title: Reconstruction of genealogical relationships with applications to Phase III of HapMap.
abstract: BACKGROUND
  Accurate inference of genealogical relationships between pairs of individuals is paramount in association studies, forensics and evolutionary analyses of wildlife populations. Current methods for relationship inference consider only a small set of close relationships and have limited to no power to distinguish between relationships with the same number of meioses separating the individuals under consideration (e.g. aunt-niece versus niece-aunt or first cousins versus great aunt-niece).
  
  
  RESULTS
  We present CARROT (ClAssification of Relationships with ROTations), a novel framework for relationship inference that leverages linkage information to differentiate between rotated relationships, that is, between relationships with the same number of common ancestors and the same number of meioses separating the individuals under consideration. We demonstrate that CARROT clearly outperforms existing methods on simulated data. We also applied CARROT on four populations from Phase III of the HapMap Project and detected previously unreported pairs of third- and fourth-degree relatives.
  
  
  BACKGROUND
  Source code for CARROT is freely available at http://carrot.stanford.edu.
  
  
  BACKGROUND
  sofiakp@stanford.edu.
authors.affiliation: Department of Computer Science, Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA. sofiakp@stanford.edu
authors.forename: Sofia
authors.initials: S
authors.lastname: Kyriazopoulou-Panagiotopoulou
authors.forename: Dorna
authors.initials: D
authors.lastname: Kashef Haghighi
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Aerni
authors.forename: Andreas
authors.initials: A
authors.lastname: Sundquist
authors.forename: Sivan
authors.initials: S
authors.lastname: Bercovici
authors.forename: Serafim
authors.initials: S
authors.lastname: Batzoglou
mesh_terms: D000465:Algorithms; D000818:Animals; D005789:Genealogy and Heraldry; D006801:Humans; D008390:Markov Chains