title: Identifying malignant transformations in recurrent low grade gliomas using high resolution magic angle spinning spectroscopy.
abstract: OBJECTIVE
  The objective of this study was to determine whether metabolic parameters derived from ex vivo analysis of tissue samples are predictive of biologic characteristics of recurrent low grade gliomas (LGGs). This was achieved by exploring the use of multivariate pattern recognition methods to generate statistical models of the metabolic characteristics of recurrent LGGs that correlate with aggressive biology and poor clinical outcome.
  
  
  METHODS
  Statistical models were constructed to distinguish between patients with recurrent gliomas that had undergone malignant transformation to a higher grade and those that remained grade 2. The pattern recognition methods explored in this paper include three filter-based feature selection methods (chi-square, gain ratio, and two-way conditional probability), a genetic search wrapper-based feature subset selection algorithm, and five classification algorithms (linear discriminant analysis, logistic regression, functional trees, support vector machines, and decision stump logit boost). The accuracy of each pattern recognition framework was evaluated using leave-one-out cross-validation and bootstrapping.
  
  
  METHODS
  The population studied included fifty-three patients with recurrent grade 2 gliomas. Among these patients, seven had tumors that transformed to grade 4, twenty-four had tumors that transformed to grade 3, and twenty-two had tumors that remained grade 2. Image-guided tissue samples were obtained from these patients using surgical navigation software. Part of each tissue sample was examined by a pathologist for histological features and for consistency with the tumor grade diagnosis. The other part of the tissue sample was analyzed with ex vivo nuclear magnetic resonance (NMR) spectroscopy.
  
  
  RESULTS
  Distinguishing between recurrent low grade gliomas that transformed to a higher grade and those that remained grade 2 was achieved with 96% accuracy, using areas of the ex vivo NMR spectrum corresponding to myoinositol, 2-hydroxyglutarate, hypo-taurine, choline, glycerophosphocholine, phosphocholine, glutathione, and lipid. Logistic regression and decision stump boosting models were able to distinguish between recurrent gliomas that transformed to a higher grade and those that did not with 100% training accuracy (95% confidence interval [93-100%]), 96% leave-one-out cross-validation accuracy (95% confidence interval [87-100%]), and 96% bootstrapping accuracy (95% confidence interval [95-97%]). Linear discriminant analysis, functional trees, and support vector machines were able to achieve leave-one-out cross-validation accuracy above 90% and bootstrapping accuracy above 85%. The three feature ranking methods were comparable in performance.
  
  
  CONCLUSIONS
  This study demonstrates the feasibility of using quantitative pattern recognition methods for the analysis of metabolic data from brain tissue obtained during the surgical resection of gliomas. All pattern recognition techniques provided good diagnostic accuracies, though logistic regression and decision stump boosting slightly outperform the other classifiers. These methods identified biomarkers that can be used to detect malignant transformations in individual low grade gliomas, and can lead to a timely change in treatment for each patient.
authors.affiliation: Electrical Engineering and Computer Science, Sutardja Dai Hall, University of California, Berkeley, Berkeley, CA 94709, USA. alexandra@berkeley.edu
authors.forename: Alexandra
authors.initials: A
authors.lastname: Constantin
authors.forename: Adam
authors.initials: A
authors.lastname: Elkhaled
authors.forename: Llewellyn
authors.initials: L
authors.lastname: Jalbert
authors.forename: Radhika
authors.initials: R
authors.lastname: Srinivasan
authors.forename: Soonmee
authors.initials: S
authors.lastname: Cha
authors.forename: Susan M
authors.initials: SM
authors.lastname: Chang
authors.forename: Ruzena
authors.initials: R
authors.lastname: Bajcsy
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Nelson
mesh_terms: D000465:Algorithms; D001706:Biopsy; D001932:Brain Neoplasms / Q000145:classification / Q000473:pathology* / Q000601:surgery; D002471:Cell Transformation, Neoplastic / Q000145:classification*; D003198:Computer Simulation; D016002:Discriminant Analysis; D005910:Glioma / Q000145:classification / Q000473:pathology* / Q000601:surgery; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D066298:In Vitro Techniques; D016015:Logistic Models; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D015233:Models, Statistical; D060787:Neoplasm Grading; D009364:Neoplasm Recurrence, Local / Q000145:classification / Q000473:pathology* / Q000601:surgery; D010363:Pattern Recognition, Automated