title: Simplified fluorescent multiplex PCR method for evaluation of the T-cell receptor V beta-chain repertoire.
abstract: BACKGROUND
  Evaluation of the T-cell receptor (TCR) V beta-chain repertoire by PCR-based CDR3 length analysis allows fine resolution of the usage of the TCR V beta repertoire and is a sensitive tool to monitor changes in the T-cell compartment. A multiplex PCR method employing 24 labeled upstream V beta primers instead of the conventionally labeled downstream C beta primer is described.
  
  
  METHODS
  RNA was isolated from purified CD4 and CD8 T-cell subsets from umbilical cord blood and clinical samples using TRI reagent followed by reverse transcription using a C beta primer and an Omniscript RT kit. The 24 V beta primers were multiplexed based on compatibility and product sizes into seven reactions. cDNA was amplified using 24 V beta primers (labeled with tetrachloro-6-cardoxyfluorescein, 6-carboxyfluorescein, and hexachloro-6-carboxyfluorescein), an unlabeled C beta primer, and Taqgold polymerase. The fluorescent PCR products were resolved on an automated DNA sequencer and analyzed using the Genotyper 2.1 software.
  
  
  RESULTS
  V beta spectratypes of excellent resolution were obtained with RNA amounts of 250 ng using the labeled V beta primers. The resolution was superior to that obtained with the labeled C beta primer assay. Also the numbers of PCRs were reduced to 7 from the 12 required in the C beta labeling method, and the sample processing time was reduced by half.
  
  
  CONCLUSIONS
  The method described for T-cell receptor V beta-chain repertoire analysis eliminates tedious dilutions and results in superior resolution with small amounts of RNA. The fast throughput makes this method suitable for automation and offers the feasibility to perform TCR V beta repertoire analyses in clinical trials.
authors.affiliation: Immunology and Inflammation Center of Excellence, North Shore--Long Island Jewish Research Institute, North Shore University Hospital--NYU School of Medicine, Manhasset, NY 11030, USA.
authors.forename: Sanjit
authors.initials: S
authors.lastname: Fernandes
authors.forename: Surendra
authors.initials: S
authors.lastname: Chavan
authors.forename: Vivek
authors.initials: V
authors.lastname: Chitnis
authors.forename: Nina
authors.initials: N
authors.lastname: Kohn
authors.forename: Savita
authors.initials: S
authors.lastname: Pahwa
mesh_terms: D015704:CD4 Antigens / Q000378:metabolism; D016827:CD8 Antigens / Q000378:metabolism; D022801:Complementarity Determining Regions / Q000097:blood* / Q000235:genetics; D005312:Fetal Blood / Q000378:metabolism; D005453:Fluorescence; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000097:blood* / Q000235:genetics / Q000276:immunology; D012016:Reference Values; D013601:T-Lymphocytes / Q000378:metabolism*
chemical_list: D015704:CD4 Antigens; D016827:CD8 Antigens; D022801:Complementarity Determining Regions; D016693:Receptors, Antigen, T-Cell, alpha-beta