title: Detection of DNA copy number alterations using penalized least squares regression.
abstract: BACKGROUND
  Genomic DNA copy number alterations are characteristic of many human diseases including cancer. Various techniques and platforms have been proposed to allow researchers to partition the whole genome into segments where copy numbers change between contiguous segments, and subsequently to quantify DNA copy number alterations. In this paper, we incorporate the spatial dependence of DNA copy number data into a regression model and formalize the detection of DNA copy number alterations as a penalized least squares regression problem. In addition, we use a stationary bootstrap approach to estimate the statistical significance and false discovery rate.
  
  
  RESULTS
  The proposed method is studied by simulations and illustrated by an application to an extensively analyzed dataset in the literature. The results show that the proposed method can correctly detect the numbers and locations of the true breakpoints while appropriately controlling the false positives.
  
  
  BACKGROUND
  http://bioinformatics.med.yale.edu/DNACopyNumber
  
  
  BACKGROUND
  hongyu.zhao@yale.edu
  
  
  BACKGROUND
  http://bioinformatics.med.yale.edu/DNACopyNumber.
authors.affiliation: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Baolin
authors.initials: B
authors.lastname: Wu
authors.forename: Paul
authors.initials: P
authors.lastname: Lizardi
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018628:Gene Dosage / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D016018:Least-Squares Analysis; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D012044:Regression Analysis; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*