title: Genomics, transcriptomics, proteomics, and numbers.
abstract: OBJECTIVE
  To review the advances in clinically useful molecular biologic techniques and to identify their applications in clinical practice, as presented at the 11th Annual William Beaumont Hospital DNA Symposium.
  
  
  METHODS
  The 8 manuscripts submitted were reviewed, and their major findings were compared with literature on the same or related topics.
  
  
  METHODS
  Manuscripts address the use of molecular techniques in microbiology to evaluate infectious disease and epidemiology; molecular microbiology methods, including rapid-cycle real-time polymerase chain reaction; peroxisome proliferator-activated receptor gamma as a potential therapeutic target in inflammatory bowel disease or colon cancer; the effect of nonapoptotic doses of the bisbenizamide dye Hoechst 33342 on luciferase expression in plasmid-transfected BC3H-1 myocytes; the routine use of cystic fibrosis screening and its challenges; and the use of flow cytometry and/or chromosomal translocation in the diagnostic evaluation of hematopoietic malignancies.
  
  
  RESULTS
  Three current issues related to the use of molecular tests in clinical laboratories are (1) the restriction on introducing new tests secondary to existing patents or licenses; (2) the preanalytic variables for the different specimen types currently in use, including whole blood, plasma, serum, fresh or frozen tissues, and free-circulating DNA; and (3) the interpretation of studies evaluating the association of complex diseases with a single mutation or single-nucleotide polymorphism. Molecular methods have had a major impact on infectious disease through the rapid identification of organisms, the evaluation of outbreaks, and the characterization of drug resistance when compared with standard culture techniques. The activation of peroxisome proliferator-activated receptor gamma stimulated by thiazolidinedione is useful in the treatment of type II diabetes mellitus and may have value in preventing inflammatory bowel disease or colon cancer. Hoechst 33342 binding to adenine-thymine-rich regions in the minor groove of DNA is a fluorescent stain for DNA and initiates apoptosis at >10 microg/mL. Lower doses of Hoechst 33342 promote luciferase expression by a mechanism that may involve binding to cryptic promoters facilitated by dye-associated misalignment of the tertiary structure of DNA. The routine use of cystic fibrosis screening is complicated by the more than 1000 mutations associated with the disease. The use of 4-color flow cytometry and the detection of chromosomal translocation are both invaluable aids in establishing the diagnosis of lymphoid or myeloid hematopoietic malignancies.
  
  
  CONCLUSIONS
  The current postgenomic era will continue to emphasize the use of microarrays and database software for genomic, transcriptomic, and proteomic screening in the search for useful clinical assays. The number of molecular pathologic techniques will expand as additional disease-associated mutations are defined.
authors.affiliation: Department of Clinical Pathology, William Beaumont Hospital, Royal Oak, Mich 48073, USA. fkiechle@beaumont.edu
authors.forename: Frederick L
authors.initials: FL
authors.lastname: Kiechle
authors.forename: Carol A
authors.initials: CA
authors.lastname: Holland-Staley
mesh_terms: D003550:Cystic Fibrosis / Q000175:diagnosis / Q000235:genetics; D005820:Genetic Testing / Q000379:methods; D023281:Genomics / Q000379:methods* / Q000639:trends; D006801:Humans; D010338:Pathology, Clinical / Q000379:methods / Q000639:trends; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D040901:Proteomics / Q000379:methods* / Q000639:trends; D014158:Transcription, Genetic / Q000235:genetics*