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Patients who have myelofibrosis with myeloid metaplasia (MMM) display recurrent, albeit nonspecific cytogenetic abnormalities that are diverse prognostically. For the current study, the authors explored the relation between specific cytogenetic clones and JAK2V617F mutational status in patients with MMM and the effects on treatment response to erythropoietin (Epo).Concomitantly collected blood granulocytes and bone marrow were processed for JAK2V617F mutation analysis and cytogenetic studies, respectively. Genomic DNA was amplified by polymerase chain reaction, and fluorescent dye chemistry sequencing was performed by using the same primers that were used for amplification.Among 105 study patients, cytogenetic abnormalities were detected in 47 patients (45%), and the JAK2V617F mutation was detected in 52 patients (50%). Comparison of mutational frequencies between favorable (normal, sole 13q−, or 20q− clones; n = 70 patients) and unfavorable (all other abnormalities; n = 35 patients) cytogenetic categories revealed a significantly different incidence of homozygous JAK2V617F between them (9% vs. 23%, respectively; P = .04). Furthermore, the mutant allele coexisted with several recurrent cytogenetic lesions. Among 25 patients who received Epo either alone (n = 17 patients) or in combination with hydroxyurea (n = 8 patients), 4 patients (16%) achieved a response, and none of them were homozygous for JAK2V617F. Conversely, a response was more likely (P = .0001) in the presence of favorable cytogenetic abnormalities (i.e., 3 of 4 responders carried sole 13q− or 20q− clones).Unfavorable and favorable cytogenetic clones in MMM clustered with homozygosity for JAK2V617F and treatment response to Epo-based therapy, respectively. Cancer 2006. © 2006 American Cancer Society.