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Whole-genome-amplified DNA as a source for mutational analysis underestimates the frequency of mutations in pediatric acute myeloid leukemia

Leukemia volume 27, pages 510–512 (2013)Cite this article

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Acute myeloid leukemia (AML) is the most common acute leukemia in adults, whereas it constitutes only ∼15–20% of childhood leukemias. AML is a biologically and clinically heterogeneous disease, for which cytogenetic findings have proved essential for stratifying patients into prognostic subgroups. Although a large proportion of AML display normal karyotype (adults 35–50%, children 25%),1 recent developments have revealed molecular markers, such as the mutational status of the FMS-related tyrosine kinase 3 (FLT3), Nucleophosmin (NPM1) and CEBPA genes, to aid further subdivision of AML patients with normal karyotype. To date, these molecular prognosticators are well established in adult AML,2 whereas they have been less studied in pediatric AML. In a recent study, we performed an extensive analysis of DNA-based markers (for example, FLT3, NPM1, CEBPA and WT1 genes) and RNA-based markers in a large cohort of uniformly treated patients from the Nordic countries, further supporting FLT3 and NPM1 as key prognostic markers also in pediatric AML.3

One of the major obstacles when working with DNA samples with great clinical/scientific value, such as tumor samples from leukemia patients, is the limited amounts of DNA for genetic analysis. Whole-genome amplification (WGA) has therefore emerged as an important method for reproducing abundant quantities of DNA as an alternative source of DNA for genetic analysis. In recent years, implementation of WGA DNA has increased drastically for different type of applications, such as genome-wide analysis of single-nucleotide polymorphisms (SNP) and copy number variations (CNV).4, 5 However, the usefulness of WGA method is mainly based on the presumption that the entire genome is amplified with minimal amplification bias. One of the most commonly used WGA methods is the multiple displacement amplification (MDA), which replicates the genome isothermally using random hexamer primers and DNA polymerase, such as Phi29, followed by strand displacement. Even though several studies on Phi29 have demonstrated that it has high genome coverage, little amplification bias and high accuracy compared with genomic DNA controls,6, 7 controversial results have also been reported.8, 9

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Acknowledgements

This work was supported by a Young Investigator grant awarded to Dr Meena Kanduri by the Swedish Research Council.

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Authors and Affiliations

  1. Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden

    R Rosenquist

  2. Department of Clinical Genetics, Lund University, Lund, Sweden

    H Ehrencrona

  3. Department of Pediatrics, Aarhus University Hospital Skejby, Aarhus, Denmark

    H Hasle

  4. Department of Women’s and Children’s Health, University Children’s Hospital, Uppsala, Sweden

    J Palle

  5. Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden

    M Kanduri

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Correspondence to M Kanduri.

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Rosenquist, R., Ehrencrona, H., Hasle, H. et al. Whole-genome-amplified DNA as a source for mutational analysis underestimates the frequency of mutations in pediatric acute myeloid leukemia. Leukemia 27, 510–512 (2013). https://doi.org/10.1038/leu.2012.250

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