[more]

PMID: 31055023

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Dataset Information

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

Publications

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

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