Detection of CALR Mutation in Clonal and Nonclonal Hematologic Diseases Using Fragment Analysis and Next-Generation Sequencing

• Published in: American journal of clinical pathology 2016-10, Vol.146 (4), p.448-455
• Main Authors: Gardner, Juli-Anne, Peterson, Jason D., Turner, Scott A., Soares, Barbara L., Lancor, Courtney R., dos Santos, Luciana L., Kaur, Prabhjot, Ornstein, Deborah L., Tsongalis, Gregory J., de Abreu, Francine B.
• Format: Article
• Language: English
• Subjects: Calreticulin - genetics; DNA Mutational Analysis; Fusion Proteins, bcr-abl - genetics; High-Throughput Nucleotide Sequencing; Humans; Janus Kinase 2 - genetics; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - diagnosis; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - genetics; Leukemia, Myeloid, Acute - diagnosis; Leukemia, Myeloid, Acute - genetics; Mutation; Polycythemia Vera - diagnosis; Polycythemia Vera - genetics; Primary Myelofibrosis - diagnosis; Primary Myelofibrosis - genetics; Thrombocythemia, Essential - diagnosis; Thrombocythemia, Essential - genetics
• ISSN: 0002-9173; 1943-7722
• DOI: 10.1093/ajcp/aqw129

Abstract Objectives: To describe three methods used to screen for frameshift mutations in exon 9 of the CALR gene. Methods: Genomic DNA from 47 patients was extracted from peripheral blood and bone marrow using the EZ1 DNA Blood Kit (Qiagen, Valencia, CA) and quantified by the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, San Diego, CA). After clinical history, cytogenetics, and molecular tests, patients were diagnosed with either clonal or nonclonal hematologic diseases. CALR screening was primarily performed using fragment analysis polymerase chain reaction, then next-generation sequencing and Sanger sequencing. Results: Among the 18 patients diagnosed with clonal diseases, one had acute myeloid leukemia (positive for trisomy 8), and 17 had myeloproliferative neoplasms (MPNs), including chronic myeloid leukemia (CML), essential thrombocythemia (ET), primary myelofibrosis (PMF), and polycythemia vera (PV). Patients with CML were positive for the BCR-ABL1 fusion. Ten patients were positive for JAK2 (PMF, n = 1; ET, n = 2; PV, n = 7), and three were CALR positive (ET, n = 1; PMF, n = 2). Patients diagnosed with a nonclonal disease were negative for JAK2, BCR-ABL, and CALR mutations. Conclusions: Screening for CALR mutations is essential in BCR-ABL–negative MPNs since it not only provides valuable diagnostic and prognostic information but also identifies potential treatment targets. Since this study describes the importance of screening for known and novel biomarkers, we described in detail three methods that could be easily integrated into a clinical laboratory.