Clinical Validation of a Multipurpose Assay for Detection and Genotyping of CALR Mutations in Myeloproliferative Neoplasms

Objectives: To develop a polymerase chain reaction (PCR) based approach to detect CALR mutations in myeloproliferative neoplasms (MPNs) in a clinical laboratory. Methods: DNA was extracted from bone marrow aspirate samples of 67 JAK2 MPNs (22 with matched peripheral blood), 54 cases of unclassifiable myelodysplastic syndrome/MPN, and 16 cases of atypical chronic myeloid leukemia. We used genomic DNA to detect somatic mutations in exon 9 of CALR and PCR with fluorescently labeled and M13-tagged primers and subjected the products to capillary electrophoresis (CE) followed by Sanger sequencing. Detailed assay performance characteristics were established. Results: We identified CALR mutations in 19 (28.4%) of 67 JAK2-negative MIDNs, including 14 type I (52 base pair [bp] deletion), four type II (5-bp insertions), and one type III (18-bp deletion). All mutations were confirmed by Sanger sequencing. Sensitivity studies showed 2.5% and 5% mutation detection levels by CE and Sanger sequencing, respectively, with high reproducibility. Conclusions: This assay allows for rapid, convenient screening for CALR mutations in MPNs, thereby reducing the number of cases that require assessment by Sanger sequencing, reducing labor and improving turnaround time.