title: Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves.
abstract: BACKGROUND
  High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst.
  
  
  METHODS
  We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately.
  
  
  RESULTS
  Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability.
  
  
  CONCLUSIONS
  We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.
authors.affiliation: Canon U.S. Life Sciences, Rockville, MD, United States of America.
authors.forename: Sami
authors.initials: S
authors.lastname: Kanderian
authors.affiliation: Canon U.S. Life Sciences, Rockville, MD, United States of America.
authors.forename: Lingxia
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Canon U.S. Life Sciences, Rockville, MD, United States of America.
authors.forename: Ivor
authors.initials: I
authors.lastname: Knight
mesh_terms: D000465:Algorithms; D057205:Automation, Laboratory; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D000069550:Machine Learning; D016133:Polymerase Chain Reaction / Q000379:methods; D012984:Software; D044366:Transition Temperature
chemical_list: D004247:DNA