Myeloproliferative Disorders |
1 Laboratoire dHématologie, CHU, Bordeaux, France
2 Laboratoire dHématologie, CHU, Dijon, France
3 Murdoch University, Perth, Australia
4 University of Texas MD Anderson Cancer Center, Houston, Texas, USA
5 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA
6 Uniklinik Eppendorf, Hamburg, Germany
7 Molecular Genetics, Royal Devon and Exeter Hospital, Exeter, UK
8 Molecular Diagnostics, Jeroen Bosch Hospital, s-Hertogenbosch, Netherlands
9 Laboratoire dHématologie, CHU, Clermont-Ferrand, France
10 Hematology Division, University of Utah School of Medicine, Salt Lake City, Utah, USA
11 Laboratoire dHématologie, CHU, Brest, France
12 Laboratoire de Cytologie Clinique et Cytogénétique, CHU, Nîmes, France
13 Laboratoire d'Hématologie, Hôtel-Dieu, Paris, France
14 Department of Hematology, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
15 Experimental Hematology, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
16 Laboratoire dHématologie, CHU, Nantes, France
Correspondence: Sylvie Hermouet, Laboratoire dHématologie, Centre Hospitalier Universitaire, Institut de Biologie, 9 quai Moncousu, 44093 Nantes, France., E-mail:sylvie.hermouet{at}chu-nantes.fr
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Design and Methods: JAK2V617F quantification techniques were compared among 16 centers using 11 assays based on quantitative polymerase chain reaction (with mutation-specific primers or probes, or fluorescent resonance energy transfer/melting curve analysis), allele-specific polymerase chain reaction, conventional sequencing or pyrosequencing.
Results: A first series of blinded samples (granulocyte DNA, n=29) was analyzed. Seven assays (12 centers) reported values inside the mean±2SD; the mean coefficient of variation was 31%. Sequencing techniques lacked sensitivity, and strong discrepancies were observed with four techniques, which could be attributed to inadequate standards or to different modes of expression of results. Indeed, quantification of JAK2V617F in relation to another control gene produced higher than expected values, suggesting the possibility of more than two JAK2 copies/cell. After calibration of assays with common 1% to 100% JAK2V617F standards (dilutions of UKE-1 cells in normal leukocytes), 14 centers tested ten new samples. JAK2V617F allelic burdens greater or equal than 1% were then reliably quantified by five techniques – one allele specific-polymerase chain reaction and four TaqMan allele-specific quantitative polymerase chain reaction assays, including one previously giving results outside the mean±2SD – with a lower mean coefficient of variation (21%). Of these, only the two TaqMan allele-specific quantitative polymerase chain reaction assays with primer-based specificity could detect 0.2% JAK2V617F.
Conclusions: Techniques expressing the allelic burden as JAK2V617F/total JAK2 and using a common set of standards produced similar quantification results but with variable sensitivity. Calibration to a reference standard improved reproducibility.
Key words: JAK2V617F, quantification, standardization, allele-specific PCR, myeloproliferative diseases, multicenter study.
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We previously reported that JAK2V617F burdens are higher in polycythemia vera than in essential thrombocythemia.7,8 In addition, a high %JAK2V617F has been associated with increased risk of thrombotic events in essential thrombocythemia; increased risk of cardiovascular events, larger spleen and greater treatment requirement in polycythemia vera; and higher leukocytosis and risk of acute transformation in primary myelofibrosis.9–11 Some of these findings, however, are controversial: Pemmaraju et al.12 found no correlation between the %JAK2V617F in neutrophils and occurrence of thrombotic events. Thus reproducible quantification of the JAK2V617F burden is of major interest in the evaluation of myeloproliferative neoplasms. Quantification of JAK2V617F may also be important in the follow-up of patients who have received a bone marrow transplant or treatment with interferon
-2a and the soon-to-come JAK2 inhibitors.13,14
Understanding the discrepancies between the results of the studies reported here is partly dependent on the comparison of the techniques used for quantification. We, therefore, undertook a study comparing 11 different techniques, carried out in 16 laboratories using various instruments. After a first round of analyses, we distributed dilutions of JAK2V617F-positive DNA to standardize the assays. With adjustment for the mode of expression of the results and the use of common standards, five techniques were similarly reliable for the quantification of JAK2V617F loads greater than or equal to 1% of total JAK2; two of these techniques could detect 0.2% JAK2V617F. The advantages and disadvantages of the five techniques are presented.
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The standards used by eight participating centers were analyzed in center 7 using an allele-specific quantitative polymerase chain reaction (AS-qPCR).7,15 Subsequently, a set of standards based on a JAK2V617F-positive, diploid cell line (UKE-1) was defined and distributed to all centers. Following the calibration of local standards, a second series of test samples, comprising ten samples from patients and a series of DNA dilutions of two cell lines (HEL/Karpas 299, prepared in center 9), were assessed blindly. The HEL/Karpas series included four samples with a JAK2V617F allelic burden lower than or equal to 2%, to provide further information on the sensitivity of the various techniques. Technical issues prevented centers 8 and 13 from participating in this part of the study.
