Background. The development of myelofibrosis (MF) is driven by complex molecular genetic events that include driver somatic mutations responsible for the constitutive activation of the JAK/STAT signaling pathway (JAK2, CALR, and MPL), additional mutations affecting epigenetic regulators (TET2, ASXL1, IDH1/2, etc.) and RNA splicing (SRSF2, U2AF1, SF3B1, etc.), as well as genetic aberrations that contribute to genomic instability and disease progression.Aim. To analyze driver (JAK2, CALR, MPL) and prognostic (ASXL1) somatic mutations in patients with MF and evaluate their impact on survival.Materials and methods. The study included 29 patients diagnosed with MF, selected by hematologists from the City Clinical Hospital No. 7 and Regional Clinical Hospital (Krasnoyarsk).Results. 26 (89.6 %) out of 29 examined patients had some driver mutations in JAK2, CALR, MPL genes. The p.V617F mutation in the JAK2 gene was found in 20 (68.9 %) patients. Mutations in the CALR gene were detected in 4 (13.8 %) patients, mutations in the MPL gene were found in 3 patients (10.3 %). In 1 of 26 patients, 2 driver mutations were present simultaneously. 3 (10.3 %) patients were triple negative. Mutations in the ASXL1 gene were detected in 12 (41.4 %) out of 29 examined patients. Conducted targeted NGS (next generation sequencing) for 13 out of 29 patients revealed additional genetic variants that contribute to the understanding of the development mechanism and disease course. When evaluating the overall survival in the groups of patients diagnosed with MF examined by us, depending on the combination of driver (JAK2, CALR, MPL) and prognostic (ASXL1) mutations, no statistically significant differences were found (p = 0.12). This appears to be due to the small sample size. At the same time, assessment of patient survival depending on ASXL1 status showed that in the presence of mutations in the ASXL1 gene, the median survival was 45 months (range 7–120 months), while in the absence of mutations it was 48 months (range 21–359 months) (p = 0.03).Conclusion. The results obtained allow us to assume that the presence of mutations in the ASXL1 gene is an unfavorable factor in the course of the disease.

Background. The presence of the FLT3-ITD mutations in patients with AML serves as a marker of poor prognosis, which is included in the ELN 2017 risk stratification guideline. The main criterion for dividing patients into groups according to the predicted outcomes was the allelic ratio (AR) with a cutoff of 0.5: an AR value <0.5 is considered low, and ≥0.5 is considered high. At the same time, if the importance of AR determination is beyond doubt, the value of information about the length of the repeat and localization is still controversial. There are two common approaches for FLT3-ITD screening. The first, more accessible and cheaper method is the method of pCR electrophoresis and the second, more expensive and requiring special equipment, is the fragment analysis method, which allows not only to detect a mutation and determine the repeat length, but also to quantify or calculate AR.Aim. To compare fragment analysis and pCR electrophoresis in the search for the FLT3-ITD mutations in dNA samples from AML patients.Materials and methods. for the period of 2020–2022 fragment analysis and pCR electrophoresis were used to analyze blood and/or bone marrow samples taken from 45 patients with a confirmed diagnosis of AML who were treated at the Regional Clinical Hospital (Krasnoyarsk). Confirmation and identification of the FLT3-ITD mutations was performed by means of Sanger sequencing.Results. both methods revealed the FLT3-ITD mutations in 11 (24.45 %) patients among the 45 patients studied. According to the results of fragment analysis, the median repeat length was 42.70 base pairs (range 26.01–99.84 base pairs), AR was 0.532 (0.027–3.328), and the allelic frequency (Af) was 34.71 (2.67–76.90) %. Three different ITds were identified in one sample. Sanger sequencing identified mutations in 9 of 11 patients.Conclusion. fragment analysis and pCR electrophoresis showed similar results when analyzing samples with different ITd lengths and with different allelic ratios. but it can be assumed that in the case of a small ITd and low AR and Af values, when using pCR electrophoresis, the mutant allele will not be visualized, which can lead to a false negative result. The disadvantage of using the pCR electrophoresis method is also that without the use of special programs that allow determining the size and intensity of the band corresponding to the mutant allele, it is impossible to determine the AR value, which is important for AML risk stratification. Thus, for detection of the FLT3-ITD we recommend using the fragment analysis method.

