title: Structural variation on the human Y chromosome from population-scale resequencing.
abstract: OBJECTIVE
  To investigate the information about Y-structural variants (SVs) in the general population that could be obtained by low-coverage whole-genome sequencing.
  
  
  METHODS
  We investigated SVs on the male-specific portion of the Y chromosome in the 70 individuals from Africa, Europe, or East Asia sequenced as part of the 1000 Genomes Pilot project, using data from this project and from additional studies on the same samples. We applied a combination of read-depth and read-pair methods to discover candidate Y-SVs, followed by validation using information from the literature, independent sequence and single nucleotide polymorphism-chip data sets, and polymerase chain reaction experiments.
  
  
  RESULTS
  We validated 19 Y-SVs, 2 of which were novel. Non-reference allele counts ranged from 1 to 64. The regions richest in variation were the heterochromatic segments near the centromere or the DYZ19 locus, followed by the ampliconic regions, but some Y-SVs were also present in the X-transposed and X-degenerate regions. In all, 5 of the 27 protein-coding gene families on the Y chromosome varied in copy number.
  
  
  CONCLUSIONS
  We confirmed that Y-SVs were readily detected from low-coverage sequence data and were abundant on the chromosome. We also reported both common and rare Y-SVs that are novel.
authors.forename: Jose Rodrigo Flores
authors.initials: JR
authors.lastname: Espinosa
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Chris Tyler-Smith,The Wellcome Trust Sanger Institute, Hinxton, Cambs. CB10 1SA, UK, cts@sanger.ac.uk.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000235:genetics*; D005787:Gene Frequency; D023281:Genomics / Q000379:methods; D006801:Humans; D008297:Male; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D044469:Racial Groups / Q000235:genetics*; D017422:Sequence Analysis, DNA; D044465:White People / Q000235:genetics