Patients
The diagnosis of myeloproliferative neoplasm was established according to WHO guidelines for all JAK2V617F-positive patients. Diagnoses were, for the two series of samples, respectively, secondary erythrocytosis (1; 1), atopic hypereosinophilia (1; 0), essential thrombocythemia (16; 3), polycythemia vera (10; 5) and primary myelofibrosis (1; 1).
Cell line characterization and DNA preparations
UKE-1 cells, kindly provided by Dr. Walter Fiedler (Hamburg, Germany), were grown as described elsewhere.16 DNA content was assessed by flow cytometry after treatment of ethanol-permeabilized cells with RNAse and staining with propidium iodide. The karyotype was established using standard cytogenetic techniques, synchronization with synchroset (Amplitech, France), heat denaturation and Giemsa staining of R bands. For preparation of JAK2V617F standards, UKE-1 cells were counted with a hemocytometer and diluted with leukocytes (buffy coat white blood cells, WBC) obtained from normal healthy individuals. Pellets of each mix of UKE-1 and WBC (100% UKE-1, 75% UKE-1 + 25% WBC, 50% UKE-1 + 50% WBC, ...) were kept frozen at –20°C. Genomic DNA was extracted using the QiaAmp kit. An additional cell line dilution series was obtained by diluting HEL into Karpas-299 cells. A mixture of 20% HEL + 80% Karpas 299 was found to have 50% JAK2V617F. Further dilutions were performed, taking this percentage into account.
Plasmids
Three sets of plasmids were used for quantification. Plasmids A and B were prepared in center 4 as described elsewhere.7 Briefly, a PCR fragment obtained by reverse transcriptase PCR of U937 or HEL (respectively wild type and mutant) with primers 3'-TTATGGACAACAGTCAAACAACA ATTCT-5' and 3'-AACTCCTGTTAAAT-TATAGTTTACTGACACC-5', was cloned into a TopoTA vector (Invitrogen, Carlsbad, CA, USA). Plasmids C and D were generated in center 8 by amplification of an 881 bp fragment with primers 3'-GATTCACTAATCATACCCAG-5' and 3'-TTGAACCTGCCATAATCTCT-5', cloned into pGEM T Easy (Promega, WI, USA). Plasmid E (mutant only) was prepared in center 15 as described by Hammond et al.20 The fragment obtained with primers 5'-TATCCCAAAGGACAGAAGTATTCATT-3' and 5'-TTGTGTTTCCCTCCCT GTTGGA-3' was cloned into Zero Blunt Topo (Invitrogen).
JAK2V617F quantification
The characteristics of the 11 techniques, used either for diagnosis/follow-up of patients with myeloproliferative neoplasms or for research, are presented in Table 1, while sequences of primers and probes can be found in the Online Supplementary Table S1. Most (13/16) centers had developed a quantitative real time PCR assay, predominantly (11/13) involving hydrolysis probe-based quantification. The same Taqman assay was used in five centers (centers 4, 5, 6, 7, and 8) with different real-time PCR machines; another assay was used in centers 9 and 10 on different qPCR platforms. Center 2 used fluorescent resonance energy transfer (FRET) probes, center 13 used SYBRgreen chemistry. Five assays based the specificity of detection on a primer, which at centers 9 and 10 was modified by inclusion of a mismatch and a locked nucleic acid. Center 12 quantified the products of a final point allele-specific PCR. Centers 3 and 16 performed DNA sequencing, with pyrosequencing and conventional Big Dye terminator chemistry, respectively. The assay used in center 1 was based on the TaqMan allelic discrimination assay principle. Results were expressed as percentages of mutated allele (%JAK2V617F) by all laboratories but center 15, which determined the ratio of JAK2V617F versus a control gene, human growth hormone (HGH). The different standards used for calibration included plasmids, cell lines or genomic DNA from patients.
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Table 1. Overview of JAK2V617F assays employed by the participating centers.
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Table 2. %JAK2V617F of total JAK2 n DNA of the first series of 29 clinical samples as determined by the 16 participating centers.
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Figure 1. Comparison of JAK2 plasmids. TaqMan AS-qPCR were performed in center 7 to determine the crossing points for five concentrations of plasmids A, C [wild type (WT) A], and B,D, and E (JAK2V617F, B).
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Assessment of %JAK2V617F using common UKE-1 standards
Fourteen laboratories, using ten assays, participated in this second part of the comparisons. The UKE-1 standards were distributed to all centers, with the instruction to calibrate local standards if necessary. A new series of samples from ten patients plus a series of DNA dilutions of HEL/Karpas 299 cells including four samples with lower or equal than 2% JAK2V617F, were then blindly assessed.
