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Inter-Laboratory Evaluation of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia

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Abstract

Introduction

Acute myeloid leukemia (AML) is a heterogeneous clonal disorder often associated with dismal overall survival. The clinical diversity of AML is reflected in the range of recurrent somatic mutations in several genes, many of which have a prognostic and therapeutic value. Targeted next-generation sequencing (NGS) of these genes has the potential for translation into clinical practice. In order to assess this potential, an inter-laboratory evaluation of a commercially available AML gene panel across three diagnostic centres in the UK and Ireland was performed.

Methods

DNA from six AML patient samples was distributed to each centre and processed using a standardised workflow, including a common sequencing platform, sequencing chips and bioinformatics pipeline. A duplicate sample in each centre was run to assess inter- and intra-laboratory performance.

Results

An average sample read depth of 2725X (range 629–5600) was achieved using six samples per chip, with some variability observed in the depth of coverage generated for individual samples and between centres. A total of 16 somatic mutations were detected in the six AML samples, with a mean of 2.7 mutations per sample (range 1–4) representing nine genes on the panel. 15/16 mutations were identified by all three centres. Allelic frequencies of the mutations ranged from 5.6 to 53.3 % (median 44.4 %), with a high level of concordance of these frequencies between centres, for mutations detected.

Conclusion

In this inter-laboratory comparison, a high concordance, reproducibility and robustness was demonstrated using a commercially available NGS AML gene panel and platform.

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Correspondence to Karl Haslam.

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Conflict of interest

Karl Haslam, Mark A. Catherwood, Edwina Dobbin, Anne Sproul, Stephen E. Langabeer and Ken I. Mills declare that they have no competing interests.

Funding

Ken I. Mills was employed by Queen’s University Belfast, and part of this work was supported from the development Grant (R2536CNR) awarded from Leukaemia and Lymphoma Northern Ireland.

Ethical Approval and Informed Consent

All procedures performed involving human participants were in accordance with the ethical standards of the institution and the 1964 Helsinki declaration or comparable ethical standards.

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Haslam, K., Catherwood, M.A., Dobbin, E. et al. Inter-Laboratory Evaluation of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia. Mol Diagn Ther 20, 457–461 (2016). https://doi.org/10.1007/s40291-016-0222-3

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  • DOI: https://doi.org/10.1007/s40291-016-0222-3

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