title: PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes.
abstract: PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. We demonstrate that discordances in mtDNA and NRY haplotypes substantially reduce the number of potential pedigrees, and often lead to the identification of the correct pedigree.
  
  
  METHODS
  We have implemented PRIMUS updates in PERL and it is available at primus.gs.washington.edu.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Staples
authors.affiliation: College of Public Service, Jackson State University, Jackson Heart Study, Jackson, MS 39213, USA.
authors.forename: Lynette
authors.initials: L
authors.lastname: Ekunwe
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Ethan
authors.initials: E
authors.lastname: Lange
authors.affiliation: Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA and.
authors.forename: James G
authors.initials: JG
authors.lastname: Wilson
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Nickerson
authors.affiliation: Department of Epidemiology, University of Texas Health Science Center, Houston, TX 77225, USA.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Below
mesh_terms: D000465:Algorithms; D041322:Chromosomes, Human, Y / Q000235:genetics*; D003198:Computer Simulation; D004272:DNA, Mitochondrial / Q000235:genetics*; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D010375:Pedigree; D012984:Software
chemical_list: D004272:DNA, Mitochondrial