International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA

Cleo Keppens, Elisabeth M C Dequeker, Simon J Patton, Nicola Normanno, Francesca Fenizia, Rachel Butler, Melanie Cheetham, Jennifer A Fairley, Hannah Williams, Jacqueline A Hall, Ed Schuuring, Zandra C Deans

Research output: Contribution to journalArticle

Abstract

BACKGROUND: Molecular analysis of circulating tumour DNA (ctDNA) is becoming increasingly important in clinical treatment decisions. A pilot External Quality Assessment (EQA) scheme for ctDNA analysis was organized by four European EQA providers under the umbrella organization IQN Path, in order to investigate the feasibility of delivering an EQA to assess the detection of clinically relevant variants in plasma circulating cell-free DNA (cfDNA) and to analyze reporting formats.

METHODS: Thirty-two experienced laboratories received 5 samples for EGFR mutation analysis and/or 5 samples for KRAS and NRAS mutation analysis. Samples were artificially manufactured to contain 3 mL of human plasma with 20 ng/mL of fragmented ctDNA and variants at allelic frequencies of 1 and 5%.

RESULTS: The scheme error rate was 20.1%. Higher error rates were observed for RAS testing when compared to EGFR analysis, for allelic frequencies of 1% compared to 5%, and for cases including 2 different variants. The reports over-interpreted wild-type results and frequently failed to comment on the amount of cfDNA extracted.

CONCLUSIONS: The pilot scheme demonstrated the feasibility of delivering a ctDNA EQA scheme and the need for such a scheme due to high error rates in detecting low frequency clinically relevant variants. Recommendations to improve reporting of cfDNA are provided.

Original languageEnglish
Pages (from-to)804
JournalBMC Cancer
Volume18
Issue number1
DOIs
Publication statusPublished - Aug 9 2018

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DNA
Neoplasms
Mutation
Needs Assessment
Plasma Cells
Organizations

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International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA. / Keppens, Cleo; Dequeker, Elisabeth M C; Patton, Simon J; Normanno, Nicola; Fenizia, Francesca; Butler, Rachel; Cheetham, Melanie; Fairley, Jennifer A; Williams, Hannah; Hall, Jacqueline A; Schuuring, Ed; Deans, Zandra C.

In: BMC Cancer, Vol. 18, No. 1, 09.08.2018, p. 804.

Research output: Contribution to journalArticle

Keppens, C, Dequeker, EMC, Patton, SJ, Normanno, N, Fenizia, F, Butler, R, Cheetham, M, Fairley, JA, Williams, H, Hall, JA, Schuuring, E & Deans, ZC 2018, 'International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA', BMC Cancer, vol. 18, no. 1, pp. 804. https://doi.org/10.1186/s12885-018-4694-x
Keppens, Cleo ; Dequeker, Elisabeth M C ; Patton, Simon J ; Normanno, Nicola ; Fenizia, Francesca ; Butler, Rachel ; Cheetham, Melanie ; Fairley, Jennifer A ; Williams, Hannah ; Hall, Jacqueline A ; Schuuring, Ed ; Deans, Zandra C. / International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA. In: BMC Cancer. 2018 ; Vol. 18, No. 1. pp. 804.
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abstract = "BACKGROUND: Molecular analysis of circulating tumour DNA (ctDNA) is becoming increasingly important in clinical treatment decisions. A pilot External Quality Assessment (EQA) scheme for ctDNA analysis was organized by four European EQA providers under the umbrella organization IQN Path, in order to investigate the feasibility of delivering an EQA to assess the detection of clinically relevant variants in plasma circulating cell-free DNA (cfDNA) and to analyze reporting formats.METHODS: Thirty-two experienced laboratories received 5 samples for EGFR mutation analysis and/or 5 samples for KRAS and NRAS mutation analysis. Samples were artificially manufactured to contain 3 mL of human plasma with 20 ng/mL of fragmented ctDNA and variants at allelic frequencies of 1 and 5{\%}.RESULTS: The scheme error rate was 20.1{\%}. Higher error rates were observed for RAS testing when compared to EGFR analysis, for allelic frequencies of 1{\%} compared to 5{\%}, and for cases including 2 different variants. The reports over-interpreted wild-type results and frequently failed to comment on the amount of cfDNA extracted.CONCLUSIONS: The pilot scheme demonstrated the feasibility of delivering a ctDNA EQA scheme and the need for such a scheme due to high error rates in detecting low frequency clinically relevant variants. Recommendations to improve reporting of cfDNA are provided.",
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AU - Keppens, Cleo

AU - Dequeker, Elisabeth M C

AU - Patton, Simon J

AU - Normanno, Nicola

AU - Fenizia, Francesca

AU - Butler, Rachel

AU - Cheetham, Melanie

AU - Fairley, Jennifer A

AU - Williams, Hannah

AU - Hall, Jacqueline A

AU - Schuuring, Ed

AU - Deans, Zandra C

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N2 - BACKGROUND: Molecular analysis of circulating tumour DNA (ctDNA) is becoming increasingly important in clinical treatment decisions. A pilot External Quality Assessment (EQA) scheme for ctDNA analysis was organized by four European EQA providers under the umbrella organization IQN Path, in order to investigate the feasibility of delivering an EQA to assess the detection of clinically relevant variants in plasma circulating cell-free DNA (cfDNA) and to analyze reporting formats.METHODS: Thirty-two experienced laboratories received 5 samples for EGFR mutation analysis and/or 5 samples for KRAS and NRAS mutation analysis. Samples were artificially manufactured to contain 3 mL of human plasma with 20 ng/mL of fragmented ctDNA and variants at allelic frequencies of 1 and 5%.RESULTS: The scheme error rate was 20.1%. Higher error rates were observed for RAS testing when compared to EGFR analysis, for allelic frequencies of 1% compared to 5%, and for cases including 2 different variants. The reports over-interpreted wild-type results and frequently failed to comment on the amount of cfDNA extracted.CONCLUSIONS: The pilot scheme demonstrated the feasibility of delivering a ctDNA EQA scheme and the need for such a scheme due to high error rates in detecting low frequency clinically relevant variants. Recommendations to improve reporting of cfDNA are provided.

AB - BACKGROUND: Molecular analysis of circulating tumour DNA (ctDNA) is becoming increasingly important in clinical treatment decisions. A pilot External Quality Assessment (EQA) scheme for ctDNA analysis was organized by four European EQA providers under the umbrella organization IQN Path, in order to investigate the feasibility of delivering an EQA to assess the detection of clinically relevant variants in plasma circulating cell-free DNA (cfDNA) and to analyze reporting formats.METHODS: Thirty-two experienced laboratories received 5 samples for EGFR mutation analysis and/or 5 samples for KRAS and NRAS mutation analysis. Samples were artificially manufactured to contain 3 mL of human plasma with 20 ng/mL of fragmented ctDNA and variants at allelic frequencies of 1 and 5%.RESULTS: The scheme error rate was 20.1%. Higher error rates were observed for RAS testing when compared to EGFR analysis, for allelic frequencies of 1% compared to 5%, and for cases including 2 different variants. The reports over-interpreted wild-type results and frequently failed to comment on the amount of cfDNA extracted.CONCLUSIONS: The pilot scheme demonstrated the feasibility of delivering a ctDNA EQA scheme and the need for such a scheme due to high error rates in detecting low frequency clinically relevant variants. Recommendations to improve reporting of cfDNA are provided.

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