title: Copy number variation in the human Y chromosome in the UK population.
abstract: We have assessed copy number variation (CNV) in the male-specific part of the human Y chromosome discovered by array comparative genomic hybridization (array-CGH) in 411 apparently healthy UK males, and validated the findings using SNP genotype intensity data available for 149 of them. After manual curation taking account of the complex duplicated structure of Y-chromosomal sequences, we discovered 22 curated CNV events considered validated or likely, mean 0.93 (range 0-4) per individual. 16 of these were novel. Curated CNV events ranged in size from <1 kb to >3 Mb, and in frequency from 1/411 to 107/411. Of the 24 protein-coding genes or gene families tested, nine showed CNV. These included a large duplication encompassing the AMELY and TBL1Y genes that probably has no phenotypic effect, partial deletions of the TSPY cluster and AZFc region that may influence spermatogenesis, and other variants with unknown functional implications, including abundant variation in the number of RBMY genes and/or pseudogenes, and a novel complex duplication of two segments overlapping the AZFa region and including the 3' end of the UTY gene.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Tomas W
authors.initials: TW
authors.lastname: Fitzgerald
authors.forename: Tomas
authors.initials: T
authors.lastname: Fitzgerald
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.forename: Andrea
authors.initials: A
authors.lastname: Massaia
authors.forename: Blair H
authors.initials: BH
authors.lastname: Smith
authors.forename: Blair B
authors.initials: BB
authors.lastname: Smith
authors.forename: Anna F
authors.initials: AF
authors.lastname: Dominiczak
authors.forename: Anna A
authors.initials: AA
authors.lastname: Dominiczak
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Morris
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Morris
authors.forename: David J
authors.initials: DJ
authors.lastname: Porteous
authors.forename: David D
authors.initials: DD
authors.lastname: Porteous
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Hurles
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
mesh_terms: D053523:Amelogenin / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000235:genetics*; D056915:DNA Copy Number Variations; D006801:Humans; D008297:Male; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D011544:Pseudogenes; D015293:Transducin / Q000235:genetics; D006113:United Kingdom
chemical_list: C507202:AMELY protein, human; D053523:Amelogenin; D018797:Cell Cycle Proteins; C485612:TBL1Y protein, human; C497749:TSPY1 protein, human; D015293:Transducin