title: Pharmacogenomic analysis of cytogenetic response in chronic myeloid leukemia patients treated with imatinib.
abstract: OBJECTIVE
  To better understand the molecular basis of cytogenetic response in chronic myeloid leukemia patients treated with imatinib, we studied gene expression profiles from a total of 100 patients from a large, multinational Phase III clinical trial (International Randomized Study of IFN-alpha versus STI571).
  
  
  METHODS
  Gene expression data for >12,000 genes were generated from whole blood samples collected at baseline (before imatinib treatment) using Affymetrix oligonucleotide microarrays. Cytogenetic response was determined based on the percentage of Ph(+) cells from bone marrow following a median of 13 months of treatment.
  
  
  RESULTS
  A genomic profile of response was developed using a subset of individuals that exhibited the greatest divergence in cytogenetic response; those with complete response (0% Ph(+) cells; n = 53) and those with minimal or no response (>65% Ph(+) cells; n = 13). A total of 55 genes was identified that were differentially expressed between these two groups. Using a "leave-one-out" strategy, we identified the optimum 31 genes from this list to use as our genomic profile of response. Using this genomic profile, we were able to distinguish between individuals that achieved major cytogenetic response (0-35% Ph(+) cells) and those that did not, with a sensitivity of 93.4% (71 of 76 patients), specificity of 58.3% (14 of 24 patients), positive predictive value of 87.7%, and negative predictive value of 73.7%.
  
  
  CONCLUSIONS
  Interestingly, many of the genes identified appear to be strongly related to reported mechanisms of BCR-ABL transformation and warrant additional research as potential drug targets. The validity and clinical implications of these results should be explored in future studies.
authors.affiliation: Clinical Pharmacogenetics Department, Novartis Pharmaceuticals Corporation, Gaithersburg, Maryland, USA. leanne.mclean@pharma.novartis.com
authors.forename: Lee Anne
authors.initials: LA
authors.lastname: McLean
authors.forename: Insa
authors.initials: I
authors.lastname: Gathmann
authors.forename: Renaud
authors.initials: R
authors.lastname: Capdeville
authors.forename: Mihael H
authors.initials: MH
authors.lastname: Polymeropoulos
authors.forename: Marlene
authors.initials: M
authors.lastname: Dressman
mesh_terms: D000970:Antineoplastic Agents / Q000627:therapeutic use*; D001549:Benzamides; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D001853:Bone Marrow / Q000378:metabolism / Q000473:pathology; D020732:Cytogenetic Analysis; D005260:Female; D016044:Fusion Proteins, bcr-abl / Q000378:metabolism; D020869:Gene Expression Profiling; D006801:Humans; D000068877:Imatinib Mesylate; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000188:drug therapy* / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D010597:Pharmacogenetics; D010879:Piperazines / Q000627:therapeutic use*; D011505:Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors; D011743:Pyrimidines / Q000627:therapeutic use*; D012334:RNA, Neoplasm / Q000378:metabolism; D016896:Treatment Outcome
chemical_list: D000970:Antineoplastic Agents; D001549:Benzamides; D014408:Biomarkers, Tumor; D010879:Piperazines; D011743:Pyrimidines; D012334:RNA, Neoplasm; D000068877:Imatinib Mesylate; D011505:Protein-Tyrosine Kinases; D016044:Fusion Proteins, bcr-abl