JAK2 mutations can be associated with any phenotypic form of chronic myeloproliferative neoplasia, while MPL and CALR mutations occur, as a rule, in cases of essential thrombocythemia and primary myelofibrosis and they are not observed in polycythemia vera. In this article we describe a clinical case of CALR mutation (c.1154_1155insGTGTC; p.E386fs*46) presence in a JAK2 -negative polycythemia vera patient at age 36. In January 2018 changes in his hemogramm were recorded for the first time. In June 2018, based on a diagnostic study of bone marrow trepanobiopsy, a diagnosis of polycythemia vera was made. Molecular genetic study of the patient’s DNA didn’t reveal mutations in the JAK2 (12 and 14 exons) and the MPL genes. CALR mutation was revealed during the screening by heteroduplex analysis with the electrophoresis in polyacrylamide gel. Then the mutation was identified by Sanger’s DNA sequencing as с.1154_1155insGTGTC; p.E386fs*46. The allelic burden level as determined by pyrosequencing was 20 % (June 2018). In conclusion we can suppose that the revealed CALR mutation с.1154_1155insGTGTC; p.E386fs*46 plays its role in our patient’s polycythemia phenotype.

JAK2 mutations can be associated with any phenotypic form of chronic myeloproliferative neoplasia, while MPL and CALR mutations occur, as a rule, in cases of essential thrombocythemia and primary myelofibrosis and they are not observed in polycythemia vera. In this article we describe a clinical case of CALR mutation (c.1154_1155insGTGTC; p.E386fs*46) presence in a JAK2-negative polycythemia vera patient at age 36. In January 2018 changes in his hemogramm were recorded for the first time. In June 2018, based on a diagnostic study of bone marrow trepanobiopsy, a diagnosis of polycythemia vera was made. Molecular genetic study of the patient’s DNA didn’t reveal mutations in the JAK2 (12 and 14 exons) and the MPL genes. CALR mutation was revealed during the screening by heteroduplex analysis with the electrophoresis in polyacrylamide gel. Then the mutation was identified by Sanger’s DNA sequencing as с.1154_1155insGTGTC; p.E386fs*46. The allelic burden level as determined by pyrosequencing was 20 % (June 2018). In conclusion we can suppose that the revealed CALR mutation с.1154_1155insGTGTC; p.E386fs*46 plays its role in our patient’s polycythemia phenotype.

Background:JAK2 exon 12 mutations are seen in about 2-5% of JAK2V617F-negative cases of polycythemia vera (PV). Nowadays about 40 different JAK2 exon 12 mutations associated with PV have been identified and classified. To identify all possible variants, it is necessary to use sequencing. However, due to the high cost of sequencing, developing a two-stage algorithm for detect mutations in JAK2 exon 12 using inexpensive screening is of immediate practically necessity. We have previously proposed a two-stage algorithm for detect mutations in JAK2 exon 12 using inexpensive screening test by heteroduplex analysis (Subbotina T et al, Haematologica 2017). Aims: The aim of this study was to demonstrate the feasibility of HRM analysis using the CFX96 thermocycler and the Precision Melt Analysis software (Bio-Rad, USA) as the preliminary screening test for detection of JAK2 exon 12 mutations. Methods: DNA samples of 5 JAK2 exon 12 mutation positive PV patients were included in this study. The identification of the JAK2 exon 12 mutation types and allele burden measurement was carried out by pyrosequencing (Subbotina T et al, Haematologica 2014). All 5 patients have different mutation variant in the 12 exon of the JAK2 and different levels of allelic burden: c.1624_1629delAATGAA – 67%; с.1619_1627TCAgAAATg>AAA – 14%; c.1623_1628delAAATGA – 15%; c.1622_1627delGAAATG – 33%; c.1612_1616CACAA>TT – 21%. HRM analysis was performed using a Precision Melt Supermix reagent kit in the presence of Eva Green dye (Bio-Rad, USA). PCR with an additional high-resolution melting step was carried out on a CFX96 thermocycler (Bio-Rad, USA) according to the following program: denaturation at 95°C for 2 minutes, then 40 cycles at 95°C for 10 seconds, 58°C in for 30 seconds. The high resolution melting program consisted of denaturation at 95°C for 30 seconds, renaturation at 60°C for 1 minute, and melting at 65°C to 95°C with a 0.2°C gradient in 10 seconds. Each DNA sample was analyzed in duplicate. For the two out five JAK2 exon 12 mutations a threshold determination of the mutant allele presence was analyzed. To analyze the threshold for determining the proportion of the mutant allele, dilution of cloned wild-type and mutated samples was performed to obtain samples with different levels of allelic burden: 50%, 25%, 12.5%, 6.25%, 3.13%, 1.56%, 0.78%. Results:Figure 1 shows the differential melting plots of the DNA fragments. The analyzed samples were divided into five clusters: first cluster – melting curves of wild type DNA; second cluster – melting curves of DNA from samples with deletion type mutations: c.1624_1629delAATGAA and c.1622_1627delGAAATG; the third cluster – the DNA melting curves from the sample with the combined mutation: c.1612_161616CACAA>TT; the fourth cluster – DNA melting curves from the sample with deletion type mutation: c.1623 _1628delAAATGA; fifth cluster – DNA melting curves from a sample with the combined mutation: c.1619_1627TCAGAAATG>AAA. The detection thresholds in case of the c.1624_1629delAATGAA and с.1619_1627TCAgAAATg>AAA mutation analysis are 6.25% of the presence of the mutant allele in the samples (data not shown). Image:Summary/Conclusion: Therefore, the HRM analysis that was conducted on the CFX96 allows to screen highly specific for the PV diagnosis mutations in exon 12 of the JAK2 gene. The inclusion of this screening research in the laboratory testing algorithm improves the efficiency and accessibility of molecular genetic technologies in the diagnosis of PV.

