Development of E-ice-COLD-PCR assay combined with HRM analysis for Nucleophosmin1 gene mutation detection in acute myelogenous leukemia

PLoS One. 2022 Sep 14;17(9):e0274034. doi: 10.1371/journal.pone.0274034. eCollection 2022.

Abstract

Mutations of the nucleophosmin1 (NPM1) gene represent the most frequent molecular alteration in acute myelogenous leukemia (AML), especially in patients with AML who have a normal karyotype. These alterations have been shown to carry favorable prognostic significance in patients with AML. Several methods have been developed for detection of NPM1 gene mutations. However, their ability to detect low levels of mutations in a wild-type background is limited. In this study, the Enhance improved and complete enrichment Co-amplification at Lower Denaturation temperature Polymerase Chain Reaction (E-ice-COLD-PCR) assay combined with High Resolution Melting (HRM) analysis was developed and validated for highly specific and sensitive screening for NPM1 gene mutations. A total of 83 blood samples from patients with AML were collected, and their DNA was extracted. For mutational analysis, the E-ice-COLD-PCR assay for the detection of NPM1 gene mutations was developed. PCR products were analyzed by HRM analysis. All positive samples were confirmed by direct sequencing. This assay enabled detection specificity and sensitivity of NPM1 mutations in 9/83 patients with AML. Direct sequencing results were 100% concordant with this method. In addition, the limit of detection was 12.5% mutant in the final concentration of 5 ng genomic DNA. The E-ice-COLD-PCR assay with HRM analysis is a highly specific and sensitive screening method for enrichment of detecting NPM1 gene mutations. This method has both a short turn around time and easier interpretation compared to those of other methods.

MeSH terms

  • Humans
  • Ice*
  • Leukemia, Myeloid, Acute* / diagnosis
  • Leukemia, Myeloid, Acute* / genetics
  • Mutation
  • Nuclear Proteins / genetics
  • Nucleophosmin / genetics*
  • Polymerase Chain Reaction / methods

Substances

  • Ice
  • NPM1 protein, human
  • Nuclear Proteins
  • Nucleophosmin

Grants and funding

We are grateful for research fund from National Research Council of Thailand (NRCT), grant no. GSCMU (NRCT)/15/2563 to RK, Health System Research Institute (HSRI), grant no. HSRI 63-079 to SD, Chiang Mai University Grant for New Researcher to SD.