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. 2018 Mar 1;35(1):49-53.
doi: 10.4274/tjh.2017.0095. Epub 2017 Nov 13.

NPM1 Mutation Analysis in Acute Myeloid Leukemia: Comparison of Three Techniques - Sanger Sequencing, Pyrosequencing, and Real-Time Polymerase Chain Reaction

Dushyant Kumar  1 , Anurag Mehta  2 , Manoj Kumar Panigrahi  1 , Sukanta Nath  1 , Kandarpa Kumar Saikia  1
Affiliations

NPM1 Mutation Analysis in Acute Myeloid Leukemia: Comparison of Three Techniques - Sanger Sequencing, Pyrosequencing, and Real-Time Polymerase Chain Reaction

Dushyant Kumar et al. Turk J Haematol. .

Abstract
in English, Turkish

Objective: Nucleophosmin-1 (NPM1) mutations have prognostic importance in acute myeloid leukemia (AML) patients with intermediate-risk karyotype at diagnosis. Approximately 30% of newly diagnosed cytogenetically normal AML (CN-AML) patients harbor the NPM1 mutation in India. In this study we compared the efficiency of three molecular techniques in detecting NPM1 mutation in peripheral blood and bone marrow samples.

Materials and methods: In a single-center cohort we analyzed 165 CN-AML bone marrow/peripheral blood samples for NPM1 mutation analysis. About 30% of the CN-AML samples revealed NPM1 mutations. For the detection, three methods were compared: Sanger sequencing, pyrosequencing, and real-time polymerase chain reaction (PCR).

Results: NPM1 exon 12 mutations were observed in 52 (31.51%) of all CN-AML cases. The sensitivity of Sanger sequencing, pyrosequencing, and real-time PCR was 80%, 90%, and 95%, whereas specificity was 95%, 100%, and 100%, respectively. The minimum limit of mutation detection was 20%-30% for Sanger sequencing, 1%-5% for pyrosequencing, and 0.1%-1% for real-time PCR.

Conclusion: The sequencing method, which is the reference method, has the lowest sensitivity and is sometimes difficult to interpret. Real-time PCR is a highly sensitive method for mutation detection but is limited for specific mutation types. In our study, pyrosequencing emerged as the most suitable technique for the detection of NPM1 mutations on the basis of its easy interpretation and less time-consuming processes than Sanger sequencing.

Amaç: Nükleofosmin-1 (NPM1) mutasyonları tanı anında orta risk akut miyeloid lösemi (AML) hastalarında prognostik öneme sahiptir. Hindistan’da, yeni teşhis normal sitogenetiğe sahip AML (CN-AML) hastalarının yaklaşık %30’u NPM1 pozitiftir. Bu çalışmada periferik kan ve kemik iliği örneklerinde NPM1 mutasyonu saptamada kullanılan üç moleküler tekniğin etkinliğini karşılaştırdık. Gereç ve Yöntemler: Tek merkezli bu kohortta, 165 CN-AML kemik iliği/periferik kan örneklerinde NPM1 mutasyon analizi yapıldı. CN-AML örneklerinin yaklaşık %30’unda NPM1 mutasyonu saptandı. Mutasyonun taranmasında üç yöntem karşılaştırıldı: Sanger dizileme, pirodizileme, gerçek-zamanlı polimeraz zincir reaksiyonu (PCR). Bulgular: Tüm CN-AML olgularının 52’sinde (%31,51) NPM1 exon12 mutasyonları gözlendi. Sanger dizileme, pirodizileme ve gerçek zamanlı PCR’nin duyarlılıkları sırasıyla %80, %90 ve %95 iken, özgünlükleri %95, %100 ve %100’dü. Mutasyonun saptanmasında minimum limit Sanger dizileme yöntemi için %20-%30, pirodizilemede %1-5, ve gerçek-zamanlı PCR için %0,1-%1 idi. Sonuç: Referans yöntemi olan dizileme yöntemi, en düşük duyarlılığa sahiptir ve bazen yorumlaması güçtür. Gerçek-zamanlı PCR mutasyon saptamada yüksek duyarlılığa sahip bir yöntemdir fakat özel mutasyon tipleri için sınırlıdır. Çalışmamızda, pirodizileme yönteminin kolay yorumlanması ve Sanger dizileme yönteminden daha az zaman harcanan işlem olması esasına dayanarak NPM1 mutasyonun saptanmasında en uygun teknik olduğu sonucuna varılmıştır.

Keywords: Acute myeloid leukemia Mutation analysis.; NPM1; Pyrosequencing.

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Conflict of interest statement

Conflict of Interest: The authors of this paper have no conflicts of interest, including specific financial interests, relationships, and/or affiliations relevant to the subject matter or materials included.

Figures

Figure 1
Figure 1. NPM1 mutation detection by pyrosequencing detection by pyrosequencing.
Figure 2
Figure 2. A) NPM1 mutation detection by real-time polymerase chain reaction using Ipsogen MutaScreen Kit. B) Sanger sequencing.
See this image and copyright information in PMC

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