The predominant circulating cells in chronic myelogenous leukemia (CML) morphologically resemble normal myeloid precursors; however, certain characteristics indicate the two are not identical. Approximately 88% of the patients with clinically typical CML present with a cytogenetic abnormality known as the Philadelphia chromosome (Ph1). Additionally, the leukocyte alkaline phosphatase (LAP) value is decreased in CML. To investigate if there are selected genes expressed in the CML cell population, poly(A+)RNA from a chronic-phase, Ph1-positive CML patient was used for construction of a complementary DNA (cDNA) library. Recombinant clones representing moderately to abundantly transcribed sequences were selected by annealing [32P]-cDNA transcribed from homologous RNA to the library sequences and assessing radioactivity in the hybrids. From an initial 729 colonies, 417 (57.2%) displayed a hybridization signal more intense than controls, indicating these recombinant plasmids contained sequences homologous to moderately or highly expressed RNAs from this particular patient. Screening of the 417 clones--utilizing 32P-cDNAs derived from normal human placenta, an acute myelomonocytic leukemia (AMML), and two other CML samples--was used to select clones likely to represent sequences preferentially expressed in CML. Sixteen recombinants were initially selected that repeatedly failed to display hybridization with the placenta and AMML- derived probes. Further analysis of eight of these clones indicated that six contain sequences preferentially expressed in CML. One clone, C-A3, has been studied with 63 different RNA samples. This sequence is found to be highly expressed in peripheral blood cells from the chronic phase of both Ph1-positive and Ph1-negative CML as well as in a Ph1- positive acute myelogenous leukemia (AML). Expression is reduced in lymphoblastic crisis of CML (L BC-CML) and essentially absent in myeloblastic crisis of CML (M BC-CML). While preliminary, the results suggest that this probe may be useful as an aid in diagnosing Ph1- negative CML and in distinguishing M BC-CML from L BC-CML and Ph1- positive AML.