title: Development of a cost-effective high-throughput process of microsatellite analysis involving miniaturized multiplexed PCR amplification and automated allele identification.
abstract: BACKGROUND
  Microsatellites are nucleotide sequences of tandem repeats occurring throughout the genome, which have been widely used in genetic linkage analysis, studies of loss of heterozygosity, determination of lineage and clonality, and the measurement of genome instability or the emergence of drug resistance reflective of mismatch repair deficiency. Such analyses may involve the parallel evaluation of many microsatellite loci, which are often limited by sample DNA, are labor intensive, and require large data processing.
  
  
  RESULTS
  To overcome these challenges, we developed a cost-effective high-throughput approach of microsatellite analysis, in which the amplifications of microsatellites are performed in miniaturized, multiplexed polymerase chain reaction (PCR) adaptable to 96 or 384 well plates, and accurate automated allele identification has been optimized with a collective reference dataset of 5,508 alleles using the GeneMapper software.
  
  
  CONCLUSIONS
  In this investigation, we have documented our experience with the optimization of multiplex PCR conditions and automated allele identification, and have generated a unique body of data that provide a starting point for a cost-effective, high-throughput process of microsatellite analysis using the studied markers.
authors.affiliation: Department of Pediatrics, Vermont Cancer Center, University of Vermont, Burlington, VT 05401, USA.
authors.forename: Truc T M
authors.initials: TT
authors.lastname: Nguyen
authors.forename: Shaheen E
authors.initials: SE
authors.lastname: Lakhan
authors.forename: Barry A
authors.initials: BA
authors.lastname: Finette
mesh_terms: D000465:Algorithms; D000483:Alleles; D001483:Base Sequence; D016022:Case-Control Studies; D056426:Genetic Loci; D005819:Genetic Markers / Q000235:genetics; D042822:Genomic Instability; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics; D015448:Leukemia, B-Cell / Q000235:genetics; D019656:Loss of Heterozygosity; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software; D013601:T-Lymphocytes / Q000473:pathology
chemical_list: D005819:Genetic Markers