title: NPM1 Mutation Detection in Acute Myeloid Leukemia: A Method Comparison Study.
abstract: BACKGROUND
  Mutations in the nucleophosmin (NPM1) gene have been used as molecular biomarkers for prognostication of patients with adult acute myeloid leukemia (AML).
  
  
  METHODS
  We designed a rapid and sensitive method using the allele-specific-refractory mutation system-polymerase chain reaction (ARMS-PCR) to detect the most common mutations of NPM1 gene, which are mostly four base pair insertions and compared its efficacy with direct sequencing and capillary electrophoresis which served as the gold standards.
  
  
  RESULTS
  The incidence of mutation was 22% (33% of patients with normal karyotypes had mutation compared with 16% of patients with abnormal karyotypes) based on the results obtained with capillary electrophoresis analysis and direct sequencing. All of the specimens determined to be mutation-positive by the gold standard tests were also positive by the ARMS-PCR method. Significantly, the ARMS-PCR test also helped determine the mutation status of an extra set of patients who had low call rates on capillary electrophoresis and appeared normal on direct sequencing.
  
  
  CONCLUSIONS
  The low mutation rate in some patients hindered its detection in the gold standard assays because of the interference of the mutation signal by high background noise. The low sensitivity of the gold standard assays for detecting low copy number mutations rates thus increase their risk of producing false negative results that adversely affects prognostication and therapy. Our results suggest that the mutation detection rate of the ARMS-PCR assay is better than existing tests. This is most probably because of the fact that in an ARMS-PCR-based method, the mutated variant is specifically amplified, based on a mutation-specific primer.
  
  
  CONCLUSIONS
  We conclude that the high sensitivity of the ARMS-based method together with its rapidity and low expense should make it a suitable choice for clinical laboratories.
authors.affiliation: 1 Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences , Tehran, Iran .|2 Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran , Tehran, Iran .
authors.forename: Aileen
authors.initials: A
authors.lastname: Azari-Yam
authors.affiliation: 3 Kawsar Human Genetics Research Center , Tehran, Iran .
authors.forename: Samira Dabbagh
authors.initials: SD
authors.lastname: Bagheri
authors.affiliation: 1 Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences , Tehran, Iran .
authors.forename: Javad
authors.initials: J
authors.lastname: Tavakkoly-Bazzaz
authors.affiliation: 3 Kawsar Human Genetics Research Center , Tehran, Iran .|4 Science and Research Branch, Islamic Azad University , Tehran, Iran .
authors.forename: Ameneh Bandehi
authors.initials: AB
authors.lastname: Sarhaddi
authors.affiliation: 3 Kawsar Human Genetics Research Center , Tehran, Iran .|5 Tehran North Branch, Islamic Azad University , Tehran, Iran .
authors.forename: Leili
authors.initials: L
authors.lastname: Rejali
authors.affiliation: 6 Hematology Oncology, and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences , Tehran, Iran .
authors.forename: Kamran
authors.initials: K
authors.lastname: Alimoghaddam
authors.affiliation: 6 Hematology Oncology, and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences , Tehran, Iran .
authors.forename: Marjan
authors.initials: M
authors.lastname: Yaghmaie
authors.affiliation: 6 Hematology Oncology, and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences , Tehran, Iran .
authors.forename: Ardeshir
authors.initials: A
authors.lastname: Ghavamzadeh
authors.affiliation: 2 Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran , Tehran, Iran .
authors.forename: Sirous
authors.initials: S
authors.lastname: Zeinali
mesh_terms: D000328:Adult; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000175:diagnosis / Q000235:genetics*; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics*; D000090243:Nucleophosmin; D016133:Polymerase Chain Reaction / Q000379:methods*; D011379:Prognosis
chemical_list: C000716967:NPM1 protein, human; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D000090243:Nucleophosmin