Background. In accordance with the World health organization clinical guidelines, the analysis of somatic mutations in the CALR gene, as well as mutations in the JAK2 and MPL genes, are included in the list of criteria for the Ph-myeloproliferative neoplasms diagnosis.More than 50 different mutation variants have been found in the CALR gene, among which the most frequent are a 52 bp deletion (c.1092_1143del), also called type 1, and a 5 bp insertion (c.1154_1155insTTGTC), also called type 2 (88 %).The remaining 12 % are other type less frequent indels or combinations thereof.It is most convenient to use sequencing methods to identify all possible variants of CALR mutations. It is also important to develop inexpensive screening test that can detect any mutations in the analyzed DNA fragment of CALR gene. This method can be heteroduplex analysis followed by electrophoresis on polyacrylamide gel (PAGE).The objective: to develop and demonstrate the feasibility of using heteroduplex analysis with separation of the PCR product by electrophoresis on non-denaturing PAGE for the CALR exon 9 mutations detection as the screening test. Materials and methods. DNA samples of 13 CALR-positive patients with different phenotypic variants of Ph-myeloproliferative neoplasms were screened by heteroduplex analysis. For the most common variants of CALR mutations (c.1092_1143del and c.1154_1155insTTGTC), a threshold determination of the mutant allele presence was analyzed.Nucleotide sequence of exon 9 fragment was determined using Sanger sequencing. Also, all 13 samples were analyzed using the pyrosequencing method to assess the allelic burden level.Results. Heteroduplex analysis revealed mutations in exon 9 of the CALR gene in all 13 patients. The threshold determinations of the method in the case of the c.1154_1155insTTGTC and c.1092_1143del analysis are 6.25 % and 3.13 % of the mutant allele presence in the patient sample, respectively.Conclusion. The proposed variant of the heteroduplex analysis with separation of the PCR product by electrophoresis on non-denaturing PAGE can be recommended for use as the preliminary screening test which is carried out before the confirming sequencing methods for the different indels (or combinations thereof) CALR mutations determine.The presence of heteroduplexes indicates the presence of a mutation, even if the mutant product is not visualized (in case of small mutations).

Somatic mutations associated with oncological diseases, including Ph-myeloproliferative neoplasms (Ph-MPN), are very diverse, occur with different frequencies and different allelic burden levels. Therefore, at the initial stage of performing molecular-genetic diagnostic procedures, it is desirable to be able to conduct screening tests in the laboratory. This is especially important when analyzing rare and diverse mutations. Analysis of high resolution melting curves (HRM analysis), which has high sensitivity and is suitable for screening all types of mutations, in a number of studies is proposed for the analysis of Ph-MPN associated mutations in the JAK2 and CALR genes. For analysis of somatic mutations in the majority of literature sources that we reviewed, the authors use the LightCycler (Roche) thermocycler and much rarely the CFX96 (Bio-Rad), which is often presented in Russian scientific and practical and medical organizations. The aim of the study was to screen the somatic JAK2 and CALR mutations by HRM analysis using the CFX96 thermocycler and the Precision Melt Analysis software (Bio-Rad, USA) for patients with Ph-MPN. In the present research, HRM analysis was conducted on the DNA samples from patients with mutations in the JAK2 or in the CALR gene. The Precision Melt Analysis software identified all variants of the analyzed mutations, both a single nucleotide substitution in the JAK2 gene (with allelic burden level in the range of 5-40%), and various indel mutations in the CALR gene (with allelic burden level in the range of 40-50%) Therefore, the HRM analysis that was conducted on the CFX96 allows screening of highly specific mutation for the diagnosis of Ph-MPN in the exon 14 of the JAK2 gene and in the exon 9 of the CALR gene. The inclusion of this screening research in the laboratory testing algorithm improves the efficiency and accessibility of molecular genetic technologies in the diagnosis of Ph-MPN.