Only one false positive result was reported (DNA pool of healthy individuals declared to contain 0.15% JAK2V617F) (Table 3). The sample with the lowest theoretical mutation load (0.15% JAK2V617F) was found to be positive by only four of the ten techniques. Three other samples with low mutation burden (0.2–1.8%) were declared negative by centers 3 and 16. Center 16 also reported two samples with 1.6% and 2.1% JAK2V617F (mean values) as negative.
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Table 3. Quantification of JAK2V617F using common UKE-1 standards.
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Figure 2. Observed %JAK2V617F values compared to average and theoretical %JAK2V617F values. A and B. Results obtained by the various techniques giving values inside the mean±2 SD were compared to mean values (open diamonds) for samples from patients in the first (A) and second (B) series. Mean plus 2 SD (closed circles) and mean minus 2 SD (closed triangles) are indicated. C and D: results obtained by the various techniques giving values inside the mean±2 SD were compared to theoretical values (open diamonds) for dilutions of the Karpas (C) and UKE-1 (D) cell lines. Mean plus 2 SD (asterisk) and mean minus 2 SD (cross) obtained by all 14 laboratories or by the 11 laboratories producing values inside the mean±2 SD (closed triangles and closed squares) are represented.
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Table 4. Advantages and disadvantages of the seven JAK2V617F assays providing results inside the mean±2 SD.
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The study also underlined the necessity to use a single mode of expression of results, the percentage of total JAK2 represented by JAK2V617F (%JAK2V617F). Centers that expressed JAK2V617F as percentages of genes other than JAK2 consistently reported values outside the mean±2 SD. However, the %JAK2V617F values reported by center 15 that were more than two-fold the average values were exclusively found in samples from patients with polycythemia vera and primay myelofibrosis. Cells with more than two copies of wild type or mutated JAK2 may be found in cases of myeloproliferative neoplasms with chromosome 9 trisomy, which occurs in approximately one third of cases of polycythemia vera.23 Future studies with techniques evaluating the absolute number of copies of JAK2 per cell by quantifying against one or several control genes20,22 may bring useful information on the status and evolution of patients with myeloproliferative neoplasms.
Remarkably, using common UKE-1 standards, seven assays – conventional sequencing, pyrosequencing, one AS-PCR assay and four TaqMan assays – were found to assess JAK2V617F similarly. The mean CV in assessing 1% or more JAK2V617F in granulocyte DNA using the TaqMan and AS-PCR assays was relatively low (21%). Hence, the choice of technique depends on the desired sensitivity and equipment available. Not surprisingly, the two techniques with the poorest sensitivity were sequencing techniques. Both techniques allow rapid processing of large series of samples; pyro-sequencing also enables the detection of potential additional mutations present less than six to eight bases downstream of 1849G>T (V617F). Less expected was the finding of three very different techniques providing values inside the mean±2 SD with 1% sensitivity: one was quantitative (TaqMan assay with sensitivity based on probes, center 11) but two were semi-quantitative assays (TaqMan with double dye probe, center 1; AS-PCR, center 12).
The best sensitivity – 0.2% JAK2V617F – was achieved by three assays. One was reliable only for mutation loads of less than 10% JAK2V617F. Thus only two TaqMan AS-qPCR assays with primer-based specificity, using plasmid dilutions for wild type and mutated JAK2 quantification, consistently provided values inside the mean±2 SD with a sensitivity estimated at 0.2%. Both assays require two PCR reactions. The assay using LNA-modified primers gave the only false positive result (less than 0.2%). One might question the necessity to detect less than 1% JAK2V617F. However, highly sensitive techniques are required to study residual disease, notably for those patients who have received allografts or treatment with interferon
-2a.13,14 Moreover, we and others also recently demonstrated that hydroxyurea treatment can reduce JAK2V617F burden to very low or undetectable levels.24,25 Obviously, for a less than 1% sensitivity to be meaningful, JAK2V617F assays should be performed on purified cells, not on the highly variable mix of cells of whole blood.26
Finally, none of the assays tested can guarantee accurate quantification of JAK2V617F for all patients. Any unsuspected additional mutation occurring within the sequence of primers can potentially reduce or prevent amplification of the concerned allele, resulting in inaccurate quantification of JAK2V617F and possible false negative results. In these instances, a second assay based on primers or probes with non-overlapping sequences will confirm the initial assessment of %JAK2V617F.
The online version of this article contains a supplementary appendix.
EL: performed analyses, provided samples, analysed the data and wrote the paper; FG: performed analyses and provided samples; EH: performed analyses, provided samples and plasmids, NSR: performed analyses and provided samples; JJ, BF, KH, MH, CR, SS, VU, SC, VH, CM, DP, MS, MM, SE, NK, RH, JTP, RCS: designed assays and performed analyses; MM: performed statistical analyses; SH: designed the study, performed analyses, provided plasmids, and wrote the paper.
The authors reported no potential conflicts of interest.
Received for publication June 11, 2008. Revision received August 14, 2008. Accepted for publication August 25, 2008.
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