title: Design of an automated multicapillary instrument with fraction collection for DNA mutation discovery by constant denaturant capillary electrophoresis (CDCE).
abstract: A fundamental goal ingenomics is the discovery of genetic variation that contributes to disease states or to differential drug responses. Single nucleotide polymorphism (SNP) detection has been the focus of much attention in the study of genetic variation over the last decade. These SNPs typically occur at a frequency greater than 1% in the human genome. Recently, low-frequency alleles are also being increasingly recognized as critical to obtain an improved understanding of the correlation between genetic variation and disease. Although many methods have been reported for the discovery and scoringof SNPs, sensitive, automated, and cost-effective methods and platforms for the discovery of low-frequency alleles are not yet readily available. We describe here an automated multicapillary instrument for high-throughput detection of low-frequency alleles from pooled samples using constant denaturant capillary electrophoresis. The instrument features high optical sensitivity (1 x 10(-12) M fluorescein detection limit), precise and stable temperature control (+/- 0.01degrees C), and automation for sample delivery, injection, matrix replacement, and fraction collection. The capillary array is divided into six groups of four capillaries, each of which can be independently set at any temperature ranging from room temperature to 90 degrees C. The key performance characteristics of the instrument are reported.
authors.affiliation: SpectruMedix LLC, State College, PA, USA. qzl101@psu.edu
authors.forename: Qingbo
authors.initials: Q
authors.lastname: Li
authors.forename: Chiranjit
authors.initials: C
authors.lastname: Deka
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Glassner
authors.forename: Kevin
authors.initials: K
authors.lastname: Arnold
authors.forename: Xiao-Cheng
authors.initials: XC
authors.lastname: Li-Sucholeiki
authors.forename: Aoy
authors.initials: A
authors.lastname: Tomita-Mitchell
authors.forename: William G
authors.initials: WG
authors.lastname: Thilly
authors.forename: Barry L
authors.initials: BL
authors.lastname: Karger
mesh_terms: D015703:Antigens, CD; D000943:Antigens, Differentiation / Q000235:genetics; D001483:Base Sequence; D060908:CTLA-4 Antigen; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification*; D019075:Electrophoresis, Capillary / Q000295:instrumentation / Q000379:methods* / Q000706:statistics & numerical data; D004867:Equipment Design; D023281:Genomics / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data; D006801:Humans; D008780:Methyltransferases / Q000235:genetics; D009154:Mutation; D009691:Nucleic Acid Denaturation; D055095:Optics and Photonics / Q000295:instrumentation; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000295:instrumentation / Q000379:methods; D013696:Temperature
chemical_list: D015703:Antigens, CD; D000943:Antigens, Differentiation; D060908:CTLA-4 Antigen; C556706:CTLA4 protein, human; D004247:DNA; D008780:Methyltransferases; C022745:thiopurine methyltransferase