title: Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants.
abstract: High resolution melt (HRM) is gaining considerable popularity as a simple and robust method for genotyping sequence variants. However, accurate genotyping of an unknown sample for which a large number of possible variants may exist will require an automated HRM curve identification method capable of comparing unknowns against a large cohort of known sequence variants. Herein, we describe a new method for automated HRM curve classification based on machine learning methods and learned tolerance for reaction condition deviations. We tested this method in silico through multiple cross-validations using curves generated from 9 different simulated experimental conditions to classify 92 known serotypes of Streptococcus pneumoniae and demonstrated over 99% accuracy with 8 training curves per serotype. In vitro verification of the algorithm was tested using sequence variants of a cancer-related gene and demonstrated 100% accuracy with 3 training curves per sequence variant. The machine learning algorithm enabled reliable, scalable, and automated HRM genotyping analysis with broad potential clinical and epidemiological applications.
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Pornpat
authors.initials: P
authors.lastname: Athamanolap
authors.affiliation: Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America; The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Medicine, Baltimore, Maryland, United States of America.
authors.forename: Vishwa
authors.initials: V
authors.lastname: Parekh
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America; Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, Maryland, United States of America.
authors.forename: Stephanie I
authors.initials: SI
authors.lastname: Fraley
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Vatsal
authors.initials: V
authors.lastname: Agarwal
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Dong J
authors.initials: DJ
authors.lastname: Shin
authors.affiliation: The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Medicine, Baltimore, Maryland, United States of America; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, United States of America.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Jacobs
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America; Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Tza-Huei
authors.initials: TH
authors.lastname: Wang
authors.affiliation: Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, Maryland, United States of America.
authors.forename: Samuel
authors.initials: S
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000235:genetics; D017931:DNA Primers / Q000378:metabolism; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008274:Magnesium / Q000494:pharmacology; D009691:Nucleic Acid Denaturation / Q000235:genetics*; D011188:Potassium / Q000494:pharmacology; D015203:Reproducibility of Results; D012703:Serotyping; D012964:Sodium / Q000494:pharmacology; D013296:Streptococcus pneumoniae / Q000145:classification / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D017931:DNA Primers; C411762:RASSF1 protein, human; D025521:Tumor Suppressor Proteins; D004247:DNA; D012964:Sodium; D008274:Magnesium; D011188:Potassium